From f207504a0b20d9696bbc9e12bf6b9255d173755c Mon Sep 17 00:00:00 2001 From: adokter Date: Fri, 21 Feb 2020 08:19:13 -0500 Subject: [PATCH 01/18] update news --- NEWS.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/NEWS.md b/NEWS.md index 9ea0e65d7..c48a8479d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +# bioRad 0.5.0.9xxx + +* extend the functionality of composite_ppi() and improve its documentation (partial fix of #59) + +* fix a bug in the color legend of map() when providing a custom color scale with palette argument (#324) + # bioRad 0.5.0 New CRAN release. All issues included in this release can be found [here](https://github.com/adokter/bioRad/milestone/6?closed=1). From a5c90480f64de460fcce8adbaf953c66bb525a6c Mon Sep 17 00:00:00 2001 From: adokter Date: Thu, 27 Feb 2020 16:26:05 -0500 Subject: [PATCH 02/18] bugfix that occurred when compositing already composited ppi's with idw method --- R/composite_ppi.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/R/composite_ppi.R b/R/composite_ppi.R index eaf9c4c39..bc7d91928 100644 --- a/R/composite_ppi.R +++ b/R/composite_ppi.R @@ -144,7 +144,8 @@ composite_ppi <- function(x, param = "DBZH", nx = 100, ny = 100, xlim, ylim, res #weights<-raster::pointDistance(as.matrix(data.frame(x=lons.radar,y=lats.radar)), coordinates(raster(spGrid)),lonlat=T) for(i in 1:length(projs)){ brick_data <- raster::setValues(brick_data, projs[[i]], layer=i) - weights<-raster::pointDistance(as.matrix(data.frame(x=lons.radar,y=lats.radar))[i,], coordinates(raster(spGrid)),lonlat=T) + latlon.radar <- unique(data.frame(lat=c(lats.radar), lon=c(lons.radar))) + weights<-raster::pointDistance(as.matrix(data.frame(x=latlon.radar$lon,y=latlon.radar$lat))[i,], coordinates(raster(spGrid)),lonlat=T) if(!is.na(idw_max_distance)) weights[weights>idw_max_distance]=NA weights = 1/(weights^idp) From 569509b111cb09cb5ff675d6ef4cc677fe56077c Mon Sep 17 00:00:00 2001 From: adokter Date: Thu, 27 Feb 2020 16:41:19 -0500 Subject: [PATCH 03/18] temporary fix #328, pending vol2bird update --- R/read_pvolfile.R | 3 +++ 1 file changed, 3 insertions(+) diff --git a/R/read_pvolfile.R b/R/read_pvolfile.R index 1781521cb..c4053c5fd 100644 --- a/R/read_pvolfile.R +++ b/R/read_pvolfile.R @@ -329,6 +329,9 @@ read_pvolfile_quantity <- function(file, quantity, radar, datetime, geo) { data <- replace(data, data == as.numeric(attr$nodata), NA) data <- replace(data, data == as.numeric(attr$undetect), NaN) data <- as.numeric(attr$offset) + as.numeric(attr$gain) * data + if(attr$quantity == "RHOHV"){ + data <- replace(data, data > 10, NaN) + } class(data) <- c("param", class(data)) attributes(data)$radar <- radar attributes(data)$datetime <- datetime From 043aa73f4a26994dc27a8073f18836c6257e4e91 Mon Sep 17 00:00:00 2001 From: adokter Date: Thu, 27 Feb 2020 17:38:44 -0500 Subject: [PATCH 04/18] fix mapping of composites of composites --- R/map.R | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/R/map.R b/R/map.R index 0f0ac51f8..636383622 100644 --- a/R/map.R +++ b/R/map.R @@ -216,21 +216,23 @@ map.ppi <- function(x, map, param, alpha = 0.7, xlim, ylim, # these declarations prevent generation of NOTE "no visible binding for # global variable" during package Check lon <- lat <- y <- z <- NA + # extract unique radar locations + latlon_radar <- unique(data.frame(lat=c(x$geo$lat), lon=c(x$geo$lon))) # symbols for the radar position # dummy is a hack to be able to include the ggplot2 color scale, # radarpoint is the actual plotting of radar positions. dummy <- geom_point(aes(x = lon, y = lat, colour = z), size = 0, data = data.frame( - lon = x$geo$lon, - lat = x$geo$lat, + lon = latlon_radar$lon, + lat = latlon_radar$lat, z = 0 ) ) radarpoint <- geom_point(aes(x = lon, y = lat), colour = radar_color, size = radar_size, - data = data.frame(lon = x$geo$lon, lat = x$geo$lat) + data = data.frame(lon = latlon_radar$lon, lat = latlon_radar$lat) ) # bounding box bboxlatlon <- attributes(map)$geo$bbox @@ -248,4 +250,5 @@ map.ppi <- function(x, map, param, alpha = 0.7, xlim, ylim, scale_y_continuous(limits = ylim, expand = c(0, 0)) ) suppressWarnings(mymap) + } From 93ad0a446c304e4ef20f7f88a16aafabfca38180 Mon Sep 17 00:00:00 2001 From: adokter Date: Tue, 10 Mar 2020 15:55:34 -0400 Subject: [PATCH 05/18] bugfix read_cajun --- R/read_cajun.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/read_cajun.R b/R/read_cajun.R index ceff52212..9dc65bc71 100644 --- a/R/read_cajun.R +++ b/R/read_cajun.R @@ -55,7 +55,7 @@ read_cajun <- function(file, rcs = 11, wavelength = "S") { data$n_all <- NA # remove redundant quantities - data$height <- NULL + data$height_mean <- NULL # sort into bioRad order data <- data[, header.names.sorted] From 0a240d6b32fb0cc15637f5fb59bbdfa1a081cc25 Mon Sep 17 00:00:00 2001 From: adokter Date: Tue, 31 Mar 2020 12:28:53 -0400 Subject: [PATCH 06/18] add keep_datetime option to regularize_vpts.R --- R/filter.R | 4 ++-- R/regularize_vpts.R | 10 +++++++--- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/R/filter.R b/R/filter.R index acaae526b..134c8cc72 100644 --- a/R/filter.R +++ b/R/filter.R @@ -1,8 +1,8 @@ #' Time selection in a time series of vertical profiles ('vpts') #' #' @param x A \code{vpts} object. -#' @param min Minimum datetime to be included. POSIXct value or charater string convertable to POSIXct. -#' @param max Maximum datetime to be included. POSIXct value or charater string convertable to POSIXct. +#' @param min Minimum datetime to be included. POSIXct value or character string convertable to POSIXct. +#' @param max Maximum datetime to be included. POSIXct value or character string convertable to POSIXct. #' @param nearest If specified, \code{min} and \code{max} are ignored and the profile nearest to the #' specified datetime is returned. POSIXct value or charater string convertable to POSIXct. #' @return An object of class '\link[=summary.vpts]{vpts}', or an object of class '\link[=summary.vp]{vp}' diff --git a/R/regularize_vpts.R b/R/regularize_vpts.R index 79c40ff28..1b0905403 100644 --- a/R/regularize_vpts.R +++ b/R/regularize_vpts.R @@ -16,6 +16,8 @@ #' @param fill Logical, whether to fill missing timesteps with the values of #' the closest neighboring profile. #' @param verbose Logical, when \code{TRUE} prints text to console. +#' @param keep_datetime Logical, when \code{TRUE} keep original radar acquisition timestamps, +#' and do not update to values of the regularized time grid. #' #' @return An object of class \code{vpts} with regular time steps. #' @@ -41,7 +43,7 @@ #' tsRegular <- regularize_vpts(ts, interval = 300) regularize_vpts <- function(ts, interval = "auto", date_min = ts$daterange[1], date_max = ts$daterange[2], units = "secs", - fill = FALSE, verbose = TRUE) { + fill = FALSE, verbose = TRUE, keep_datetime = FALSE) { stopifnot(inherits(ts, "vpts")) stopifnot(inherits(date_min, "POSIXct")) stopifnot(inherits(date_max, "POSIXct")) @@ -99,8 +101,10 @@ regularize_vpts <- function(ts, interval = "auto", date_min = ts$daterange[1], } } names(ts$data) <- quantity.names - ts$datetime <- grid - ts$timesteps <- rep(as.double(dt, units = "secs"), length(grid) - 1) + if(!keep_datetime){ + ts$datetime <- grid + ts$timesteps <- rep(as.double(dt, units = "secs"), length(grid) - 1) + } ts$regular <- TRUE return(ts) } From 8e1bc04d06295ae1a6f8b5285c2ef71330da9c3c Mon Sep 17 00:00:00 2001 From: adokter Date: Tue, 31 Mar 2020 15:19:42 -0400 Subject: [PATCH 07/18] partial addressing of issue #333 --- R/regularize_vpts.R | 13 ++++++++++--- R/vpts.R | 2 +- man/filter_vpts.Rd | 4 ++-- man/regularize_vpts.Rd | 6 +++++- 4 files changed, 18 insertions(+), 7 deletions(-) diff --git a/R/regularize_vpts.R b/R/regularize_vpts.R index 1b0905403..8a286506b 100644 --- a/R/regularize_vpts.R +++ b/R/regularize_vpts.R @@ -16,8 +16,6 @@ #' @param fill Logical, whether to fill missing timesteps with the values of #' the closest neighboring profile. #' @param verbose Logical, when \code{TRUE} prints text to console. -#' @param keep_datetime Logical, when \code{TRUE} keep original radar acquisition timestamps, -#' and do not update to values of the regularized time grid. #' #' @return An object of class \code{vpts} with regular time steps. #' @@ -43,11 +41,15 @@ #' tsRegular <- regularize_vpts(ts, interval = 300) regularize_vpts <- function(ts, interval = "auto", date_min = ts$daterange[1], date_max = ts$daterange[2], units = "secs", - fill = FALSE, verbose = TRUE, keep_datetime = FALSE) { + fill = FALSE, verbose = TRUE) { stopifnot(inherits(ts, "vpts")) stopifnot(inherits(date_min, "POSIXct")) stopifnot(inherits(date_max, "POSIXct")) + # @param keep_datetime Logical, when \code{TRUE} keep original radar acquisition timestamps, + # and do not update to values of the regularized time grid. + keep_datetime <- FALSE # option under development + if (!(units %in% c("secs", "mins", "hours", "days", "weeks"))) { stop( "Invalid 'units' argument. Should be one of", @@ -87,6 +89,7 @@ regularize_vpts <- function(ts, interval = "auto", date_min = ts$daterange[1], ts$data[[x]][, index] } ) + index2 <- integer(0) if (!fill) { index2 <- which(abs(ts$datetime[index] - grid) > as.double(dt, units = "secs")) if (length(index2) > 0) { @@ -104,6 +107,10 @@ regularize_vpts <- function(ts, interval = "auto", date_min = ts$daterange[1], if(!keep_datetime){ ts$datetime <- grid ts$timesteps <- rep(as.double(dt, units = "secs"), length(grid) - 1) + } else{ + ts$datetime <- ts$datetime[index] + ts$timesteps <- difftime(ts$datetime[-1], ts$datetime[-length(ts$datetime)], units = "secs") + ts$timesteps[index2] <- dt } ts$regular <- TRUE return(ts) diff --git a/R/vpts.R b/R/vpts.R index d21878b95..3381e2ff8 100644 --- a/R/vpts.R +++ b/R/vpts.R @@ -187,7 +187,7 @@ print.vpts <- function(x, digits = max(3L, getOption("digits") - 3L), ...) { } else { stepMin <- stepMax <- NA } - if (x$regular) { + if (x$regular & stepMin == stepMax) { cat(" time step (s): ", stepMin, "\n") } else { cat(" time step (s): ", "min:", stepMin, " max: ", stepMax, "\n") diff --git a/man/filter_vpts.Rd b/man/filter_vpts.Rd index 7c71f9c9f..7adce2a0f 100644 --- a/man/filter_vpts.Rd +++ b/man/filter_vpts.Rd @@ -9,9 +9,9 @@ filter_vpts(x, min, max, nearest) \arguments{ \item{x}{A \code{vpts} object.} -\item{min}{Minimum datetime to be included. POSIXct value or charater string convertable to POSIXct.} +\item{min}{Minimum datetime to be included. POSIXct value or character string convertable to POSIXct.} -\item{max}{Maximum datetime to be included. POSIXct value or charater string convertable to POSIXct.} +\item{max}{Maximum datetime to be included. POSIXct value or character string convertable to POSIXct.} \item{nearest}{If specified, \code{min} and \code{max} are ignored and the profile nearest to the specified datetime is returned. POSIXct value or charater string convertable to POSIXct.} diff --git a/man/regularize_vpts.Rd b/man/regularize_vpts.Rd index 87159696d..dba8d6cb3 100644 --- a/man/regularize_vpts.Rd +++ b/man/regularize_vpts.Rd @@ -12,7 +12,8 @@ regularize_vpts( date_max = ts$daterange[2], units = "secs", fill = FALSE, - verbose = TRUE + verbose = TRUE, + keep_datetime = FALSE ) } \arguments{ @@ -35,6 +36,9 @@ Taken from \code{ts} when '\code{auto}'.} the closest neighboring profile.} \item{verbose}{Logical, when \code{TRUE} prints text to console.} + +\item{keep_datetime}{Logical, when \code{TRUE} keep original radar acquisition timestamps, +and do not update to values of the regularized time grid.} } \value{ An object of class \code{vpts} with regular time steps. From 736a10aec6ae764fe27855967bd41af578c66584 Mon Sep 17 00:00:00 2001 From: adokter Date: Tue, 31 Mar 2020 16:53:44 -0400 Subject: [PATCH 08/18] fix issue #331 --- DESCRIPTION | 2 +- NEWS.md | 4 +++- R/read_pvolfile.R | 2 ++ man/regularize_vpts.Rd | 6 +----- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 6fff36bf1..ec071aa7e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: bioRad Title: Biological Analysis and Visualization of Weather Radar Data -Version: 0.5.0.9325 +Version: 0.5.1 Description: Extract, visualize and summarize aerial movements of birds and insects from weather radar data. See for a software paper describing package and methodologies. diff --git a/NEWS.md b/NEWS.md index c48a8479d..f1fd5270f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,9 +1,11 @@ -# bioRad 0.5.0.9xxx +# bioRad 0.5.1 * extend the functionality of composite_ppi() and improve its documentation (partial fix of #59) * fix a bug in the color legend of map() when providing a custom color scale with palette argument (#324) +* resolving conflict with CRAN dependency + # bioRad 0.5.0 New CRAN release. All issues included in this release can be found [here](https://github.com/adokter/bioRad/milestone/6?closed=1). diff --git a/R/read_pvolfile.R b/R/read_pvolfile.R index c4053c5fd..3efe645ab 100644 --- a/R/read_pvolfile.R +++ b/R/read_pvolfile.R @@ -325,6 +325,8 @@ read_pvolfile_scan <- function(file, scan, param, radar, datetime, geo) { read_pvolfile_quantity <- function(file, quantity, radar, datetime, geo) { data <- h5read(file, quantity)$data + # convert storage mode from raw to numeric: + storage.mode(data) <- "numeric" attr <- h5readAttributes(file, paste(quantity, "/what", sep = "")) data <- replace(data, data == as.numeric(attr$nodata), NA) data <- replace(data, data == as.numeric(attr$undetect), NaN) diff --git a/man/regularize_vpts.Rd b/man/regularize_vpts.Rd index dba8d6cb3..87159696d 100644 --- a/man/regularize_vpts.Rd +++ b/man/regularize_vpts.Rd @@ -12,8 +12,7 @@ regularize_vpts( date_max = ts$daterange[2], units = "secs", fill = FALSE, - verbose = TRUE, - keep_datetime = FALSE + verbose = TRUE ) } \arguments{ @@ -36,9 +35,6 @@ Taken from \code{ts} when '\code{auto}'.} the closest neighboring profile.} \item{verbose}{Logical, when \code{TRUE} prints text to console.} - -\item{keep_datetime}{Logical, when \code{TRUE} keep original radar acquisition timestamps, -and do not update to values of the regularized time grid.} } \value{ An object of class \code{vpts} with regular time steps. From 0e937a57158ec2c60b630fe39620d4556337097f Mon Sep 17 00:00:00 2001 From: adokter Date: Tue, 31 Mar 2020 17:16:09 -0400 Subject: [PATCH 09/18] update cran-comments.md --- DESCRIPTION | 2 +- cran-comments.md | 31 ++++++++++++++----------------- man/example_scan.Rd | 4 +++- man/example_vp.Rd | 4 +++- man/example_vpts.Rd | 4 +++- 5 files changed, 24 insertions(+), 21 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index ec071aa7e..bbe14f796 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -44,4 +44,4 @@ Suggests: LazyData: true Encoding: UTF-8 VignetteBuilder: knitr -RoxygenNote: 7.0.2 +RoxygenNote: 7.1.0 diff --git a/cran-comments.md b/cran-comments.md index 493833e3f..23440357f 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,7 +1,14 @@ +## bioRad 0.5.1 +This version includes a minor bugfix associated with the +upcoming R 0.4.0 release. I only found out today that our +package had been removed from CRAN because of this, without +any notice, is there a way for me to subscribe to a notification +when my package is pending to be removed? + ## Test environments -* local OS X install, R 3.6.2 -* local Ubuntu 18.04 LTS, R 3.6.2 -* local Windows 10 Enterprise, R 3.6.2 +* local OS X install, R 3.6.3 +* local Ubuntu 18.04 LTS, R 3.6.3 +* local Windows 10 Enterprise, R 3.6.3 ## R CMD check results There were no ERRORs or WARNINGs. @@ -18,20 +25,10 @@ There was 1 NOTE: The tarball is however below the required 5 Mb ## r-hub builder -Building bioRad with r-hub (using `check_rhub()` fails because gdal is -not available on the r-hub build system. The rgdal package is a -dependency of bioRad. rgdal documentations explains in detail -how to install gdal on all platforms, so this seems more an -rgdal issue than a bioRad issue. - -Resulting PREPERROR: -``` -#> configure: GDAL: 1.11.3 -#> checking GDAL version >= 1.11.4... no -#> configure: error: upgrade GDAL to 1.11.4 or later -#> ERROR: configuration failed for package ‘rgdal’ -#> * removing ‘/home/docker/R/rgdal’ -``` +There was one warning: + +* checking package dependencies ... WARNING +Requires orphaned package: 'ggmap' ## Downstream dependencies There are currently no downstream dependencies for this package diff --git a/man/example_scan.Rd b/man/example_scan.Rd index 9c537a809..9d9e9caf5 100644 --- a/man/example_scan.Rd +++ b/man/example_scan.Rd @@ -4,7 +4,9 @@ \name{example_scan} \alias{example_scan} \title{Example object of class \code{scan}} -\format{An object of class \code{scan} of dimension 5 x 480 x 360.} +\format{ +An object of class \code{scan} of dimension 5 x 480 x 360. +} \usage{ example_scan } diff --git a/man/example_vp.Rd b/man/example_vp.Rd index 50b9e027c..5f42e0274 100644 --- a/man/example_vp.Rd +++ b/man/example_vp.Rd @@ -4,7 +4,9 @@ \name{example_vp} \alias{example_vp} \title{Example object of class \code{vp}} -\format{An object of class \code{vp} with 25 rows and 16 columns.} +\format{ +An object of class \code{vp} with 25 rows and 16 columns. +} \usage{ example_vp } diff --git a/man/example_vpts.Rd b/man/example_vpts.Rd index 20bb1755c..4b7ddb3fe 100644 --- a/man/example_vpts.Rd +++ b/man/example_vpts.Rd @@ -4,7 +4,9 @@ \name{example_vpts} \alias{example_vpts} \title{Example object of class \code{vpts}} -\format{An object of class \code{vpts} of dimension 25 x 1934 x 15.} +\format{ +An object of class \code{vpts} of dimension 25 x 1934 x 15. +} \usage{ example_vpts } From 930d0f26228d50357aa7ee830e673520c94ac69a Mon Sep 17 00:00:00 2001 From: adokter Date: Tue, 31 Mar 2020 17:21:30 -0400 Subject: [PATCH 10/18] update news --- NEWS.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index f1fd5270f..1d98fef0b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,10 +1,12 @@ # bioRad 0.5.1 +Minor bugfixes. All issues included in this release can be found [here](https://github.com/adokter/bioRad/pull/334) + * extend the functionality of composite_ppi() and improve its documentation (partial fix of #59) * fix a bug in the color legend of map() when providing a custom color scale with palette argument (#324) -* resolving conflict with CRAN dependency +* resolve a conflict with upcoming R 0.4 release # bioRad 0.5.0 From 13e8ee588c046e699daf370193136724eae8626c Mon Sep 17 00:00:00 2001 From: adokter Date: Tue, 31 Mar 2020 17:25:03 -0400 Subject: [PATCH 11/18] update codemeta and readme --- README.md | 4 ++-- codemeta.json | 22 +++++++++++++++++----- 2 files changed, 19 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 0f450c580..937fc64ff 100644 --- a/README.md +++ b/README.md @@ -67,8 +67,8 @@ Then load the package with: ``` r library(bioRad) -#> Welcome to bioRad version 0.5.0 -#> Docker daemon running, Docker functionality enabled (vol2bird version 0.5.0, MistNet available) +#> Welcome to bioRad version 0.5.1 +#> Docker daemon running, Docker functionality enabled (vol2bird version 0.5.1, MistNet available) ``` #### Required system libraries on Linux (Ubuntu) diff --git a/codemeta.json b/codemeta.json index 77afc50d6..f4fce7517 100644 --- a/codemeta.json +++ b/codemeta.json @@ -5,7 +5,7 @@ ], "@type": "SoftwareSourceCode", "identifier": "bioRad", - "description": "Extract, visualize and summarize aerial movements of birds and\n insects from weather radar data. See \n for a software paper describing package and methodologies.", + "description": "Extract, visualize and summarize aerial movements of birds and\n insects from weather radar data. See \n for a software paper describing package and methodologies.", "name": "bioRad: Biological Analysis and Visualization of Weather Radar Data", "codeRepository": "https://github.com/adokter/bioRad", "relatedLink": [ @@ -15,14 +15,14 @@ ], "issueTracker": "https://github.com/adokter/bioRad/issues", "license": "https://spdx.org/licenses/MIT", - "version": "0.5.0", + "version": "0.5.1", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", - "version": "3.6.2", + "version": "3.6.3", "url": "https://r-project.org" }, - "runtimePlatform": "R version 3.6.2 (2019-12-12)", + "runtimePlatform": "R version 3.6.3 (2020-02-29)", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -271,6 +271,18 @@ "identifier": "utils", "name": "utils" }, + { + "@type": "SoftwareApplication", + "identifier": "viridisLite", + "name": "viridisLite", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=viridisLite" + }, { "@type": "SoftwareApplication", "identifier": "viridis", @@ -394,5 +406,5 @@ ], "releaseNotes": "https://github.com/adokter/bioRad/blob/master/NEWS.md", "readme": "https://github.com/adokter/bioRad/blob/master/README.md", - "fileSize": "5887.639KB" + "fileSize": "4947.408KB" } From 7cb612762df3912022f898aec17c3b402dfe2d77 Mon Sep 17 00:00:00 2001 From: adokter Date: Tue, 31 Mar 2020 17:29:49 -0400 Subject: [PATCH 12/18] build site --- docs/404.html | 37 +- docs/CODE_OF_CONDUCT.html | 37 +- docs/CONTRIBUTING.html | 39 +- docs/LICENSE-text.html | 37 +- docs/articles/bioRad.html | 61 ++- docs/articles/index.html | 44 ++- docs/articles/rad_aero_19.html | 383 +++++++++---------- docs/articles/range_correction.html | 127 +++--- docs/authors.html | 31 +- docs/docsearch.json | 2 +- docs/index.html | 87 +++-- docs/news/index.html | 61 +-- docs/pkgdown.css | 109 ++++++ docs/pkgdown.js | 5 - docs/pkgdown.yml | 7 +- docs/reference/add_expected_eta_to_scan.html | 41 +- docs/reference/apply_mistnet.html | 65 ++-- docs/reference/as.data.frame.vp.html | 42 +- docs/reference/as.data.frame.vpts.html | 42 +- docs/reference/beam_distance.html | 42 +- docs/reference/beam_height.html | 42 +- docs/reference/beam_profile.html | 42 +- docs/reference/beam_profile_overlap.html | 42 +- docs/reference/beam_range.html | 42 +- docs/reference/beam_width.html | 41 +- docs/reference/bind_into_vpts.html | 42 +- docs/reference/bioRad-deprecated.html | 115 ++---- docs/reference/bioRad-package.html | 56 +-- docs/reference/c.vp.html | 40 +- docs/reference/calculate_param.html | 43 +-- docs/reference/calculate_vp.html | 139 ++----- docs/reference/check_date_format.html | 40 +- docs/reference/check_docker.html | 47 ++- docs/reference/check_night.html | 42 +- docs/reference/check_radar_codes.html | 40 +- docs/reference/composite_ppi.html | 152 ++++++-- docs/reference/dbz_to_eta.html | 41 +- docs/reference/download_basemap.html | 62 +-- docs/reference/download_vpfiles.html | 47 +-- docs/reference/eta_to_dbz.html | 41 +- docs/reference/example_scan.html | 44 +-- docs/reference/example_vp.html | 44 +-- docs/reference/example_vpts.html | 47 +-- docs/reference/filter_vpts.html | 46 ++- docs/reference/gaussian_beam_profile.html | 41 +- docs/reference/get_elevation_angles.html | 42 +- docs/reference/get_odim_object_type.html | 41 +- docs/reference/get_param.html | 41 +- docs/reference/get_quantity.html | 42 +- docs/reference/get_scan.html | 42 +- docs/reference/index.html | 107 ++++-- docs/reference/integrate_profile.html | 45 +-- docs/reference/integrate_to_ppi.html | 68 ++-- docs/reference/is.nan.data.frame.html | 40 +- docs/reference/is.pvolfile.html | 42 +- docs/reference/is.vpfile.html | 41 +- docs/reference/map.html | 73 ++-- docs/reference/match_filenames.html | 40 +- docs/reference/nexrad_to_odim.html | 53 +-- docs/reference/nyquist_velocity.html | 41 +- docs/reference/plot.ppi.html | 43 +-- docs/reference/plot.scan.html | 53 ++- docs/reference/plot.vp.html | 40 +- docs/reference/plot.vpi.html | 43 +-- docs/reference/plot.vpts.html | 43 +-- docs/reference/print.param.html | 39 +- docs/reference/print.ppi.html | 39 +- docs/reference/print.pvol.html | 39 +- docs/reference/print.scan.html | 39 +- docs/reference/print.vp.html | 39 +- docs/reference/print.vpts.html | 39 +- docs/reference/proj_to_wgs.html | 40 +- docs/reference/project_as_ppi.html | 43 +-- docs/reference/rcs-set.html | 41 +- docs/reference/rcs.html | 43 +-- docs/reference/read_cajun.html | 40 +- docs/reference/read_pvolfile.html | 46 ++- docs/reference/read_vp.html | 40 +- docs/reference/read_vpfiles.html | 53 ++- docs/reference/read_vpts.html | 41 +- docs/reference/regularize_vpts.html | 42 +- docs/reference/scan_to_raster.html | 42 +- docs/reference/scan_to_spatial.html | 42 +- docs/reference/sd_vvp_threshold-set.html | 41 +- docs/reference/sd_vvp_threshold.html | 43 +-- docs/reference/select_vpfiles.html | 41 +- docs/reference/sub-.ppi.html | 40 +- docs/reference/sub-.vpts.html | 40 +- docs/reference/summary.param.html | 46 ++- docs/reference/summary.ppi.html | 48 ++- docs/reference/summary.pvol.html | 48 ++- docs/reference/summary.scan.html | 46 ++- docs/reference/summary.vp.html | 46 ++- docs/reference/summary.vpts.html | 44 +-- docs/reference/sunrise_sunset.html | 44 +-- docs/reference/update_docker.html | 48 ++- docs/reference/vol2bird_version.html | 48 ++- docs/reference/vplist_to_vpts.html | 48 +-- docs/reference/wgs_to_proj.html | 40 +- 99 files changed, 2585 insertions(+), 2530 deletions(-) diff --git a/docs/404.html b/docs/404.html index 4599931a5..9b0864022 100644 --- a/docs/404.html +++ b/docs/404.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,7 +54,6 @@ - @@ -68,7 +71,7 @@ - +
@@ -121,7 +124,7 @@
  • - + @@ -152,6 +155,12 @@

    Page not found (404)

+ + @@ -162,7 +171,7 @@

Page not found (404)

-

Site built with pkgdown 1.4.1.9000.

+

Site built with pkgdown 1.5.0.

diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html index ac21401f8..c461c948c 100644 --- a/docs/CODE_OF_CONDUCT.html +++ b/docs/CODE_OF_CONDUCT.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,7 +54,6 @@ - @@ -68,7 +71,7 @@ - +
@@ -121,7 +124,7 @@
  • - + @@ -160,6 +163,12 @@

    Contributor Code of Conduct

+ + @@ -170,7 +179,7 @@

Contributor Code of Conduct

-

Site built with pkgdown 1.4.1.9000.

+

Site built with pkgdown 1.5.0.

diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html index f1c4bd73c..03b6536b0 100644 --- a/docs/CONTRIBUTING.html +++ b/docs/CONTRIBUTING.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,7 +54,6 @@ - @@ -68,7 +71,7 @@ - +
@@ -121,7 +124,7 @@
  • - + @@ -233,7 +236,7 @@

  • Write your code.
  • Test your code (bonus points for adding unit tests).
  • Document your code (see function documentation above).
    • -
  • Do an R CMD check using devtools::check() and aim for 0 errors and warnings.
    • +
  • Do an R CMD check using devtools::check() and aim for 0 errors and warnings.

  • Commit and push your changes.
    • @@ -244,6 +247,12 @@

    + + @@ -254,7 +263,7 @@

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index ca8e13e75..f4fd713a6 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,7 +54,6 @@ - @@ -68,7 +71,7 @@ - +
    @@ -121,7 +124,7 @@
    • - + @@ -154,6 +157,12 @@

      License

    + + @@ -164,7 +173,7 @@

    License

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/articles/bioRad.html b/docs/articles/bioRad.html index 8d60a367f..26366899b 100644 --- a/docs/articles/bioRad.html +++ b/docs/articles/bioRad.html @@ -12,22 +12,22 @@ - - - - - + + + + + + - + - - +
    +
    -

    Introduction to bioRad

    +

    Introduction to bioRad

    Adriaan M. Dokter & Peter Desmet

    @@ -137,7 +137,7 @@

    Figure 2

    -

    Figure 2 from Dokter et al. (2019)

    +Figure 2 from Dokter et al. (2019)

    Figure 2 from Dokter et al. (2019)

    The figure shows the structure and interrelation of bioRad’s main class objects, functions, and plotting methods. (A) objects (rounded box), functions (fixed width font) and their relation (arrows). (B–K) output of the default plot methods for a European radar (left row, Offenthal radar, Germany, 2016-10-04 15:15 UTC–2016-10-05 08:45 UTC) and US radar (right row, KBRO radar, Texas, 2017-05-14 00:09 UTC–2017-05-14 13:25 UTC). The dotted line in (H) and (K) indicates the time slice of (B), (D), (F) and (C), (E), (J) respectively. Grey shading indicates night time (time on the x-axis is in UTC). Altitudes are relative to mean sea level.

    @@ -256,7 +251,7 @@

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/articles/index.html b/docs/articles/index.html index 51d170a96..d6809f8e2 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,7 +54,6 @@ - @@ -68,7 +71,7 @@ - +
    @@ -121,7 +124,7 @@
    @@ -168,7 +174,7 @@

    All vignettes

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/articles/rad_aero_19.html b/docs/articles/rad_aero_19.html index 152500a93..3c599eba9 100644 --- a/docs/articles/rad_aero_19.html +++ b/docs/articles/rad_aero_19.html @@ -12,22 +12,22 @@ - - - - - + + + + + + - + - - +
    +
    -

    Introductory exercises with bioRad

    +

    Introductory exercises with bioRad

    Adriaan M. Dokter

    @@ -124,87 +124,87 @@

    Radar data needed for this practical can be downloaded here.

    Follow bioRad’s install instructions, and install the latest development version to be fully up-to-date.

    Execute each of the code examples provided below in RStudio, and try to complete the exercises.

    -
    # make sure you start with a fresh R session
-# load the bioRad package
-library(bioRad)
-# check the package version
-packageVersion("bioRad")
    +
    # make sure you start with a fresh R session
+# load the bioRad package
+library(bioRad)
+# check the package version
+packageVersion("bioRad")

    Make sure you have the latest version (0.4.0.9243). If you have an older version, download and reinstall as follows:

    -
    library(devtools)
-install_github("adokter/bioRad")
    +
    library(devtools)
+install_github("adokter/bioRad")

    All bioRad’s functions are documented in an extensive function refererence online, as well as in manual pages within R:

    -
    # bring up the package general help page:
-?bioRad
    +
    # bring up the package general help page:
+?bioRad

    Start by making a new directory on your local machine that you will use for this practical:

    -
    # make a new local directory on your machine where to download data for this practical
-# replace the string below with the path of that directory:
-HOME <- "your/personal/working/directory/"
-# check that the directory exists. If the next statement evaluates to FALSE, something went wrong: the directory does not exist or you didn't specify its path correctly
-file.exists(HOME)
-# we will make HOME our work directory, the default folder in which R will look
-# for files, and where it will output newly generated files.
-setwd(HOME)
-# Finally, we set the local time zone to UTC, so all plotted time axes will be in UTC
-Sys.setenv(TZ = "UTC")
    +
    # make a new local directory on your machine where to download data for this practical
+# replace the string below with the path of that directory:
+HOME <- "your/personal/working/directory/"
+# check that the directory exists. If the next statement evaluates to FALSE, something went wrong: the directory does not exist or you didn't specify its path correctly
+file.exists(HOME)
+# we will make HOME our work directory, the default folder in which R will look
+# for files, and where it will output newly generated files.
+setwd(HOME)
+# Finally, we set the local time zone to UTC, so all plotted time axes will be in UTC
+Sys.setenv(TZ = "UTC")

    Your R session is now properly set up.

    To work with US NEXRAD data, bioRad currently requires a working installation of Docker (Linux/Mac) or Docker for Windows (not Docker Toolbox, this is an older implementation of Docker for Windows operating systems that is not supported). If you managed to successfully install Docker, test whether it works:

    -
    # start your local Docker installation
-# we first test whether R can communicate with Docker:
-check_docker()
    +
    # start your local Docker installation
+# we first test whether R can communicate with Docker:
+check_docker()

    The message “running docker image with vol2bird version 0.4.0” indicates everything is working.

    If you did not manage to install Docker, you will be able to continue with all of below exercises, but not be able to load NEXRAD data into R at this time.

    1.2 The structure of polar volumes

    -
    # the bioRad package comes with an example radar volume file, that we will inspect first
-# first locate this example file on our computer:
-my_filename <- system.file("extdata", "volume.h5", package = "bioRad")
-# print the local path of the volume file:
-my_filename
-# load the file into R:
-my_pvol <- read_pvolfile(my_filename)
-## print some information about the polar volume
-my_pvol
-# print information about the polar scans contained in this polar volume:
-my_pvol$scans
    +
    # the bioRad package comes with an example radar volume file, that we will inspect first
+# first locate this example file on our computer:
+my_filename <- system.file("extdata", "volume.h5", package = "bioRad")
+# print the local path of the volume file:
+my_filename
+# load the file into R:
+my_pvol <- read_pvolfile(my_filename)
+## print some information about the polar volume
+my_pvol
+# print information about the polar scans contained in this polar volume:
+my_pvol$scans

    Exercise 1: Load the polar volume file, example_pvol.h5 from the files downloaded in section 1.1. Put it in your working directory and load it into R. What is the minimum and maximum scan elevation contained in the volume? And which scan parameters are available? (See manual page of the read_pvolfile() function for the nomenclature of various available quantities).

    1.3 Plotting radar scans

    -
    # (if you haven't done so already) load the polar volume data from the example_pvol.h5 file you just downloaded
-my_pvol <- read_pvolfile("example_pvol.h5")
-# let's extract the third scan, which was collected at 1.5 degree elevation:
-my_scan <- my_pvol$scans[[3]]
-# print some information about this scan:
-my_scan
-# let's plot the reflectivity factor parameter of the scan in a range - azimuth coordinate system:
-plot(my_scan, param = "DBZH")
    +
    # (if you haven't done so already) load the polar volume data from the example_pvol.h5 file you just downloaded
+my_pvol <- read_pvolfile("example_pvol.h5")
+# let's extract the third scan, which was collected at 1.5 degree elevation:
+my_scan <- my_pvol$scans[[3]]
+# print some information about this scan:
+my_scan
+# let's plot the reflectivity factor parameter of the scan in a range - azimuth coordinate system:
+plot(my_scan, param = "DBZH")

    Usually it is more intuitive to explore radar scans as a PPI (plan position indicator), which is a projection of the scan on a Cartesian (X,Y) or (lat,lon) grid:

    -
    # before we can plot the scan, we need to project it on a Cartesian grid,
-# i.e. we need to make a Plan Position Indicator (PPI)
-my_ppi <- project_as_ppi(my_scan)
-# print some information about this ppi:
-my_ppi
-# you can see we projected it on a 500 meter grid
-# (check the manual of the project_as_ppi function to see how you can
-# change the grid size (argument grid_size) and the maximum distance
-# from the radar up to where to plot data (argument range_max))
-#
-# Now we are ready to plot the ppi, for example let's plot reflectivity factor DBZH:
-plot(my_ppi, param = "DBZH")
    +
    # before we can plot the scan, we need to project it on a Cartesian grid,
+# i.e. we need to make a Plan Position Indicator (PPI)
+my_ppi <- project_as_ppi(my_scan)
+# print some information about this ppi:
+my_ppi
+# you can see we projected it on a 500 meter grid
+# (check the manual of the project_as_ppi function to see how you can
+# change the grid size (argument grid_size) and the maximum distance
+# from the radar up to where to plot data (argument range_max))
+#
+# Now we are ready to plot the ppi, for example let's plot reflectivity factor DBZH:
+plot(my_ppi, param = "DBZH")

    Exercise 2: This case contains convective precipitation, characterized by localized but intense thunderstorms, as well as biological scattering. Make also a ppi plot of the correlation coefficient (RHOHV) and radial velocity (VRADH). Verify how the texture of the radial velocity, and the values of correlation coefficient of the precipitative areas differs from the areas with biological scattering.

    Exercise 3: Based on the radial velocity image, are the biological scatterers birds or insects? Why?

    1.4 Overlaying radar scans on maps

    -
    # It is often informative to plot radar data on a base layer.
-# first download the background image:
-basemap <- download_basemap(my_ppi)
-# then overlay the PPI on the satellite image, restricting the color scale from -20 to 15 dBZ:
-map(my_ppi, map = basemap, param = "DBZH", zlim = c(-20, 15))
    +
    # It is often informative to plot radar data on a base layer.
+# first download the background image:
+basemap <- download_basemap(my_ppi)
+# then overlay the PPI on the satellite image, restricting the color scale from -20 to 15 dBZ:
+map(my_ppi, map = basemap, param = "DBZH", zlim = c(-20, 15))

    bioRad provides several functions to convert radar scans to other common spatial formats in R (cf. package raster and package sp), see scan_to_raster() and scan_to_spatial(), allowing you to process and overlay the radar data further with these spatial analysis toolkits.

    @@ -216,72 +216,72 @@

    2.1 Loading processed vertical profiles

    -
    # Usually we would load processed vertical profiles (vp files) by:
-# my_vplist <- read_vpfiles("./your/directory/with/processed/profiles/goes/here")
-# my_vplist contains after running the command a list of vertical profile (vp) objects
-# To save time, we load these data directly from file
-load("KBRO20170514.RData")
-# print the length of the vplist object. It should contain 95 profiles
-length(my_vplist)
    +
    # Usually we would load processed vertical profiles (vp files) by:
+# my_vplist <- read_vpfiles("./your/directory/with/processed/profiles/goes/here")
+# my_vplist contains after running the command a list of vertical profile (vp) objects
+# To save time, we load these data directly from file
+load("KBRO20170514.RData")
+# print the length of the vplist object. It should contain 95 profiles
+length(my_vplist)

    2.2 Inspecting single vertical profiles

    Now that you have loaded a list of vertical profiles, we can start exploring them. We will start with plotting and inspecting single vertical profiles, i.e. a single profile from the list of vp objects you have just loaded.

    -
    # let's extract a profile from the list, in this example the 41st profile:
-my_vp <- my_vplist[[41]]
-# print some info for this profile to the console
-my_vp
-# test whether this profile was collected at day time:
-check_night(my_vp)
-# plot the vertical profile, in terms of reflectivity factor
-plot(my_vp, quantity = "dbz")
-# plot the vertical profile, in terms of (linear) reflectivity
-plot(my_vp, quantity = "eta")
    +
    # let's extract a profile from the list, in this example the 41st profile:
+my_vp <- my_vplist[[41]]
+# print some info for this profile to the console
+my_vp
+# test whether this profile was collected at day time:
+check_night(my_vp)
+# plot the vertical profile, in terms of reflectivity factor
+plot(my_vp, quantity = "dbz")
+# plot the vertical profile, in terms of (linear) reflectivity
+plot(my_vp, quantity = "eta")

    eta and dbz are closely related, the main difference is that reflectivity factors are logarithmic, and reflectivities linear. You can convert one into the other using eta_to_dbz() and dbz_to_eta() functions, which follow this simple formula:

    eta = (radar-wavelength dependent constant) * 10^(dbz/10)

    The reflectivity factor dBZ is the quantity used by most meteorologist. It has the useful property that at different radar wavelengths (e.g. S-band versus C-band) the same amount of precipitation shows up at similar reflectivity factors. The same holds for insects, as well as any other target that is much smaller than the radar wavelength (S-band = 10 cm, C-band = 5 cm), the so-called Rayleigh-scattering limit.

    In the case of birds we are outside the Rayleigh limit, because birds are of similar size as the radar wavelength. In this limit reflectivity eta is more similar between S-band and C-band. eta is also more directly related to the density of birds, since eta can be expressed as (bird density) x (radar cross section per bird). For these two reasons, for weather radar ornithologists not reflectivity factor dBZ but reflectivity eta is the more conventional unit.

    -
    # let'splot the vertical profile, in terms of bird density
-plot(my_vp, quantity = "dens")
-# print the currently assumed radar cross section (RCS) per bird:
-rcs(my_vp)
    +
    # let'splot the vertical profile, in terms of bird density
+plot(my_vp, quantity = "dens")
+# print the currently assumed radar cross section (RCS) per bird:
+rcs(my_vp)

    Exercise 4: If you change your assumption on the bird’s radar cross section in the previous example, and assume it is 10 times as large, what will be the effect on the bird density profile?

    The radar cross section you assume can be changed as follows:

    -
    # let's change the RCS to 110 cm^2
-rcs(my_vp) <- 110
    +
    # let's change the RCS to 110 cm^2
+rcs(my_vp) <- 110

    Exercise 5: Verify your answers on the previous two questions, by re-plotting the vertical profiles for the bird density quantity.

    2.3 Plotting vertical profile time series

    We will now examine multiple vertical profiles at once that are ordered into a time series, e.g. the vertical profiles obtained from a single radar over a full day.

    -
    # convert the list of vertical profiles into a time series:
-my_vpts <- bind_into_vpts(my_vplist)
-# print summary information
-my_vpts
-# time series objects can be subsetted, just as you may be used to with vectors
-# here we subset the first 50 timesteps:
-my_vpts[1:50]
-# here we extract a single timestep, which gives you back a vertical profile class object:
-my_vpts[100]
-# to extract all the dates of all profiles in the time series:
-my_vpts$datetime
-# to plot the full time series:
-plot(my_vpts)
-# check the help file for the plotting function of profile time series
-# Because profile timeseries are of class 'vpts', it's associated plotting function
-# is called plot.vpts:
-?plot.vpts
    +
    # convert the list of vertical profiles into a time series:
+my_vpts <- bind_into_vpts(my_vplist)
+# print summary information
+my_vpts
+# time series objects can be subsetted, just as you may be used to with vectors
+# here we subset the first 50 timesteps:
+my_vpts[1:50]
+# here we extract a single timestep, which gives you back a vertical profile class object:
+my_vpts[100]
+# to extract all the dates of all profiles in the time series:
+my_vpts$datetime
+# to plot the full time series:
+plot(my_vpts)
+# check the help file for the plotting function of profile time series
+# Because profile timeseries are of class 'vpts', it's associated plotting function
+# is called plot.vpts:
+?plot.vpts

    Let’s make a plot for a subselection of the time series:

    -
    # make a subselection for night time only
-index_night <- check_night(my_vpts)
-# index_night is a logical vector that specifies each profile whether it occurred at night or not:
-index_night
-# now subset our vpts using this selection:
-my_vpts_night <- my_vpts[index_night]
-# plot this smaller time series:
-plot(my_vpts_night)
    +
    # make a subselection for night time only
+index_night <- check_night(my_vpts)
+# index_night is a logical vector that specifies each profile whether it occurred at night or not:
+index_night
+# now subset our vpts using this selection:
+my_vpts_night <- my_vpts[index_night]
+# plot this smaller time series:
+plot(my_vpts_night)

    Exercise 6: Interpret the wind barbs in the profile time series figure: what is the approximate speed and direction at 1500 meter at 6 UTC? In the speed barbs, each half flag represents 2.5 m/s, each full flag 5 m/s, [each pennant (triangle) 25 m/s, not occurring in this case].

    Exercise 7: Extract the vertical profile at 6 UTC from the time series and plot the vertical profile of ground speed (quantity ff). Hint: use function filter_vpts() to extract the 6 UTC profile. Check whether your answer to the previous question was approximately correct.

    @@ -294,31 +294,31 @@

  • Note that the VID quantity doesn’t depend on the speed of the migrants. A common measure that reflects both the density and speed of the migration is migration traffic rate (MTR). This is flux measure that gives you how many migrants are passing the radar station per unit of time and per unit of distance perpendicular to the migratory direction (unit individuals/km/hour).

    • We will be using bioRad’s integrate_profile() function to calculate these quantities:

    -
    # Let's continue with the vpts object created in the previous example.
-# The vertically integrated quantities are calculated as follows:
-my_vpi <- integrate_profile(my_vpts)
-# The my_vpi object you created is a vpi class object, which is an acronym for "vertical profile integrated". It has its own plot method, which by default plots migration traffic rate (MTR):
-plot(my_vpi)
-# you can also plot vertically integrated densities (VID):
-plot(my_vpi, quantity = "vid")
-# the gray and white shading indicates day and night, which is calculated
-# from the date and the radar position. You can also turn this off:
-plot(my_vpi, night_shade = FALSE)
-# plot the cumulative number of birds passing the radar, i.e. migration traffic (mt):
-plot(my_vpi, quantity = "mt")
-# execute `?plot.vpi` to open the help page listing all the options.
-?plot.vpi
    +
    # Let's continue with the vpts object created in the previous example.
+# The vertically integrated quantities are calculated as follows:
+my_vpi <- integrate_profile(my_vpts)
+# The my_vpi object you created is a vpi class object, which is an acronym for "vertical profile integrated". It has its own plot method, which by default plots migration traffic rate (MTR):
+plot(my_vpi)
+# you can also plot vertically integrated densities (VID):
+plot(my_vpi, quantity = "vid")
+# the gray and white shading indicates day and night, which is calculated
+# from the date and the radar position. You can also turn this off:
+plot(my_vpi, night_shade = FALSE)
+# plot the cumulative number of birds passing the radar, i.e. migration traffic (mt):
+plot(my_vpi, quantity = "mt")
+# execute `?plot.vpi` to open the help page listing all the options.
+?plot.vpi

    The following questions only require pen and paper. Assume a night migration event in which the volume density of birds from 0-1 km above ground is 200 birds per cubic kilometer, and from 1-1.5 km 100 birds per cubic kilometer. In the lower layer birds fly at 50 km/hour, and in the upper layer at 100 km/hour. Above 1500 meter there are no birds. Migration continues for exactly three hours after sunset, and then halts abruptly.

    Exercise 8: What is in this case the bird’s vertically integrated density (VID)? Give your answer in units birds/km\(^2\).

    Exercise 9: What is in this case the migration traffic rate across a transect perpendicular to the direction of movement? Give your answer in units birds/km/hour.

    Exercise 10: How many birds have passed a 1km transect perpendicular to the direction of movement in this night? Give your answer in terms of migration traffic (mt) in units birds/km.

    Both MTR, VID and MT depend on the assumed radar cross section (RCS) per bird. If you are unwilling/unable to specify RCS, you can alternatively use two closely related quantities that make no assumptions RCS:

    -
    # instead of vertically integrated density (VID), you can use vertically integrated reflectivity (VIR):
-plot(my_vpi, quantity = "vir")
-# instead of migration traffic rate (MTR), you can use the reflectivity traffic rate (RTR):
-plot(my_vpi, quantity = "rtr")
-# instead of migration traffic (MT), you can use the reflectivity traffic (RT):
-plot(my_vpi, quantity = "rt")
    +
    # instead of vertically integrated density (VID), you can use vertically integrated reflectivity (VIR):
+plot(my_vpi, quantity = "vir")
+# instead of migration traffic rate (MTR), you can use the reflectivity traffic rate (RTR):
+plot(my_vpi, quantity = "rtr")
+# instead of migration traffic (MT), you can use the reflectivity traffic (RT):
+plot(my_vpi, quantity = "rt")

    VIR gives you the total cross-sectional area of air-borne targets per square kilometer of ground surface, whereas RTR gives you the total cross-sectional area of targets flying across a one kilometer line perpendicular to the migratory flow per hour.

    @@ -327,12 +327,12 @@

    Precipitation is known to have a major influence on the timing and intensity of migration, therefore it is a useful skill to be able to inspect profiles for presence of precipitation.

    Also, although automated bird quantification algorithms become more and more reliable, distinguishing precipitation from birds remains challenging for algorithms in specific cases. It is therefore important to have the skills to inspect suspicious profiles. That may help you to identify potential errors of the automated methods, and prevent your from overinterpreting the data.

    An easy way of doing that is plotting the vertical profile of total reflectivity (quantity DBZH), which includes everything: birds, insects and precipitation. Precipitation often has higher reflectivities than birds, and also extends to much higher altitudes.

    -
    # load a time series for the KBGM radar in Binghamton, NY
-load("KBGM20170527-20170602.RData")
-# print the loaded vpts time series for this radar:
-my_vpts
-# plot the bird density over time:
-plot(my_vpts, quantity = "dens")
    +
    # load a time series for the KBGM radar in Binghamton, NY
+load("KBGM20170527-20170602.RData")
+# print the loaded vpts time series for this radar:
+my_vpts
+# plot the bird density over time:
+plot(my_vpts, quantity = "dens")

    Exercise 11: Compare the above plot for bird density (quantity dens) with a profile plot for total reflectivity (quantity DBZH, showing birds and precipitation combined). Compare the two plots to visually identify periods and altitude layers with precipitation.

    @@ -360,55 +360,55 @@

    3.2 Processing a single polar volume with the vol2bird algorithm

    The following steps take you through the process applying the vol2bird algorithm yourself. You need a working installation of Docker (Linux/Mac) or Docker for Windows (not Docker Toolbox, this is an older implementation of Docker for Windows operating systems that is not supported).

    We will generate vertical profiles with the automated algorithm vol2bird (https://github.com/adokter/vol2bird), which is included in the bioRad package.

    -
    # start your local Docker installation
-# we first test whether R can communicate with Docker:
-check_docker()
    +
    # start your local Docker installation
+# we first test whether R can communicate with Docker:
+check_docker()

    If you get a “Hello from Docker!” welcome message, everything is working and you can start processing.

    -
    # download a polar volume file you want to process and put it in your home directory.
-my_file <- "write_your_file_to_be_processed_here"
-# Alternatively, continue with the polar volume that comes with the package:
-my_file <- system.file("extdata", "volume.h5", package = "bioRad")
-# run vol2bird
-# we set autoconf to TRUE, to let vol2bird figure out the optimal settings by itself
-my_vp <- calculate_vp(my_file, autoconf = TRUE)
-# vp is now a 'vp' profile object, that you can examine as in the previous exercises
-# alternatively, you may also store the profile as a hdf5 file, which is what we will do next:
-calculate_vp(my_file, "my_vpfile.h5", autoconf = TRUE)
-# your work directory should now contain a new file 'my_vpfile.h5'
-# check that we can read this file, and retrieve the vertical profile from it:
-vp <- read_vpfiles("my_vpfile.h5")
    +
    # download a polar volume file you want to process and put it in your home directory.
+my_file <- "write_your_file_to_be_processed_here"
+# Alternatively, continue with the polar volume that comes with the package:
+my_file <- system.file("extdata", "volume.h5", package = "bioRad")
+# run vol2bird
+# we set autoconf to TRUE, to let vol2bird figure out the optimal settings by itself
+my_vp <- calculate_vp(my_file, autoconf = TRUE)
+# vp is now a 'vp' profile object, that you can examine as in the previous exercises
+# alternatively, you may also store the profile as a hdf5 file, which is what we will do next:
+calculate_vp(my_file, "my_vpfile.h5", autoconf = TRUE)
+# your work directory should now contain a new file 'my_vpfile.h5'
+# check that we can read this file, and retrieve the vertical profile from it:
+vp <- read_vpfiles("my_vpfile.h5")

    3.3 Processing multiple polar volumes

    This section contains an example for processing a directory of polar volumes into profiles:

    -
    # read the filenames of the polar volumes you want to process
-my_files <- list.files("your/directory/with/volumes/goes/here/", full.names = TRUE)
-# print the filenames
-my_files
-# create output directory for processed profiles
-outputdir <- "~/processed_data"
-dir.create(outputdir)
-# let's loop over the files and generate profiles
-for (file_in in my_files) {
-  # generate the output filename for the input file
-  file_out <- paste(outputdir, "/", basename(file_in), "_vp.h5", sep = "")
-  # generate the profile, and write it as a hdf5 file (for later reference)
-  # we turn autoconfiguration on, so vol2bird chooses the optimal settings for the file automatically
-  vp <- calculate_vp(file_in, file_out, autoconf = TRUE)
-}
    +
    # read the filenames of the polar volumes you want to process
+my_files <- list.files("your/directory/with/volumes/goes/here/", full.names = TRUE)
+# print the filenames
+my_files
+# create output directory for processed profiles
+outputdir <- "~/processed_data"
+dir.create(outputdir)
+# let's loop over the files and generate profiles
+for (file_in in my_files) {
+  # generate the output filename for the input file
+  file_out <- paste(outputdir, "/", basename(file_in), "_vp.h5", sep = "")
+  # generate the profile, and write it as a hdf5 file (for later reference)
+  # we turn autoconfiguration on, so vol2bird chooses the optimal settings for the file automatically
+  vp <- calculate_vp(file_in, file_out, autoconf = TRUE)
+}

    Having generated the profiles, we can read them into R:

    -
    # we assume outputdir contains the path to the directory with processed profiles
-my_vpfiles <- list.files(outputdir, full.names = TRUE)
-# print them
-my_vpfiles
-# read them
-my_vplist <- read_vpfiles(my_vpfiles)
    +
    # we assume outputdir contains the path to the directory with processed profiles
+my_vpfiles <- list.files(outputdir, full.names = TRUE)
+# print them
+my_vpfiles
+# read them
+my_vplist <- read_vpfiles(my_vpfiles)

    You can now continue with visualizing and post-processing as we did earlier:

    -
    # make a time series of profiles:
-my_vpts <- bind_into_vpts(my_vplist)
-# plot them between 0 - 3 km altitude:
-plot(my_vpts, ylim = c(0, 3000))
    +
    # make a time series of profiles:
+my_vpts <- bind_into_vpts(my_vplist)
+# plot them between 0 - 3 km altitude:
+plot(my_vpts, ylim = c(0, 3000))
    @@ -451,7 +444,7 @@

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/articles/range_correction.html b/docs/articles/range_correction.html index fa8f3f368..f13424cec 100644 --- a/docs/articles/range_correction.html +++ b/docs/articles/range_correction.html @@ -12,22 +12,22 @@ - - - - - + + + + + + - + - - +
    +
    -

    Correction for range effects

    +

    Correction for range effects

    Adriaan M. Dokter

    @@ -118,8 +118,8 @@

    Adriaan M. Dokter

    1 Preparations

    Load bioRad

    -
    library(bioRad)
    -
    ## Welcome to bioRad version 0.5.0
    +
    library(bioRad)
    +
    ## Welcome to bioRad version 0.5.1
    ## Docker daemon running, Docker functionality enabled (vol2bird version 0.5.0, MistNet available)
    @@ -134,38 +134,38 @@

    distance: the distance of the target from the radar as measured along the earth’s surface, also known as down range.

    The beam height is changing as a result of earth’s curvature, and beam refraction:

    -
    # define a range grid from 0 to 200 km:
-my_range <- seq(0, 200000, 1000)
-# plot the beam height for each range, for a 0.5 degree elevation beam:
-plot(my_range, beam_height(my_range, elev = .5), xlab = "range [m]", ylab = "beam height [m]")
    +
    # define a range grid from 0 to 200 km:
+my_range <- seq(0, 200000, 1000)
+# plot the beam height for each range, for a 0.5 degree elevation beam:
+plot(my_range, beam_height(my_range, elev = .5), xlab = "range [m]", ylab = "beam height [m]")

    The beam width also broadens with range:

    -
    # plot the beam width, for a beam opening angle of 1 degree (typical for most weather radars):
-plot(my_range, beam_width(my_range, beam_angle = 1), xlab = "range [m]", ylab = "beam width [m]")
    +
    # plot the beam width, for a beam opening angle of 1 degree (typical for most weather radars):
+plot(my_range, beam_width(my_range, beam_angle = 1), xlab = "range [m]", ylab = "beam width [m]")

    We can now combine the relations for beam width and beam height, to calculate the beam profile as a function of height, i.e. the altitudinal normalized distribution of radiated energy by the beam. Let’s plot the radiation profile for a 0.5 and 2 degree beam elevation at 50 km from the radar (the height axis runs from ground level straight up):

    -
    # plot the beam profile, for a 0.5 degree elevation beam at 50 km distance from the radar:
-plot(beam_profile(height = 0:4000, 50000, 0.5), 0:4000, xlab = "normalized radiated energy", ylab = "height [m]", main = "beam elevation: 0.5 deg, distance=50km")
    +
    # plot the beam profile, for a 0.5 degree elevation beam at 50 km distance from the radar:
+plot(beam_profile(height = 0:4000, 50000, 0.5), 0:4000, xlab = "normalized radiated energy", ylab = "height [m]", main = "beam elevation: 0.5 deg, distance=50km")

    -
    # plot the beam profile, for a 2 degree elevation beam at 50 km distance from the radar:
-plot(beam_profile(height = 0:4000, 50000, 2), 0:4000, xlab = "normalized radiated energy", ylab = "height [m]", main = "beam elevation: 2 deg, distance=50km")
    +
    # plot the beam profile, for a 2 degree elevation beam at 50 km distance from the radar:
+plot(beam_profile(height = 0:4000, 50000, 2), 0:4000, xlab = "normalized radiated energy", ylab = "height [m]", main = "beam elevation: 2 deg, distance=50km")

    We can also calculate the normalized radiation profile for the two beams combined:

    -
    # plot the combined beam profile for a 0.5 and 2.0 degree elevation beam at 50 km distance from the radar:
-plot(beam_profile(height = 0:4000, 50000, c(0.5, 2)), 0:4000, xlab = "normalized radiated energy", ylab = "height [m]", main = "beam elevations: 0.5,2 deg, distance=50km")
    +
    # plot the combined beam profile for a 0.5 and 2.0 degree elevation beam at 50 km distance from the radar:
+plot(beam_profile(height = 0:4000, 50000, c(0.5, 2)), 0:4000, xlab = "normalized radiated energy", ylab = "height [m]", main = "beam elevations: 0.5,2 deg, distance=50km")

    3 Vertical profiles and polar volumes

    Let us now assume we have calculated a vertical profile (of birds) for a certain polar volume file. Let’s load an example

    -
    # let's load an example polar volume:
-pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
-example_pvol <- read_pvolfile(file = pvolfile)
-# a vertical profile can also be calculated from the polar volume directly, using
-# calculate_vp(pvolfile)
-# but for now we will use bioRad's example vertical profile already calculated:
-example_vp
    +
    # let's load an example polar volume:
+pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
+example_pvol <- read_pvolfile(file = pvolfile)
+# a vertical profile can also be calculated from the polar volume directly, using
+# calculate_vp(pvolfile)
+# but for now we will use bioRad's example vertical profile already calculated:
+example_vp
    ##                Vertical profile (class vp)
 ## 
 ##        radar:  seang 
@@ -173,10 +173,10 @@ 
    
 ## nominal time:  2015-10-18 18:00:00 
 ## generated by:  vol2bird 0.3.17

    Let’s plot the vertical profile, for the quantity eta (the linear reflectivity):

    -
    plot(example_vp, quantity = "eta")
    +
    plot(example_vp, quantity = "eta")

    Note that eta is directly related to reflectivity factor (DBZH), i.e. a reflectivity factor of 5 dBZ amounts to the following eta at a radar wavelength of 5.3 cm:

    -
    dbz_to_eta(5, wavelength = 5.3)
    +
    dbz_to_eta(5, wavelength = 5.3)
    ## [1] 1060.747
    @@ -207,33 +207,33 @@

    5 Example: estimating a VID image

    Let’s first make a PPI plot of the lowest uncorrected scan:

    -
    # extract the first scan from the polar volume:
-my_scan <- example_pvol$scans[[1]]
-# project it as a PPI on the ground:
-my_ppi <- project_as_ppi(my_scan, range_max = 100000)
-# plot it
-plot(my_ppi)
    +
    # extract the first scan from the polar volume:
+my_scan <- example_pvol$scans[[1]]
+# project it as a PPI on the ground:
+my_ppi <- project_as_ppi(my_scan, range_max = 100000)
+# plot it
+plot(my_ppi)

    Now let’s calculate the range-corrected PPI

    -
    # let's use a 500 metre spatial grid (res), and restrict to 100x100 km area
-my_corrected_ppi <- integrate_to_ppi(example_pvol, example_vp, res = 500, xlim = c(-100000, 100000), ylim = c(-100000, 100000))
-my_corrected_ppi
    +
    # let's use a 500 metre spatial grid (res), and restrict to 100x100 km area
+my_corrected_ppi <- integrate_to_ppi(example_pvol, example_vp, res = 500, xlim = c(-100000, 100000), ylim = c(-100000, 100000))
+my_corrected_ppi
    ##                Plan position indicator (class ppi)
 ## 
 ##   quantities:  VIR VID R overlap eta_sum eta_sum_expected 
 ##         dims:  400 x 400 pixels

    The range corrected PPI has four parameters: VIR, VID, R, overlap. Let’s plot the adjustment factor R:

    -
    # plot the adjustment factor R:
-plot(my_corrected_ppi, param = "R")
    +
    # plot the adjustment factor R:
+plot(my_corrected_ppi, param = "R")

    Let’s also plot the vertically integrated reflectivity:

    -
    plot(my_corrected_ppi, param = "VIR")
    +
    plot(my_corrected_ppi, param = "VIR")

    Or plot the vertically integrated density on a map:

    -
    bm <- download_basemap(my_corrected_ppi)
    +
    bm <- download_basemap(my_corrected_ppi)
    ## Downloading zoom = 8 ...
    ## Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL.
    -
    map(my_corrected_ppi, bm, param = "VIR", alpha = .5)
    +
    map(my_corrected_ppi, bm, param = "VIR", alpha = .5)

    @@ -245,16 +245,16 @@

  • at large distances weak biological echoes may get below the radar’s detection level

    • We can calculate overlap between emitted radiation and the biological profile as follows:

    -
    # calculate overlap between vertical profile of birds
-# and the vertical radiation profile emitted by the radar:
-bpo <- beam_profile_overlap(example_vp, get_elevation_angles(example_pvol), seq(0, 100000, 1000), quantity = "eta")
-# plot the calculated overlap:
-plot(bpo)
    +
    # calculate overlap between vertical profile of birds
+# and the vertical radiation profile emitted by the radar:
+bpo <- beam_profile_overlap(example_vp, get_elevation_angles(example_pvol), seq(0, 100000, 1000), quantity = "eta")
+# plot the calculated overlap:
+plot(bpo)

    The function first normalizes the vertical profile altitudinal distribution. This can be either using profile quantity eta or dens, whichever is preferred (note that dens, the density, is sometimes thresholded to zero based on radial velocity standard deviation, see sd_vvp_threshold(), while eta is not)

    It then calculates the overlap between the normalized vertical profile, and the normalized radiation profile as calculated with beam_profile(), using a metric called the Bhattacharyya distance. This metric is zero when there is no overlap, and 1 when the distributions are identical.

    The range-corrected PPI also contains a field overlap, which contains the same metric but then calculated on the grid of the PPI:

    -
    plot(my_corrected_ppi, param = "overlap")
    +
    plot(my_corrected_ppi, param = "overlap")

    The overlap metric might be used in the future to show only certain section of the PPI, based on their overlap value.

    @@ -269,20 +269,9 @@

    @@ -293,7 +282,7 @@

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/authors.html b/docs/authors.html index 1ac2288cb..409e5d1ec 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,7 +54,6 @@ - @@ -68,7 +71,7 @@ - +
    @@ -121,7 +124,7 @@
    • - + @@ -211,7 +214,7 @@

      Authors

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/docsearch.json b/docs/docsearch.json index 073f8190b..11afd16ab 100644 --- a/docs/docsearch.json +++ b/docs/docsearch.json @@ -74,7 +74,7 @@ "selector": ".contents h2, .contents h3", "default_value": "Context" }, - "text": ".contents p, .contents li, .tempate-article .contents .pre" + "text": ".contents p, .contents li" } }, "selectors_exclude": [ diff --git a/docs/index.html b/docs/index.html index 6f5473a6e..b0fcf6bf2 100644 --- a/docs/index.html +++ b/docs/index.html @@ -12,24 +12,24 @@ - - - - - + + + + + + - - +
    @@ -197,12 +197,12 @@

    Radar data example

    bioRad can read weather radar data (= polar volumes) in the ODIM format and formats supported by the RSL library, such as NEXRAD data. NEXRAD data (US) are available as open data and on AWS.

    Here we read an example polar volume data file with read_pvolfile(), extract the scan/sweep at elevation angle 3 with get_scan(), project the data to a plan position indicator with project_as_ppi() and plot the radial velocity of detected targets with plot():

    -
    library(tidyverse) # To pipe %>% the steps below
-system.file("extdata", "volume.h5", package = "bioRad") %>%
-  read_pvolfile() %>%
-  get_scan(3) %>%
-  project_as_ppi() %>%
-  plot(param = "VRADH") # VRADH = radial velocity in m/s
    +
    library(tidyverse) # To pipe %>% the steps below
+system.file("extdata", "volume.h5", package = "bioRad") %>%
+  read_pvolfile() %>%
+  get_scan(3) %>%
+  project_as_ppi() %>%
+  plot(param = "VRADH") # VRADH = radial velocity in m/s

    Radial velocities towards the radar are negative, while radial velocities away from the radar are positive, so in this plot there is movement from the top right to the bottom left.

    @@ -211,22 +211,22 @@

    Vertical profile data example

    Weather radar data can be processed into vertical profiles of biological targets using calculate_vp(). This type of data is available as open data for over 100 European weather radars.

    Once vertical profile data are loaded into bioRad, these can be bound into time series using bind_into_vpts(). Here we read an example time series, project it on a regular time grid with regularize_vpts() and plot it with plot():

    -
    example_vpts %>%
-  regularize_vpts() %>%
-  plot()
-#> projecting on 300 seconds interval grid...
    +
    example_vpts %>%
+  regularize_vpts() %>%
+  plot()
+#> projecting on 300 seconds interval grid...

    The gray bars in the plot indicate gaps in the data.

    The altitudes in the profile can be integrated with integrate_profile() resulting in a dataframe with rows for datetimes and columns for quantities. Here we plot the quantity migration traffic rate (column mtr) with plot():

    -
    my_vpi <- integrate_profile(example_vpts)
-
-plot(my_vpi, quantity = "mtr") # mtr = migration traffic rate
    +
    my_vpi <- integrate_profile(example_vpts)
+
+plot(my_vpi, quantity = "mtr") # mtr = migration traffic rate

    To know the total number of birds passing over the radar during the full time series, we use the last value of the cumulative migration traffic (column mt):

    -
    my_vpi %>%
-  pull(mt) %>% # Extract column mt as a vector
-  last()
-#> [1] 173023.8
    +
    my_vpi %>%
+  pull(mt) %>% # Extract column mt as a vector
+  last()
+#> [1] 173023.8

    For more exercises, see this tutorial.

    @@ -249,7 +249,7 @@

    Links

    - +
    +

    Dev status

    +
      +
    • CRAN status
      • +
    • DOI
      • +
    +
    + @@ -300,7 +307,7 @@

    Developers

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/news/index.html b/docs/news/index.html index 7df442010..ed65b2983 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,7 +54,6 @@ - @@ -68,7 +71,7 @@ - +
    @@ -121,7 +124,7 @@
    • - + @@ -145,12 +148,23 @@
      -

      Changelog

      +

      Changelog

      Source: NEWS.md
      +
      +

      +bioRad 0.5.1 Unreleased +

      +

      Minor bugfixes. All issues included in this release can be found here

      +
        +

      • extend the functionality of composite_ppi() and improve its documentation (partial fix of #59)

        • +

      • fix a bug in the color legend of map() when providing a custom color scale with palette argument (#324)

        • +

      • resolve a conflict with upcoming R 0.4 release

        • +
      +
      -

      +

      bioRad 0.5.0 2020-02-19

      New CRAN release. All issues included in this release can be found here.

      @@ -204,7 +218,7 @@

      -

      +

      bioRad 0.4.0 2018-12-14

      First release on CRAN! All issues included in this release can be found here.

      @@ -221,7 +235,7 @@

    -

    +

    bioRad 0.3.0 Unreleased

    Release consistent with and in preparation of the bioRad methods paper (https://doi.org/10.1111/ecog.04028). All issues included in this release can be found here.

    @@ -240,14 +254,9 @@

    @@ -259,7 +268,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/pkgdown.css b/docs/pkgdown.css index fa9261632..c01e5923b 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -17,6 +17,10 @@ html, body { height: 100%; } +body { + position: relative; +} + body > .container { display: flex; height: 100%; @@ -67,6 +71,10 @@ summary { margin-top: calc(-60px + 1em); } +dd { + margin-left: 3em; +} + /* Section anchors ---------------------------------*/ a.anchor { @@ -100,6 +108,52 @@ a.anchor { margin-top: -40px; } +/* Navbar submenu --------------------------*/ + +.dropdown-submenu { + position: relative; +} + +.dropdown-submenu>.dropdown-menu { + top: 0; + left: 100%; + margin-top: -6px; + margin-left: -1px; + border-radius: 0 6px 6px 6px; +} + +.dropdown-submenu:hover>.dropdown-menu { + display: block; +} + +.dropdown-submenu>a:after { + display: block; + content: " "; + float: right; + width: 0; + height: 0; + border-color: transparent; + border-style: solid; + border-width: 5px 0 5px 5px; + border-left-color: #cccccc; + margin-top: 5px; + margin-right: -10px; +} + +.dropdown-submenu:hover>a:after { + border-left-color: #ffffff; +} + +.dropdown-submenu.pull-left { + float: none; +} + +.dropdown-submenu.pull-left>.dropdown-menu { + left: -100%; + margin-left: 10px; + border-radius: 6px 0 6px 6px; +} + /* Sidebar --------------------------*/ #pkgdown-sidebar { @@ -122,6 +176,61 @@ a.anchor { margin-bottom: 0.5em; } +/* bootstrap-toc tweaks ------------------------------------------------------*/ + +/* All levels of nav */ + +nav[data-toggle='toc'] .nav > li > a { + padding: 4px 20px 4px 6px; + font-size: 1.5rem; + font-weight: 400; + color: inherit; +} + +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 5px; + color: inherit; + border-left: 1px solid #878787; +} + +nav[data-toggle='toc'] .nav > .active > a, +nav[data-toggle='toc'] .nav > .active:hover > a, +nav[data-toggle='toc'] .nav > .active:focus > a { + padding-left: 5px; + font-size: 1.5rem; + font-weight: 400; + color: inherit; + border-left: 2px solid #878787; +} + +/* Nav: second level (shown on .active) */ + +nav[data-toggle='toc'] .nav .nav { + display: none; /* Hide by default, but at >768px, show it */ + padding-bottom: 10px; +} + +nav[data-toggle='toc'] .nav .nav > li > a { + padding-left: 16px; + font-size: 1.35rem; +} + +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 15px; +} + +nav[data-toggle='toc'] .nav .nav > .active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 15px; + font-weight: 500; + font-size: 1.35rem; +} + +/* orcid ------------------------------------------------------------------- */ + .orcid { font-size: 16px; color: #A6CE39; diff --git a/docs/pkgdown.js b/docs/pkgdown.js index 087a76227..7e7048fae 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -9,11 +9,6 @@ $('body').css('padding-top', $('.navbar').height() + 10); }); - $('body').scrollspy({ - target: '#sidebar', - offset: 60 - }); - $('[data-toggle="tooltip"]').tooltip(); var cur_path = paths(location.pathname); diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 3dd836aef..11769e4aa 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,10 +1,11 @@ -pandoc: '2.9' -pkgdown: 1.4.1.9000 -pkgdown_sha: 48e12e0fc836ec8ca423b44656b97f719cd856c7 +pandoc: '2.5' +pkgdown: 1.5.0 +pkgdown_sha: ~ articles: bioRad: bioRad.html rad_aero_19: rad_aero_19.html range_correction: range_correction.html +last_built: 2020-03-31T21:28Z urls: reference: https://adokter.github.io/bioRad/reference article: https://adokter.github.io/bioRad/articles diff --git a/docs/reference/add_expected_eta_to_scan.html b/docs/reference/add_expected_eta_to_scan.html index 1dbe16a0f..15e5c0093 100644 --- a/docs/reference/add_expected_eta_to_scan.html +++ b/docs/reference/add_expected_eta_to_scan.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -230,13 +233,9 @@

      Details

    @@ -247,7 +246,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/apply_mistnet.html b/docs/reference/apply_mistnet.html index cc6463d70..4c639eb7f 100644 --- a/docs/reference/apply_mistnet.html +++ b/docs/reference/apply_mistnet.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -221,14 +224,14 @@

      Details it can estimate a segmentation mask that identifies pixels with weather that should be removed when interested only in biological data.

      MistNet will calculate three class probabilities (from 0 to 1, with 1 corresponding -to a 100% probability) as additional scan parameters to the polar volume:

      +to a 100% probability) as additional scan parameters to the polar volume:

      "BACKGROUND"

      class probability that no signal was detected above the noise level of the radar

      "WEATHER"

      class probability that weather was detected

      "BIOLOGY"

      class probability that biological scatterers were detected

      These class probabilities are only available for the 5 input elevations used as input for the MistNet model. Based on all the class probabilities a final weather segmentation map calculated, -stored as scan parameter CELL, which is available for all elevation scans.

      +stored as scan parameter CELL, which is available for all elevation scans.

      "CELL"

      Final weather segmentation, with values > 1 indicating pixels classified as weather, and values equal to 1 indicating pixels that are located within 5 km distance of a weather pixels

      @@ -252,7 +255,7 @@

      R

      Examples

      - 
      # \dontrun{
+    
      if (FALSE) {
 # download a NEXRAD file, save as KBGM_example
 download.file(paste("https://noaa-nexrad-level2.s3.amazonaws.com/",
   "2019/10/01/KBGM/KBGM20191001_000542_V06",
@@ -270,29 +273,27 @@ 
      Examp
 my_ppi <- project_as_ppi(my_scan, range_max = 100000)
 
 # plot the reflectivity parameter:
-plot(my_ppi, param = "DBZH")
      
+plot(my_ppi, param = "DBZH")
+
 # plot the MistNet class probability [0-1] for weather
-plot(my_ppi, param = "WEATHER")
      
+plot(my_ppi, param = "WEATHER")
+
 # plot the MistNet class probability [0-1] for biology
-plot(my_ppi, param = "BIOLOGY")
      
+plot(my_ppi, param = "BIOLOGY")
+
 # plot the final segmentation result, with values >1 indicating
 # areas classified as weather, and value 1 pixels that fall within an
 # additional 5 km fringe around weather areas.
-plot(my_ppi, param = "CELL")
      
+plot(my_ppi, param = "CELL")
+
 # clean up:
-file.remove("~/KBGM_example")
      #> [1] TRUE
      # }
-
      
+file.remove("~/KBGM_example")
+}

    @@ -303,7 +304,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/as.data.frame.vp.html b/docs/reference/as.data.frame.vp.html index 9441e82ab..9d3139ee3 100644 --- a/docs/reference/as.data.frame.vp.html +++ b/docs/reference/as.data.frame.vp.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,7 +57,6 @@ on sunrise/sunset, day/night and derived quantities like migration traffic rates." /> - @@ -71,7 +74,7 @@ - +
    @@ -124,7 +127,7 @@
    • - + @@ -364,14 +367,9 @@

      Examp df <- as.data.frame(example_vp, suntime = TRUE, lat = 50, lon = 4)

    @@ -382,7 +380,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/as.data.frame.vpts.html b/docs/reference/as.data.frame.vpts.html index 754113b08..f81fc37c3 100644 --- a/docs/reference/as.data.frame.vpts.html +++ b/docs/reference/as.data.frame.vpts.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,7 +57,6 @@ data Frame, and optionally adds information on sunrise/sunset, day/night and derived quantities like migration traffic rates." /> - @@ -71,7 +74,7 @@ - +
    @@ -124,7 +127,7 @@
    • - + @@ -292,14 +295,9 @@

      Examp #> 10 519 FALSE 2016-09-01 05:03:05 2016-09-01 18:23:38

    @@ -310,7 +308,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/beam_distance.html b/docs/reference/beam_distance.html index 554f37ea6..9927f0a71 100644 --- a/docs/reference/beam_distance.html +++ b/docs/reference/beam_distance.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -201,14 +204,9 @@

      Examp beam_distance(100000, 5)

    #> [1] 99495.13
    @@ -219,7 +217,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/beam_height.html b/docs/reference/beam_height.html index f1fd190ca..435ab5173 100644 --- a/docs/reference/beam_height.html +++ b/docs/reference/beam_height.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -215,14 +218,9 @@

      Examp plot(range, beam_height(range, 0.5), ylab = "beam height [m]", xlab = "range [m]")

    @@ -233,7 +231,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/beam_profile.html b/docs/reference/beam_profile.html index c4442cff5..46bcb205f 100644 --- a/docs/reference/beam_profile.html +++ b/docs/reference/beam_profile.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -243,14 +246,9 @@

      Examp )

    @@ -261,7 +259,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/beam_profile_overlap.html b/docs/reference/beam_profile_overlap.html index 3c4386cfa..b3c1bf4fd 100644 --- a/docs/reference/beam_profile_overlap.html +++ b/docs/reference/beam_profile_overlap.html @@ -18,23 +18,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -43,7 +47,7 @@ - + @@ -55,7 +59,6 @@ and the vertical radiation profile of a set of emitted radar beams at various elevation angles as given by beam_profile." /> - @@ -73,7 +76,7 @@ - +
    @@ -126,7 +129,7 @@
    • - + @@ -292,14 +295,9 @@

      Examp plot(bpo)

    @@ -310,7 +308,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/beam_range.html b/docs/reference/beam_range.html index 50eaf4934..0088353be 100644 --- a/docs/reference/beam_range.html +++ b/docs/reference/beam_range.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -200,14 +203,9 @@

      Examp beam_range(100000, 5)

    #> [1] 100508.1
    @@ -218,7 +216,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/beam_width.html b/docs/reference/beam_width.html index 9f0ffa7c5..591fb4fdb 100644 --- a/docs/reference/beam_width.html +++ b/docs/reference/beam_width.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -185,13 +188,9 @@

      Examp plot(range, beam_width(range), ylab = "beam width [m]", xlab = "range [m]")

    @@ -202,7 +201,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/bind_into_vpts.html b/docs/reference/bind_into_vpts.html index b9df29296..5a35afa76 100644 --- a/docs/reference/bind_into_vpts.html +++ b/docs/reference/bind_into_vpts.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,7 +57,6 @@ (vpts), sorted in time. Can also bind multiple vpts of a single radar into one vpts." /> - @@ -71,7 +74,7 @@ - +
    @@ -124,7 +127,7 @@
    • - + @@ -250,14 +253,9 @@

      Examp #> time step (s): 240

    @@ -268,7 +266,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/bioRad-deprecated.html b/docs/reference/bioRad-deprecated.html index f8d379aa3..fc8609a0f 100644 --- a/docs/reference/bioRad-deprecated.html +++ b/docs/reference/bioRad-deprecated.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,7 +57,6 @@ defunct in the near future. When possible, alternative functions with similar functionality are mentioned." /> - @@ -71,7 +74,7 @@ - +
    @@ -124,7 +127,7 @@
    • - + @@ -365,14 +368,13 @@

      mt

      specified altitude band.

      Deprecated examples

      -# get example time series of vertical profiles:
-data(example_vpts)
-example_vpts
-# total migration traffic in full altitude band:
-mt(example_vpts)
-# total migration traffic in 0-1000 meter band:
-mt(example_vpts, alt.min = 0, alt.max = 1000)
-
      +# get example time series of vertical profiles: +data(example_vpts) +example_vpts +# total migration traffic in full altitude band: +mt(example_vpts) +# total migration traffic in 0-1000 meter band: +mt(example_vpts, alt.min = 0, alt.max = 1000)

      mtr

      @@ -412,15 +414,14 @@

      mtr

      positive or negative, depending on the definition of alpha.

      Deprecated examples

      -# MTR for a single vertical profile:
-mtr(example_vp)
-# MTRs for a time series of vertical profiles:
-data(example_vpts)
-# print migration traffic rates:
-mtr(example_vpts)
-# to plot migration traffic rate data, use integrate_profile:
-plot(integrate_profile(example_vpts), quantity = "mtr")
-
      +# MTR for a single vertical profile: +mtr(example_vp) +# MTRs for a time series of vertical profiles: +data(example_vpts) +# print migration traffic rates: +mtr(example_vpts) +# to plot migration traffic rate data, use integrate_profile: +plot(integrate_profile(example_vpts), quantity = "mtr")

      cmt

      @@ -439,12 +440,11 @@

      cmt

      band.

      Deprecated examples

      -# get example time series of vertical profiles:
-data(example_vpts)
+# get example time series of vertical profiles:
+data(example_vpts)
 
-# print cumulative migration traffic to console:
-cmt(example_vpts)
-
      +# print cumulative migration traffic to console: +cmt(example_vpts)

      night

      @@ -539,46 +539,9 @@

      SCAN

    @@ -589,7 +552,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/bioRad-package.html b/docs/reference/bioRad-package.html index e401c9952..7718eec42 100644 --- a/docs/reference/bioRad-package.html +++ b/docs/reference/bioRad-package.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -54,7 +58,6 @@ insects from weather radar data. See &lt;doi:10.1111/ecog.04028&gt; for a software paper describing package and methodologies." /> - @@ -72,7 +75,7 @@ - +
    @@ -125,7 +128,7 @@
    • - + @@ -187,28 +190,9 @@

      See a

    @@ -219,7 +203,7 @@

    Author

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/c.vp.html b/docs/reference/c.vp.html index 51f197304..cdf905c8e 100644 --- a/docs/reference/c.vp.html +++ b/docs/reference/c.vp.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -173,12 +176,9 @@

      Value

    @@ -189,7 +189,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/calculate_param.html b/docs/reference/calculate_param.html index c52ab7d06..0455f20c4 100644 --- a/docs/reference/calculate_param.html +++ b/docs/reference/calculate_param.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -54,7 +58,6 @@ linear reflectivity eta, depolarization ratio (Kilambi et al. 2018), or for applying clutter corrections (CCORH) to uncorrected reflectivity moments (TH), as in TH+CCORH" /> - @@ -72,7 +75,7 @@ - +
    @@ -125,7 +128,7 @@
    • - + @@ -227,15 +230,9 @@

      Examp #> dims: 480 bins x 360 rays

    @@ -246,7 +243,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/calculate_vp.html b/docs/reference/calculate_vp.html index 0edaa08ae..1c1cebb57 100644 --- a/docs/reference/calculate_vp.html +++ b/docs/reference/calculate_vp.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -405,113 +408,21 @@

      Examp # copy to a home directory with read/write permissions: file.copy(pvolfile, "~/volume.h5")

    #> [1] TRUE
    # calculate the profile: -# \dontrun{ +if (FALSE) { profile <- calculate_vp("~/volume.h5") # print some summary info: -profile
    #> Vertical profile (class vp) -#> -#> radar: seang -#> source: WMO:02606,RAD:SE50,PLC:Angelholm,NOD:seang,ORG:82,CTY:643,CMT:Swedish radar -#> nominal time: 2015-10-18 18:00:00 -#> generated by: vol2bird 0.5.0
    # convert profile to a data.frame: -as.data.frame(profile)
    #> radar datetime ff dbz dens u v -#> 1 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 2 seang 2015-10-18 18:00:00 NaN 2.8776991 61.27740 NaN NaN -#> 3 seang 2015-10-18 18:00:00 14.88610 5.5255389 112.74165 -6.467583 -13.407694 -#> 4 seang 2015-10-18 18:00:00 14.64004 4.6949205 93.11562 -6.711918 -13.010798 -#> 5 seang 2015-10-18 18:00:00 13.30489 0.4530046 35.06153 -6.556170 -11.577423 -#> 6 seang 2015-10-18 18:00:00 10.76581 -1.9438103 20.19061 -5.069613 -9.497456 -#> 7 seang 2015-10-18 18:00:00 10.33567 -1.8632607 20.56858 -5.671824 -8.640401 -#> 8 seang 2015-10-18 18:00:00 12.07231 -2.2290711 18.90703 -7.580208 -9.395803 -#> 9 seang 2015-10-18 18:00:00 10.28255 -2.5026581 17.75271 -3.064733 -9.815207 -#> 10 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 11 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 12 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 13 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 14 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 15 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 16 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 17 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 18 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 19 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 20 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> gap w n_dbz dd n DBZH height n_dbz_all eta -#> 1 1 NA 0 NA 0 NA 0 0 NA -#> 2 1 NaN 817 NaN 536 4.873434 200 10602 674.0515 -#> 3 0 6.552267 4231 205.7517 2116 8.229273 400 17421 1240.1581 -#> 4 0 -17.817648 4085 207.2880 1866 4.437433 600 8098 1024.2719 -#> 5 0 -12.915339 3897 209.5224 1155 1.342218 800 7801 385.6769 -#> 6 0 30.602781 4369 208.0927 744 -0.492405 1000 7829 222.0967 -#> 7 0 24.725313 2276 213.2821 450 -1.101062 1200 3206 226.2544 -#> 8 0 57.809780 1694 218.8954 198 -1.102251 1400 2851 207.9773 -#> 9 0 36.869717 2045 197.3406 158 10.828478 1600 3213 195.2798 -#> 10 1 NA 0 NA 0 NA 1800 0 NA -#> 11 1 NA 0 NA 0 NA 2000 0 NA -#> 12 1 NA 0 NA 0 NA 2200 0 NA -#> 13 1 NA 0 NA 0 NA 2400 0 NA -#> 14 1 NA 0 NA 0 NA 2600 0 NA -#> 15 1 NA 0 NA 0 NA 2800 0 NA -#> 16 1 NA 0 NA 0 NA 3000 0 NA -#> 17 1 NA 0 NA 0 NA 3200 0 NA -#> 18 1 NA 0 NA 0 NA 3400 0 NA -#> 19 1 NA 0 NA 0 NA 3600 0 NA -#> 20 1 NA 0 NA 0 NA 3800 0 NA -#> sd_vvp n_all lat lon height_antenna day sunrise -#> 1 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 2 3.271695 4351 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 3 3.220699 5304 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 4 3.316308 3144 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 5 3.897997 2043 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 6 4.067675 1380 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 7 4.837257 747 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 8 4.795825 483 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 9 4.506003 315 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 10 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 11 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 12 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 13 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 14 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 15 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 16 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 17 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 18 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 19 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 20 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> sunset -#> 1 2015-10-18 15:56:28 -#> 2 2015-10-18 15:56:28 -#> 3 2015-10-18 15:56:28 -#> 4 2015-10-18 15:56:28 -#> 5 2015-10-18 15:56:28 -#> 6 2015-10-18 15:56:28 -#> 7 2015-10-18 15:56:28 -#> 8 2015-10-18 15:56:28 -#> 9 2015-10-18 15:56:28 -#> 10 2015-10-18 15:56:28 -#> 11 2015-10-18 15:56:28 -#> 12 2015-10-18 15:56:28 -#> 13 2015-10-18 15:56:28 -#> 14 2015-10-18 15:56:28 -#> 15 2015-10-18 15:56:28 -#> 16 2015-10-18 15:56:28 -#> 17 2015-10-18 15:56:28 -#> 18 2015-10-18 15:56:28 -#> 19 2015-10-18 15:56:28 -#> 20 2015-10-18 15:56:28
    # } +profile +# convert profile to a data.frame: +as.data.frame(profile) +} # clean up: file.remove("~/volume.h5")
    #> [1] TRUE
    @@ -522,7 +433,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/check_date_format.html b/docs/reference/check_date_format.html index f26a19771..df4e8cf44 100644 --- a/docs/reference/check_date_format.html +++ b/docs/reference/check_date_format.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -179,12 +182,9 @@

      Value

    @@ -195,7 +195,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/check_docker.html b/docs/reference/check_docker.html index a94f96b16..25e05ed69 100644 --- a/docs/reference/check_docker.html +++ b/docs/reference/check_docker.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -175,19 +178,15 @@

      Value

      2 if Docker daemon not running, 3 if Docker daemon not found.

      Examples

      - 
      # \dontrun{
+    
      if (FALSE) {
 # check if Docker is running and vol2bird image is available:
-check_docker()
      #> Running docker image with vol2bird version 0.5.0  (MistNet available) 
      #> [1] 0
      # }
-
      
+check_docker()
+}
    @@ -198,7 +197,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/check_night.html b/docs/reference/check_night.html index 36984e9b0..86c813ecb 100644 --- a/docs/reference/check_night.html +++ b/docs/reference/check_night.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -54,7 +58,6 @@ (pvol, vp, vpts) this information is extracted from the bioRad object directly." /> - @@ -72,7 +75,7 @@ - +
    @@ -125,7 +128,7 @@
    • - + @@ -393,14 +396,9 @@

      Examp #> [1933] FALSE FALSE

    @@ -411,7 +409,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/check_radar_codes.html b/docs/reference/check_radar_codes.html index 287df4207..cac7a09b9 100644 --- a/docs/reference/check_radar_codes.html +++ b/docs/reference/check_radar_codes.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -174,12 +177,9 @@

      Value

    @@ -190,7 +190,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/composite_ppi.html b/docs/reference/composite_ppi.html index b60a7c45e..370287e01 100644 --- a/docs/reference/composite_ppi.html +++ b/docs/reference/composite_ppi.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,7 +57,6 @@ ppi. Can be used to make a composite of ppi's from multiple radars." /> - @@ -71,7 +74,7 @@ - +
    @@ -124,7 +127,7 @@
    • - + @@ -159,22 +162,77 @@

      Create a composite of multiple plan position indicators (ppi)

    - 
    composite_ppi(x, param = "DBZH", dim = c(100, 100))
    + 
    composite_ppi(
+  x,
+  param = "DBZH",
+  nx = 100,
+  ny = 100,
+  xlim,
+  ylim,
+  res,
+  crs,
+  raster = NA,
+  method = "max",
+  idp = 2,
+  idw_max_distance = NA
+)

    Arguments

    - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    x

    A list of ppi.

    A list of ppi objects.
    param

    Scan parameter to composite.
    dim

    integer. Vector with number of cells in each spatial dimension.

    		nx

    number of raster pixels in the x (longitude) dimension

    ny

    number of raster pixels in the y (latitude) dimension

    xlim

    x (longitude) range

    ylim

    y (latitude) range

    res

    numeric vector of length 1 or 2 to set the resolution of the raster (see res). +If this argument is used, arguments nx and ny are ignored. Unit is identical to xlim and ylim.

    crs

    character or object of class CRS. PROJ.4 type description of a Coordinate Reference System (map projection). +When 'NA' (default), an azimuthal equidistant projection with origin at the radar location is used. +To use a WSG84 (lat,lon) projection, use crs="+proj=longlat +datum=WGS84"

    raster

    (optional) RasterLayer with a CRS. When specified this raster topology is used for the output, and nx, ny, res +arguments are ignored.

    method

    string. Compositing method, one of "mean", "min", "max" or "idw"

    idp

    numeric. inverse distance weighting power

    idw_max_distance

    numeric. Maximum distance from the radar to consider in +inverse distance weighting. Measuruments beyond this distance will have a +weighting factor of zero.
    @@ -183,25 +241,53 @@

    Value

    A ppi.

    Details

    -

    This function is a prototype, wait for the next bioRad release -for more documentation and functionality.

    -

    The latitude/longitude of the returned ppi use the WGS84 -datum.

    +

    This function composites multiple ppi objects into a ppi object that +combines all data.

    +

    Either multiple ppi's of different scan elevation of the same radar may be combined, +or ppi's of different radars can be composited.

    +

    Argument method determines how values of different ppi's at the same +geographic location are combined.

    +
    "mean"

    Compute the average value

    +
    "max"

    Compute the maximum value. If ppi's are of the same radar +and the same polar volume, this computes a max product, showing the maximum +detected signal at that geographic location.

    +
    "min"

    Compute the minimum value

    +
    "idw"

    This option is useful primarily when compositing ppi's of +multiple radars. Performs an inverse distance weighting, where values are +weighted according to 1/(distance from the radar)^idp

    + + + +

    The coordinates system of the returned ppi is a WGS84 +(lat,lon) datum.

    +

    This function is a prototype and under active development

    Examples

    - 
    # load the example polar scan:
-data(example_scan)
-# to be written ...
    + 
    # locate example volume file:
+pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
+
+# load the file:
+example_pvol <- read_pvolfile(pvolfile)
+
+# calculate a ppi for each elevation scan
+my_ppis <- lapply(example_pvol$scans, project_as_ppi)
+
+# overlay the ppi's, calculating the maximum value observed
+# across the available scans at each geographic location
+my_composite <- composite_ppi(my_ppis, method="max")
+
+if (FALSE) {
+# download basemap
+bm <- download_basemap(my_composite)
+
+# plot the calculated max product on the basemap
+map(my_composite, bm)
+}
    @@ -212,7 +298,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/dbz_to_eta.html b/docs/reference/dbz_to_eta.html index 343a365d6..eca559ed3 100644 --- a/docs/reference/dbz_to_eta.html +++ b/docs/reference/dbz_to_eta.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -189,13 +192,9 @@

      Examp dbz_to_eta(7, 5) / 11 # C-band

    #> [1] 192.949
    dbz_to_eta(7, 10) / 11 # S-band
    #> [1] 12.05931
    @@ -206,7 +205,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/download_basemap.html b/docs/reference/download_basemap.html index 204434ac9..2ad19e459 100644 --- a/docs/reference/download_basemap.html +++ b/docs/reference/download_basemap.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -212,7 +215,7 @@

      Details enable billing and provide an API key to ggmap. See the ggmap README for details.

      To use maptype, install the development version of ggmap (>3.0.0) with -devtools::install_github("dkahle/ggmap").

      +devtools::install_github("dkahle/ggmap").

      Examples

      # load an example scan:
@@ -226,28 +229,29 @@ 
      Examp
 #>            dims:  480 bins x 360 rays
      
 # make ppi for the scan
 ppi <- project_as_ppi(example_scan)
-# \dontrun{
+if (FALSE) {
 # grab a basemap that matches the extent of the ppi:
-basemap <- download_basemap(ppi)
      #> Downloading zoom = 9 ...
      #> Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL.
      
+basemap <- download_basemap(ppi)
+
 # map the reflectivity quantity of the ppi onto the basemap:
-map(ppi, map = basemap, param = "DBZH")
      
+map(ppi, map = basemap, param = "DBZH")
+
 # increase the transparancy of the basemap:
-basemap <- download_basemap(ppi, alpha = 0.3)
      #> Downloading zoom = 9 ...
      #> Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL.
      map(ppi, map = basemap, param = "DBZH")
      
+basemap <- download_basemap(ppi, alpha = 0.3)
+map(ppi, map = basemap, param = "DBZH")
+
 # download a different type of basemap, e.g. a gray-scale image:
 # see get_map() in ggmap library for full documentation of options
-basemap <- download_basemap(ppi, maptype = "toner-lite")
      #> Downloading zoom = 9 ...
      #> Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL.
      
+basemap <- download_basemap(ppi, maptype = "toner-lite")
+
 # map the radial velocities onto the line image:
-map(ppi, map = basemap, param = "VRADH")
      # }
-
      +map(ppi, map = basemap, param = "VRADH") +}
    @@ -258,7 +262,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/download_vpfiles.html b/docs/reference/download_vpfiles.html index 39e5160c2..cee4cde52 100644 --- a/docs/reference/download_vpfiles.html +++ b/docs/reference/download_vpfiles.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,7 +57,6 @@ ENRAM data repository, where these are stored as monthly zips per radar." /> - @@ -71,7 +74,7 @@ - +
    @@ -124,7 +127,7 @@
    • - + @@ -202,7 +205,7 @@

      Examp 
      # Download data from radars "bejab" and "bewid", even if previously
 # downloaded (overwrite = TRUE). Will successfully download 2016-10 files,
 # but show 404 error for 2016-11 files (as these are not available).
-# \dontrun{
+if (FALSE) {
 dir.create("~/bioRad_tmp_files")
 download_vpfiles(
   date_min = "2016-10-01",
@@ -210,17 +213,15 @@ 
      Examp
   radar = c("bejab", "bewid"),
   directory = "~/bioRad_tmp_files",
   overwrite = TRUE
-)
      #> Downloading data from https://lw-enram.s3-eu-west-1.amazonaws.com
      #> bejab201610.zip: successfully downloaded
      #> bewid201610.zip: successfully downloaded
      #> bejab201611.zip: http error 404
      #> bewid201611.zip: http error 404
      # clean up:
+)
+# clean up:
 unlink("~/bioRad_tmp_files", recursive = T)
-# }
      +}

    @@ -231,7 +232,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/eta_to_dbz.html b/docs/reference/eta_to_dbz.html index 1d9e93549..0f680bd09 100644 --- a/docs/reference/eta_to_dbz.html +++ b/docs/reference/eta_to_dbz.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -190,13 +193,9 @@

      Examp eta_to_dbz(1000 * 11, 5) # C-band

    #> [1] 14.14557
    eta_to_dbz(1000 * 11, 10) # S-band
    #> [1] 26.18677
    @@ -207,7 +206,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/example_scan.html b/docs/reference/example_scan.html index afc9b092f..400207f33 100644 --- a/docs/reference/example_scan.html +++ b/docs/reference/example_scan.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -175,17 +178,14 @@

      Examp pvolfile <- system.file("extdata", "volume.h5", package = "bioRad") pvol <- read_pvolfile(pvolfile) example_scan <- pvol$scans[[1]] -# \dontrun{ +if (FALSE) { # save(example_scan, file = "data/example_scan.rda") -# }

    +} @@ -196,7 +196,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/example_vp.html b/docs/reference/example_vp.html index 81663e616..0a320aad5 100644 --- a/docs/reference/example_vp.html +++ b/docs/reference/example_vp.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,7 +57,6 @@ example_vp. Can be created with calculate_vp or read from file with read_vpfiles." /> - @@ -71,7 +74,7 @@ - +
    @@ -124,7 +127,7 @@
    • - + @@ -177,17 +180,14 @@

      Examp # example_vp was created with: vpfile <- system.file("extdata", "profile.h5", package = "bioRad") example_vp <- read_vpfiles(vpfile) -# \dontrun{ +if (FALSE) { # save(example_vp, file = "data/example_vp.rda") -# }

    +} @@ -198,7 +198,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/example_vpts.html b/docs/reference/example_vpts.html index 666b154f2..269081850 100644 --- a/docs/reference/example_vpts.html +++ b/docs/reference/example_vpts.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -173,24 +176,22 @@

      Examp #> time range (UTC): 2016-09-01 00:02:00 - 2016-09-10 11:56:00 #> time step (s): min: 180 max: 16320

    # example_vpts was created with: -# \dontrun{ +if (FALSE) { vptsfile <- system.file("extdata", "vpts.txt.zip", package = "bioRad") unzip(vptsfile, exdir = (dirname(vptsfile)), junkpaths = T) vptsfile <- substr(vptsfile, 1, nchar(vptsfile) - 4) example_vpts <- read_vpts(vptsfile, radar = "KBGM", wavelength = "S") -rcs(example_vpts) <- 11
    #> Warning: Threshold for sd_vvp not set, defaulting to 2 m/s
    sd_vvp_threshold(example_vpts) <- 2 +rcs(example_vpts) <- 11 +sd_vvp_threshold(example_vpts) <- 2 example_vpts$attributes$where$lat <- 42.2 example_vpts$attributes$where$lon <- -75.98 # save(example_vpts, file = "data/example_vpts.rda", compress = "xz") -# }
    +} @@ -201,7 +202,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/filter_vpts.html b/docs/reference/filter_vpts.html index 9029265bb..a5fa2c7e4 100644 --- a/docs/reference/filter_vpts.html +++ b/docs/reference/filter_vpts.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -166,11 +169,11 @@

      Arg min -

      Minimum datetime to be included. POSIXct value or charater string convertable to POSIXct.

      +

      Minimum datetime to be included. POSIXct value or character string convertable to POSIXct.

      max -

      Maximum datetime to be included. POSIXct value or charater string convertable to POSIXct.

      +

      Maximum datetime to be included. POSIXct value or character string convertable to POSIXct.

      nearest @@ -219,14 +222,9 @@

      Examp #> time step (s): min: 540 max: 600

    @@ -237,7 +235,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/gaussian_beam_profile.html b/docs/reference/gaussian_beam_profile.html index b30492206..4232166ad 100644 --- a/docs/reference/gaussian_beam_profile.html +++ b/docs/reference/gaussian_beam_profile.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -222,13 +225,9 @@

      Details

    @@ -239,7 +238,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/get_elevation_angles.html b/docs/reference/get_elevation_angles.html index 1e7ef9ab3..fc8426864 100644 --- a/docs/reference/get_elevation_angles.html +++ b/docs/reference/get_elevation_angles.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -203,14 +206,9 @@

      Examp get_elevation_angles(scan)

    #> [1] 0.5
    @@ -221,7 +219,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/get_odim_object_type.html b/docs/reference/get_odim_object_type.html index ffe3894c5..28d171a58 100644 --- a/docs/reference/get_odim_object_type.html +++ b/docs/reference/get_odim_object_type.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -179,13 +182,9 @@

      Examp get_odim_object_type(pvolfile) # > "PVOL"

    #> [1] "PVOL"
    @@ -196,7 +195,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/get_param.html b/docs/reference/get_param.html index 569740aa4..c605e6040 100644 --- a/docs/reference/get_param.html +++ b/docs/reference/get_param.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -189,13 +192,9 @@

      Examp #> dims: 480 bins x 360 rays

    @@ -206,7 +205,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/get_quantity.html b/docs/reference/get_quantity.html index 25b733543..489debf1f 100644 --- a/docs/reference/get_quantity.html +++ b/docs/reference/get_quantity.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -227,14 +230,9 @@

      Examp #> 0.0000000

    @@ -245,7 +243,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/get_scan.html b/docs/reference/get_scan.html index 76b87af50..dbaeeed53 100644 --- a/docs/reference/get_scan.html +++ b/docs/reference/get_scan.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -196,14 +199,9 @@

      Examp #> dims: 480 bins x 360 rays

    @@ -214,7 +212,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/index.html b/docs/reference/index.html index 055b06946..cadb4d98a 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,7 +54,6 @@ - @@ -68,7 +71,7 @@ - +
    @@ -121,7 +124,7 @@
    @@ -680,7 +727,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/integrate_profile.html b/docs/reference/integrate_profile.html index c53e9a76e..f17cf55c6 100644 --- a/docs/reference/integrate_profile.html +++ b/docs/reference/integrate_profile.html @@ -18,23 +18,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -43,7 +47,7 @@ - + @@ -55,7 +59,6 @@ traffic rate, and a vertical averaging of ground speed and direction weighted by density." /> - @@ -73,7 +76,7 @@ - +
    @@ -126,7 +129,7 @@
    • - + @@ -228,7 +231,7 @@

      Details

      Available quantities

      The function generates a specially classed data frame with the following -quantities:

      +quantities:

      datetime

      POSIXct date of each profile in UTC

      vid

      Vertically Integrated Density in individuals/km^2. vid is a surface density, whereas dens in vp @@ -360,15 +363,9 @@

      Examp plot(integrate_profile(example_vpts), quantity = "mt")

    @@ -379,7 +376,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/integrate_to_ppi.html b/docs/reference/integrate_to_ppi.html index 12a3a60d0..44d5639c3 100644 --- a/docs/reference/integrate_to_ppi.html +++ b/docs/reference/integrate_to_ppi.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -58,7 +62,6 @@ (overshooting) at larger distances from the radar. The methodology is described in detail in Kranstauber et al. (2020)." /> - @@ -76,7 +79,7 @@ - +
    @@ -129,7 +132,7 @@
    • - + @@ -360,15 +363,18 @@

      Examp # plot the vertically integrated reflectivity (VIR) using a 0-2000 cm^2/km^2 color scale: plot(my_ppi, zlim = c(0, 2000))

    -# \dontrun{ +if (FALSE) { # calculate the range-corrected ppi on finer 2000m x 2000m pixel raster: my_ppi <- integrate_to_ppi(example_pvol, example_vp, res = 2000) # plot the vertically integrated density (VID) using a 0-200 birds/km^2 color scale: -plot(my_ppi, param = "VID", zlim = c(0, 200))
    +plot(my_ppi, param = "VID", zlim = c(0, 200)) + # to overlay ppi objects on a background map, first # download a basemap, and map the ppi: -bm <- download_basemap(my_ppi)
    #> Downloading zoom = 7 ...
    #> Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL.
    map(my_ppi, bm)
    +bm <- download_basemap(my_ppi) +map(my_ppi, bm) + # the ppi can also be projected on a user-defined raster, as follows: # first define the raster: template_raster <- raster::raster(raster::extent(12, 13, 56, 57), crs = sp::CRS("+proj=longlat")) @@ -377,35 +383,21 @@

    Examp my_ppi <- integrate_to_ppi(example_pvol, example_vp, raster = template_raster) # extract the raster data from the ppi object: -raster::brick(my_ppi$data)

    #> class : RasterBrick -#> dimensions : 10, 10, 100, 6 (nrow, ncol, ncell, nlayers) -#> resolution : 0.1, 0.1 (x, y) -#> extent : 12, 13, 56, 57 (xmin, xmax, ymin, ymax) -#> crs : +proj=longlat +ellps=WGS84 -#> source : memory -#> names : VIR, VID, R, overlap, eta_sum, eta_sum_expected -#> min values : 0.00000000, 0.00000000, 0.00000000, 0.06252018, 0.00000000, 406.96716161 -#> max values : 6.052578e+04, 5.480034e+03, 6.151489e+01, 9.070487e-01, 6.468812e+04, 3.196694e+03 -#>
    +raster::brick(my_ppi$data) + # calculate the range-corrected ppi on an even finer 500m x 500m pixel raster, # cropping the area up to 50000 meter from the radar. my_ppi <- integrate_to_ppi(example_pvol, example_vp, res = 500, xlim = c(-50000, 50000), ylim = c(-50000, 50000) ) -plot(my_ppi, param = "VID", zlim = c(0, 200))
    # } -
    +plot(my_ppi, param = "VID", zlim = c(0, 200)) +} @@ -416,7 +408,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/is.nan.data.frame.html b/docs/reference/is.nan.data.frame.html index 886cf6f7d..8fd4d0133 100644 --- a/docs/reference/is.nan.data.frame.html +++ b/docs/reference/is.nan.data.frame.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,7 +57,6 @@ is.nan() function, which only works on vectors, by allowing data frames as input." /> - @@ -71,7 +74,7 @@ - +
    @@ -124,7 +127,7 @@
    • - + @@ -179,12 +182,9 @@

      Value

    @@ -195,7 +195,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/is.pvolfile.html b/docs/reference/is.pvolfile.html index 47a19a3e8..036f77efe 100644 --- a/docs/reference/is.pvolfile.html +++ b/docs/reference/is.pvolfile.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -190,14 +193,9 @@

      Examp is.pvolfile(pvolfile) # > TRUE

    #> [1] TRUE
    @@ -208,7 +206,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/is.vpfile.html b/docs/reference/is.vpfile.html index 0f600c55a..bfdf804cf 100644 --- a/docs/reference/is.vpfile.html +++ b/docs/reference/is.vpfile.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -181,13 +184,9 @@

      Examp is.vpfile(profile) # > TRUE

    #> [1] TRUE
    @@ -198,7 +197,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/map.html b/docs/reference/map.html index 9097a2723..004074cf2 100644 --- a/docs/reference/map.html +++ b/docs/reference/map.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -259,7 +262,7 @@

      Value

      Details

      Available scan parameters for mapping can by printed to screen by -summary(x). Commonly available parameters are:

      +summary(x). Commonly available parameters are:

      "DBZH", "DBZ"

      (Logged) reflectivity factor [dBZ]

      "TH", "T"

      (Logged) uncorrected reflectivity factor [dBZ]

      "VRADH", "VRAD"

      Radial velocity [m/s]. Radial @@ -285,36 +288,38 @@

      Examp data(example_scan) # make ppi's for all scan parameters in the scan ppi <- project_as_ppi(example_scan) -# \dontrun{ +if (FALSE) { # grab a basemap that matches the extent of the ppi: # using a gray-scale basemap: -basemap <- download_basemap(ppi, maptype = "toner-lite")

    #> Downloading zoom = 9 ...
    #> Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL.
    +basemap <- download_basemap(ppi, maptype = "toner-lite") + # map the radial velocity scan parameter onto the basemap: -map(ppi, map = basemap, param = "VRADH")
    +map(ppi, map = basemap, param = "VRADH") + # extend the plotting range of velocities, from -50 to 50 m/s: -map(ppi, map = basemap, param = "VRADH", zlim = c(-50, 50))
    +map(ppi, map = basemap, param = "VRADH", zlim = c(-50, 50)) + # map the reflectivity on a terrain basemap: -basemap <- download_basemap(ppi, maptype = "terrain")
    #> Downloading zoom = 9 ...
    #> Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL.
    map(ppi, map = basemap, param = "DBZH")
    +basemap <- download_basemap(ppi, maptype = "terrain") +map(ppi, map = basemap, param = "DBZH") + # change the color palette, e.g. Viridis colors: -map(ppi, map = basemap, param = "DBZH", palette = viridis::viridis(100), zlim=c(-10,10))
    +map(ppi, map = basemap, param = "DBZH", palette = viridis::viridis(100), zlim=c(-10,10)) + # give the data more transparency: -map(ppi, map = basemap, param = "DBZH", alpha = 0.3)
    +map(ppi, map = basemap, param = "DBZH", alpha = 0.3) + # change the appearance of the symbol indicating the radar location: -map(ppi, map = basemap, radar_size = 5, radar_color = "blue")
    +map(ppi, map = basemap, radar_size = 5, radar_color = "blue") + # crop the map: -map(ppi, map = basemap, xlim = c(12.4, 13.2), ylim = c(56, 56.5))
    #> Warning: Removed 1 rows containing missing values (geom_rect).
    # } -
    +map(ppi, map = basemap, xlim = c(12.4, 13.2), ylim = c(56, 56.5)) +} @@ -325,7 +330,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/match_filenames.html b/docs/reference/match_filenames.html index 465dbbde6..edde7eb33 100644 --- a/docs/reference/match_filenames.html +++ b/docs/reference/match_filenames.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -54,7 +58,6 @@ function basically wraps a grep to make it work on vectors by combining the vector of regex options as possible options." /> - @@ -72,7 +75,7 @@ - +
    @@ -125,7 +128,7 @@
    • - + @@ -184,12 +187,9 @@

      Value

    @@ -200,7 +200,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/nexrad_to_odim.html b/docs/reference/nexrad_to_odim.html index d4321c48c..5530b70f6 100644 --- a/docs/reference/nexrad_to_odim.html +++ b/docs/reference/nexrad_to_odim.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -191,7 +194,7 @@

      Value

      TRUE on success

      Examples

      - 
      # \dontrun{
+    
      if (FALSE) {
 # download a NEXRAD file, save as KBGM_example
 download.file(paste("https://noaa-nexrad-level2.s3.amazonaws.com/",
   "2019/10/01/KBGM/KBGM20191001_000542_V06",
@@ -199,21 +202,19 @@ 
      Examp
 ), "~/KBGM_example")
 
 # convert to ODIM format
-nexrad_to_odim("~/KBGM_example", "~/KBGM_example.h5")
      #> [1] TRUE
      
+nexrad_to_odim("~/KBGM_example", "~/KBGM_example.h5")
+
 # verify that we have generated a polar volume in ODIM hdf5 format
-get_odim_object_type("~/KBGM_example.h5")
      #> [1] "PVOL"
      
+get_odim_object_type("~/KBGM_example.h5")
+
 # clean up
-file.remove("~/KBGM_example", "~/KBGM_example.h5")
      #> [1] TRUE TRUE
      # }
-
      
+file.remove("~/KBGM_example", "~/KBGM_example.h5")
+}
    @@ -224,7 +225,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/nyquist_velocity.html b/docs/reference/nyquist_velocity.html index ec716e204..fc0aa0438 100644 --- a/docs/reference/nyquist_velocity.html +++ b/docs/reference/nyquist_velocity.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,7 +57,6 @@ and wavelength. When specifying two PRFs, the extended Nyquist velocity is given for a radar using the dual-PRF technique." /> - @@ -71,7 +74,7 @@ - +
    @@ -124,7 +127,7 @@
    • - + @@ -190,13 +193,9 @@

      Examp nyquist_velocity(5.3, 2000, 1500)

    #> [1] 79.5
    @@ -207,7 +206,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/plot.ppi.html b/docs/reference/plot.ppi.html index 913af371b..abd9ccac7 100644 --- a/docs/reference/plot.ppi.html +++ b/docs/reference/plot.ppi.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -209,7 +212,7 @@

      Arg

      Details

      Available scan paramaters for plotting can by printed to screen -by summary(x). Commonly available parameters are:

      +by summary(x). Commonly available parameters are:

      "DBZH", "DBZ"

      (Logged) reflectivity factor [dBZ]

      "TH", "T"

      (Logged) uncorrected reflectivity factor [dBZ]

      "VRADH", "VRAD"

      Radial velocity [m/s]. Radial @@ -248,13 +251,9 @@

      Examp #> will replace the existing scale.

    @@ -265,7 +264,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/plot.scan.html b/docs/reference/plot.scan.html index da15b2934..edf66736b 100644 --- a/docs/reference/plot.scan.html +++ b/docs/reference/plot.scan.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -204,7 +207,7 @@

      Arg

      Details

      Available scan parameters for plotting can by printed to screen -by summary(x). Commonly available parameters are:

      +by summary(x). Commonly available parameters are:

      "DBZH", "DBZ"

      (Logged) reflectivity factor [dBZ]

      "TH", "T"

      (Logged) uncorrected reflectivity factor [dBZ]

      "VRADH", "VRAD"

      Radial velocity [m/s]. Radial @@ -232,22 +235,18 @@

      Examp #> dims: 480 bins x 360 rays

    # make ppi for the scan # plot the reflectivity param: -plot(example_scan, param = "DBZH")
    # \dontrun{ +plot(example_scan, param = "DBZH")
    if (FALSE) { # change the range of reflectivities to plot, from -10 to 10 dBZ: -plot(example_scan, param = "DBZH", zlim = c(-10, 10))
    +plot(example_scan, param = "DBZH", zlim = c(-10, 10)) + # change the scale name and colour scheme, using viridis colors: -plot(example_scan, param = "DBZH", zlim = c(-10, 10)) + viridis::scale_fill_viridis(name = "dBZ")
    #> Scale for 'fill' is already present. Adding another scale for 'fill', which -#> will replace the existing scale.
    # } -
    +plot(example_scan, param = "DBZH", zlim = c(-10, 10)) + viridis::scale_fill_viridis(name = "dBZ") +} @@ -258,7 +257,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/plot.vp.html b/docs/reference/plot.vp.html index cc981d767..2a63101ed 100644 --- a/docs/reference/plot.vp.html +++ b/docs/reference/plot.vp.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -233,12 +236,9 @@

      Examp plot(example_vp, quantity = "DBZH")

    @@ -249,7 +249,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/plot.vpi.html b/docs/reference/plot.vpi.html index 665d118a6..e7f8b1e6c 100644 --- a/docs/reference/plot.vpi.html +++ b/docs/reference/plot.vpi.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -242,7 +245,7 @@

      Arg

      Details

      The integrated profiles can be visualized in various related quantities, as specified by -argument quantity:

      +argument quantity:

      "vid"

      Vertically Integrated Density, i.e. the aerial surface density of individuals. This quantity is dependent on the assumed radar cross section per individual (RCS)

      @@ -272,13 +275,9 @@

      Examp plot(vpi, quantity = "vid", night_shade = FALSE)

    @@ -289,7 +288,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/plot.vpts.html b/docs/reference/plot.vpts.html index 0f82a718d..e3238de09 100644 --- a/docs/reference/plot.vpts.html +++ b/docs/reference/plot.vpts.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -260,7 +263,7 @@

      Arg

      Details

      Profile can be visualized in three related quantities, as specified -by argument quantity:

      +by argument quantity:

      "dens"

      the aerial density of individuals. This quantity is dependent on the assumed radar cross section (RCS) in the x$attributes$how$rcs_bird attribute

      @@ -287,13 +290,9 @@

      Examp plot(ts[1:500], ylim = c(0, 3000), quantity = "DBZH")

    #> Warning: Irregular time-series: missing profiles will not be visible.Use 'regularize_vpts' to make time series regular.
    @@ -304,7 +303,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/print.param.html b/docs/reference/print.param.html index 2352f40b3..76b1cde76 100644 --- a/docs/reference/print.param.html +++ b/docs/reference/print.param.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -170,11 +173,9 @@

      Arg

    @@ -185,7 +186,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/print.ppi.html b/docs/reference/print.ppi.html index 404f77a10..acdfcf0cb 100644 --- a/docs/reference/print.ppi.html +++ b/docs/reference/print.ppi.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -170,11 +173,9 @@

      Arg

    @@ -185,7 +186,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/print.pvol.html b/docs/reference/print.pvol.html index 7293da10f..4b1d1153c 100644 --- a/docs/reference/print.pvol.html +++ b/docs/reference/print.pvol.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -170,11 +173,9 @@

      Arg

    @@ -185,7 +186,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/print.scan.html b/docs/reference/print.scan.html index 00663cd0d..ac2e29c5f 100644 --- a/docs/reference/print.scan.html +++ b/docs/reference/print.scan.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -170,11 +173,9 @@

      Arg

    @@ -185,7 +186,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/print.vp.html b/docs/reference/print.vp.html index c99116700..f59cece6d 100644 --- a/docs/reference/print.vp.html +++ b/docs/reference/print.vp.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -171,11 +174,9 @@

      Arg

    @@ -186,7 +187,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/print.vpts.html b/docs/reference/print.vpts.html index 61edbad79..8383f82e2 100644 --- a/docs/reference/print.vpts.html +++ b/docs/reference/print.vpts.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -171,11 +174,9 @@

      Arg

    @@ -186,7 +187,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/proj_to_wgs.html b/docs/reference/proj_to_wgs.html index 63a17af6e..7dfee4020 100644 --- a/docs/reference/proj_to_wgs.html +++ b/docs/reference/proj_to_wgs.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -180,12 +183,9 @@

      Value

    @@ -196,7 +196,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/project_as_ppi.html b/docs/reference/project_as_ppi.html index 80a93d5b6..59f49c89b 100644 --- a/docs/reference/project_as_ppi.html +++ b/docs/reference/project_as_ppi.html @@ -18,23 +18,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -43,7 +47,7 @@ - + @@ -53,7 +57,6 @@ position indicator (ppi) — project_as_ppi" /> - @@ -71,7 +74,7 @@ - +
    @@ -124,7 +127,7 @@
    • - + @@ -298,15 +301,9 @@

      Examp plot(ppi)

    @@ -317,7 +314,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/rcs-set.html b/docs/reference/rcs-set.html index 2dd95ec75..2c9174977 100644 --- a/docs/reference/rcs-set.html +++ b/docs/reference/rcs-set.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -206,13 +209,9 @@

      Examp rcs(example_vpts)

    #> [1] 11
    @@ -223,7 +222,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/rcs.html b/docs/reference/rcs.html index 1bbab4659..1d41295ea 100644 --- a/docs/reference/rcs.html +++ b/docs/reference/rcs.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -212,15 +215,9 @@

      Examp rcs(example_vpts) <- 11

    @@ -231,7 +228,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/read_cajun.html b/docs/reference/read_cajun.html index b7396163d..e69d1498c 100644 --- a/docs/reference/read_cajun.html +++ b/docs/reference/read_cajun.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -183,12 +186,9 @@

      Value

    @@ -199,7 +199,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/read_pvolfile.html b/docs/reference/read_pvolfile.html index 5bb14597f..9ef54920c 100644 --- a/docs/reference/read_pvolfile.html +++ b/docs/reference/read_pvolfile.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -233,7 +236,7 @@

      Details

      Scan parameters are named according to the OPERA data information model (ODIM), see Table 16 in the ODIM specification. -Commonly available parameters are:

      +Commonly available parameters are:

      "DBZH", "DBZ"

      (Logged) reflectivity factor [dBZ]

      "TH", "T"

      (Logged) uncorrected reflectivity factor [dBZ]

      "VRADH", "VRAD"

      Radial velocity [m/s]. Radial @@ -253,7 +256,7 @@

      Examp pvolfile <- system.file("extdata", "volume.h5", package = "bioRad") # print the local path of the volume file: -pvolfile

    #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/Rtmp5GrRDa/temp_libpath15fed6648be9d/bioRad/extdata/volume.h5"
    +pvolfile
    #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmpJinW0n/temp_libpath1aad377d5d/bioRad/extdata/volume.h5"
    # load the file: example_pvol <- read_pvolfile(pvolfile) @@ -298,14 +301,9 @@

    Examp #> dims: 480 bins x 360 rays

    @@ -316,7 +314,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/read_vp.html b/docs/reference/read_vp.html index 6c6fe5581..9f281f4d4 100644 --- a/docs/reference/read_vp.html +++ b/docs/reference/read_vp.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -173,12 +176,9 @@

      Value

    @@ -189,7 +189,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/read_vpfiles.html b/docs/reference/read_vpfiles.html index 12c56165b..af0c1637a 100644 --- a/docs/reference/read_vpfiles.html +++ b/docs/reference/read_vpfiles.html @@ -18,23 +18,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -43,7 +47,7 @@ - + @@ -54,7 +58,6 @@ - @@ -72,7 +75,7 @@ - +
    @@ -125,7 +128,7 @@
    • - + @@ -181,7 +184,7 @@

      Examp vpfile <- system.file("extdata", "profile.h5", package = "bioRad") # print the local path of the profile file: -vpfile

    #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/Rtmp5GrRDa/temp_libpath15fed6648be9d/bioRad/extdata/profile.h5"
    +vpfile
    #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmpJinW0n/temp_libpath1aad377d5d/bioRad/extdata/profile.h5"
    # load the file: read_vpfiles(vpfile)
    #> Vertical profile (class vp) #> @@ -189,21 +192,15 @@

    Examp #> source: WMO:02606,RAD:SE50,PLC:Ängelholm,NOD:seang,ORG:82,CTY:643,CMT:Swedish radar #> nominal time: 2015-10-18 18:00:00 #> generated by: vol2bird 0.3.17

    -# load multiple files at once: -# \dontrun{ -# read_vpfiles(c("my/path/profile1.h5", "my/path/profile2.h5", ...)) -# } - -
    +# load multiple files at once: +if (FALSE) { +# read_vpfiles(c("my/path/profile1.h5", "my/path/profile2.h5", ...)) +} @@ -214,7 +211,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/read_vpts.html b/docs/reference/read_vpts.html index 225130144..366d7bcc1 100644 --- a/docs/reference/read_vpts.html +++ b/docs/reference/read_vpts.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -207,13 +210,9 @@

      Examp #> time step (s): min: 540 max: 600

    @@ -224,7 +223,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/regularize_vpts.html b/docs/reference/regularize_vpts.html index 7175fbdf6..d26cfb2c3 100644 --- a/docs/reference/regularize_vpts.html +++ b/docs/reference/regularize_vpts.html @@ -18,23 +18,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -43,7 +47,7 @@ - + @@ -53,7 +57,6 @@ regular time grid — regularize_vpts" /> - @@ -71,7 +74,7 @@ - +
    @@ -124,7 +127,7 @@
    • - + @@ -231,14 +234,9 @@

      Examp tsRegular <- regularize_vpts(ts, interval = 300)

    @@ -249,7 +247,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/scan_to_raster.html b/docs/reference/scan_to_raster.html index 2cc0aed76..3ccb37048 100644 --- a/docs/reference/scan_to_raster.html +++ b/docs/reference/scan_to_raster.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -283,14 +286,9 @@

      Examp #>

    @@ -301,7 +299,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/scan_to_spatial.html b/docs/reference/scan_to_spatial.html index b88dd43fc..a6f571139 100644 --- a/docs/reference/scan_to_spatial.html +++ b/docs/reference/scan_to_spatial.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -209,14 +212,9 @@

      Examp #> max values : 359, 240000, 239848.089357779, 5695.96400438249, 23.6928958296776, 55, 7.90588282048702, 0.99959997474798, 178.588244199753

    @@ -227,7 +225,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/sd_vvp_threshold-set.html b/docs/reference/sd_vvp_threshold-set.html index 6b1d8a532..dc4ef1b75 100644 --- a/docs/reference/sd_vvp_threshold-set.html +++ b/docs/reference/sd_vvp_threshold-set.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -54,7 +58,6 @@ individuals. This method updates the migration densities in x$data$dens" /> - @@ -72,7 +75,7 @@ - +
    @@ -125,7 +128,7 @@
    #> [1] 2
    @@ -224,7 +223,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/sd_vvp_threshold.html b/docs/reference/sd_vvp_threshold.html index edb9d38c2..da413c2e9 100644 --- a/docs/reference/sd_vvp_threshold.html +++ b/docs/reference/sd_vvp_threshold.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -212,15 +215,9 @@

      Examp sd_vvp_threshold(example_vp) <- 2

    @@ -231,7 +228,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/select_vpfiles.html b/docs/reference/select_vpfiles.html index 403d02ff4..782406c3a 100644 --- a/docs/reference/select_vpfiles.html +++ b/docs/reference/select_vpfiles.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -54,7 +58,6 @@ file name (not directory structure), which should be of format radar_vp_yyyymmdd*.*, such as bewid_vp_20171123T1900Z_0x5.h5." /> - @@ -72,7 +75,7 @@ - +
    @@ -125,7 +128,7 @@
    • - + @@ -205,13 +208,9 @@

      Examp )

    #> character(0)
    @@ -222,7 +221,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/sub-.ppi.html b/docs/reference/sub-.ppi.html index d9b9ce5ad..a04423dd9 100644 --- a/docs/reference/sub-.ppi.html +++ b/docs/reference/sub-.ppi.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -196,12 +199,9 @@

      Examp #>

    @@ -212,7 +212,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/sub-.vpts.html b/docs/reference/sub-.vpts.html index 714146c39..485a19d8b 100644 --- a/docs/reference/sub-.vpts.html +++ b/docs/reference/sub-.vpts.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -199,12 +202,9 @@

      Examp #> time step (s): min: 240 max: 420

    @@ -215,7 +215,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/summary.param.html b/docs/reference/summary.param.html index 67791d767..d62bf2081 100644 --- a/docs/reference/summary.param.html +++ b/docs/reference/summary.param.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -186,7 +189,7 @@

      Value

      Details

      An object of class scan is a simple matrix, with the following -specific attributes:

      +specific attributes:

      radar

      character string with the radar identifier

      datetime

      nominal time of the volume to which this scan belongs [UTC]

      @@ -199,7 +202,7 @@

      Details

      Scan parameters are named according to the OPERA data information model (ODIM), see Table 16 in the ODIM specification. -Commonly available parameters are:

      +Commonly available parameters are:

      "DBZH", "DBZ"

      (Logged) reflectivity factor [dBZ]

      "VRADH", "VRAD"

      Radial velocity [m/s]. Radial velocities towards the radar are negative, while radial velocities away @@ -229,14 +232,9 @@

      Examp #> dims: 480 bins x 360 rays

    @@ -247,7 +245,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/summary.ppi.html b/docs/reference/summary.ppi.html index c17c0627b..a971f7e3e 100644 --- a/docs/reference/summary.ppi.html +++ b/docs/reference/summary.ppi.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -192,10 +195,10 @@

      Details

      ppi objects are generated from elevation scans (scan objects) with project_as_ppi or from polar volumes with integrate_to_ppi, producing projections of the radar data onto the earth's surface.

      -

      An object of class ppi is a list containing:

      +

      An object of class ppi is a list containing:

      data

      an object of class SpatialGridDataFrame containing the georeferenced data. Commonly available parameters are: -

      +
      "DBZH", "DBZ"

      (Logged) reflectivity factor [dBZ]

      "TH", "T"

      (Logged) uncorrected reflectivity factor [dBZ]

      "VRADH", "VRAD"

      Radial velocity [m/s]. Radial @@ -207,7 +210,7 @@

      Details
      "PHIDP"

      Differential phase [degrees]

      "ZDR"

      (Logged) differential reflectivity [dB]

      geo

      geographic data, a list with: -

      +
      lat

      latitude of the radar [decimal degrees]

      lon

      longitude of the radar [decimal degrees]

      height

      height of the radar @@ -240,14 +243,9 @@

      Examp dim(example_ppi)

    #> [1] 5 200 200
    @@ -258,7 +256,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/summary.pvol.html b/docs/reference/summary.pvol.html index c450a2fb0..d6baaa354 100644 --- a/docs/reference/summary.pvol.html +++ b/docs/reference/summary.pvol.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -183,14 +186,14 @@

      Value

      class pvol

      Details

      -

      An object of class pvol is a list containing:

      +

      An object of class pvol is a list containing:

      radar

      character string with the radar identifier

      datetime

      nominal time of the volume [UTC]

      scans

      a list with scan objects of class 'scan'

      attributes

      list with the volume's \what, \where and \how attributes

      geo

      geographic data, a list with: -

      +
      lat

      latitude of the radar [decimal degrees]

      lon

      longitude of the radar [decimal degrees]

      height

      height of the radar @@ -204,7 +207,7 @@

      Examp pvolfile <- system.file("extdata", "volume.h5", package = "bioRad") # print the local path of the volume file: -pvolfile

    #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/Rtmp5GrRDa/temp_libpath15fed6648be9d/bioRad/extdata/volume.h5"
    +pvolfile
    #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmpJinW0n/temp_libpath1aad377d5d/bioRad/extdata/volume.h5"
    # load the file: example_pvol <- read_pvolfile(pvolfile) @@ -251,14 +254,9 @@

    Examp #> dims: 480 bins x 360 rays

    is.pvol("this is not a polar volume but a string") # > FALSE
    #> [1] FALSE
    @@ -269,7 +267,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/summary.scan.html b/docs/reference/summary.scan.html index 264270823..45a6c392b 100644 --- a/docs/reference/summary.scan.html +++ b/docs/reference/summary.scan.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -187,7 +190,7 @@

      Value

      For dim.scan: dimensions of the scan.

      Details

      -

      A object of class scan is a list containing:

      +

      A object of class scan is a list containing:

      radar

      character string with the radar identifier

      datetime

      nominal time of the volume to which this scan belongs [UTC]

      @@ -195,7 +198,7 @@

      Details
      attributes

      list with the scan's \what, \where and \how attributes

      geo

      geographic data, a list with: -

      +
      lat

      latitude of the radar [decimal degrees]

      lon

      longitude of the radar [decimal degrees]

      height

      height of the radar @@ -256,14 +259,9 @@

      Examp #> dims: 480 bins x 360 rays

    is.scan("this is not a polar scan but a string") # > FALSE
    #> [1] FALSE
    @@ -274,7 +272,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/summary.vp.html b/docs/reference/summary.vp.html index e183d2380..aac6a797f 100644 --- a/docs/reference/summary.vp.html +++ b/docs/reference/summary.vp.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -193,11 +196,11 @@

      Details

      Data contained in this class object should be accessed with the get_quantity function. Information stored under attributes (see below) can be accessed directly.

      -

      A vp object is a list containing

      +

      A vp object is a list containing

      radar

      the radar identifier

      datetime

      the nominal time of the profile

      data

      the profile data, a list containing: -

      +
      height

      height above mean sea level [m]. Alt. bin from height to height+interval)

      u

      speed component west to east [m/s]

      v

      speed component north to south [m/s]

      @@ -249,14 +252,9 @@

      Examp dim(example_vp)

    #> [1] 25 16
    @@ -267,7 +265,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/summary.vpts.html b/docs/reference/summary.vpts.html index 126462f75..eeae13eff 100644 --- a/docs/reference/summary.vpts.html +++ b/docs/reference/summary.vpts.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -204,7 +207,7 @@

      Details

      Data contained in this class object should be accessed with the get_quantity function. Information stored under attributes (see below) can be accessed directly.

      -

      An object of class vpts is a list containing

      +

      An object of class vpts is a list containing

      radar

      string containing the radar identifier

      datetime

      the N nominal times of the profiles (named dates in bioRad versions < 0.4.0)

      height

      the M heights of the layers in the profile

      @@ -240,14 +243,9 @@

      Examp dim(example_vpts)

    #> [1] 25 1934 15
    @@ -258,7 +256,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/sunrise_sunset.html b/docs/reference/sunrise_sunset.html index be7f8b8cc..1e0aac76c 100644 --- a/docs/reference/sunrise_sunset.html +++ b/docs/reference/sunrise_sunset.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -203,17 +206,12 @@

      Examp # sunset in the Netherlands sunset("2016-01-01", 5, 53)

    #> [1] "2016-01-01 15:28:31 UTC"
    # civil twilight in Ithaca, NY, today -sunrise(Sys.time(), -76.5, 42.4, elev = -6)
    #> [1] "2020-02-19 06:28:50 EST"
    +sunrise(Sys.time(), -76.5, 42.4, elev = -6)
    #> [1] "2020-03-31 06:20:54 EDT"
    @@ -224,7 +222,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/update_docker.html b/docs/reference/update_docker.html index e82aa265b..515fa1b32 100644 --- a/docs/reference/update_docker.html +++ b/docs/reference/update_docker.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -182,20 +185,15 @@

      Details run update_docker(mistnet = TRUE)

      Examples

      - 
      # \dontrun{
+    
      if (FALSE) {
 # update the vol2bird docker image:
-update_docker()
      #> Succesfully installed Docker image with vol2bird version 0.5.0 , including MistNet. 
      #> [1] "2020-02-11 19:37:40 UTC"
      # }
-
      
+update_docker()
+}
    @@ -206,7 +204,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/vol2bird_version.html b/docs/reference/vol2bird_version.html index f7d809556..4ddba334f 100644 --- a/docs/reference/vol2bird_version.html +++ b/docs/reference/vol2bird_version.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,7 +57,6 @@ correctly on the local system and returns the version of the installed vol2bird algorithm in the Docker container." /> - @@ -71,7 +74,7 @@ - +
    @@ -124,7 +127,7 @@
    • - + @@ -182,20 +185,15 @@

      Details the version of this local installation.

      Examples

      - 
      # \dontrun{
+    
      if (FALSE) {
 # check installed vol2bird version:
-vol2bird_version()
      #> [1] ‘0.5.0’
      # }
-
      
+vol2bird_version()
+}
    @@ -206,7 +204,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/vplist_to_vpts.html b/docs/reference/vplist_to_vpts.html index 126395f7a..5b6f2962c 100644 --- a/docs/reference/vplist_to_vpts.html +++ b/docs/reference/vplist_to_vpts.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
    @@ -123,7 +126,7 @@
    • - + @@ -182,18 +185,15 @@

      Value

      multiple radars, containing vpts objects for each radar.

      Examples

      - 
      # \dontrun{
-vps <- read_vpfiles(c("my/path/profile1.h5", "my/path/profile2.h5", ...))
      #> Error in read_vpfiles(c("my/path/profile1.h5", "my/path/profile2.h5",     ...)): '...' used in an incorrect context
      ts <- bind_into_vpts(vps)
      #> Error in bind_into_vpts(vps): object 'vps' not found
      # }
-
      + 
      if (FALSE) {
+vps <- read_vpfiles(c("my/path/profile1.h5", "my/path/profile2.h5", ...))
+ts <- bind_into_vpts(vps)
+}
    @@ -204,7 +204,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/reference/wgs_to_proj.html b/docs/reference/wgs_to_proj.html index fb1a22a9b..4526f0657 100644 --- a/docs/reference/wgs_to_proj.html +++ b/docs/reference/wgs_to_proj.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
    @@ -122,7 +125,7 @@
    • - + @@ -180,12 +183,9 @@

      Value

    @@ -196,7 +196,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.9000.

    +

    Site built with pkgdown 1.5.0.

    From ea28c310b7bf8f36795632707fb6f3ee3bb74d7e Mon Sep 17 00:00:00 2001 From: adokter Date: Tue, 31 Mar 2020 17:31:24 -0400 Subject: [PATCH 13/18] add new files --- docs/bootstrap-toc.css | 60 ++++++++++++++++ docs/bootstrap-toc.js | 159 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 219 insertions(+) create mode 100644 docs/bootstrap-toc.css create mode 100644 docs/bootstrap-toc.js diff --git a/docs/bootstrap-toc.css b/docs/bootstrap-toc.css new file mode 100644 index 000000000..5a859415c --- /dev/null +++ b/docs/bootstrap-toc.css @@ -0,0 +1,60 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ + +/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */ + +/* All levels of nav */ +nav[data-toggle='toc'] .nav > li > a { + display: block; + padding: 4px 20px; + font-size: 13px; + font-weight: 500; + color: #767676; +} +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 19px; + color: #563d7c; + text-decoration: none; + background-color: transparent; + border-left: 1px solid #563d7c; +} +nav[data-toggle='toc'] .nav > .active > a, +nav[data-toggle='toc'] .nav > .active:hover > a, +nav[data-toggle='toc'] .nav > .active:focus > a { + padding-left: 18px; + font-weight: bold; + color: #563d7c; + background-color: transparent; + border-left: 2px solid #563d7c; +} + +/* Nav: second level (shown on .active) */ +nav[data-toggle='toc'] .nav .nav { + display: none; /* Hide by default, but at >768px, show it */ + padding-bottom: 10px; +} +nav[data-toggle='toc'] .nav .nav > li > a { + padding-top: 1px; + padding-bottom: 1px; + padding-left: 30px; + font-size: 12px; + font-weight: normal; +} +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 29px; +} +nav[data-toggle='toc'] .nav .nav > .active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 28px; + font-weight: 500; +} + +/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */ +nav[data-toggle='toc'] .nav > .active > ul { + display: block; +} diff --git a/docs/bootstrap-toc.js b/docs/bootstrap-toc.js new file mode 100644 index 000000000..1cdd573b2 --- /dev/null +++ b/docs/bootstrap-toc.js @@ -0,0 +1,159 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ +(function() { + 'use strict'; + + window.Toc = { + helpers: { + // return all matching elements in the set, or their descendants + findOrFilter: function($el, selector) { + // http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/ + // http://stackoverflow.com/a/12731439/358804 + var $descendants = $el.find(selector); + return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])'); + }, + + generateUniqueIdBase: function(el) { + var text = $(el).text(); + var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-'); + return anchor || el.tagName.toLowerCase(); + }, + + generateUniqueId: function(el) { + var anchorBase = this.generateUniqueIdBase(el); + for (var i = 0; ; i++) { + var anchor = anchorBase; + if (i > 0) { + // add suffix + anchor += '-' + i; + } + // check if ID already exists + if (!document.getElementById(anchor)) { + return anchor; + } + } + }, + + generateAnchor: function(el) { + if (el.id) { + return el.id; + } else { + var anchor = this.generateUniqueId(el); + el.id = anchor; + return anchor; + } + }, + + createNavList: function() { + return $('
      '); + }, + + createChildNavList: function($parent) { + var $childList = this.createNavList(); + $parent.append($childList); + return $childList; + }, + + generateNavEl: function(anchor, text) { + var $a = $(''); + $a.attr('href', '#' + anchor); + $a.text(text); + var $li = $('
    • '); + $li.append($a); + return $li; + }, + + generateNavItem: function(headingEl) { + var anchor = this.generateAnchor(headingEl); + var $heading = $(headingEl); + var text = $heading.data('toc-text') || $heading.text(); + return this.generateNavEl(anchor, text); + }, + + // Find the first heading level (`

      `, then `

      `, etc.) that has more than one element. Defaults to 1 (for `

      `). + getTopLevel: function($scope) { + for (var i = 1; i <= 6; i++) { + var $headings = this.findOrFilter($scope, 'h' + i); + if ($headings.length > 1) { + return i; + } + } + + return 1; + }, + + // returns the elements for the top level, and the next below it + getHeadings: function($scope, topLevel) { + var topSelector = 'h' + topLevel; + + var secondaryLevel = topLevel + 1; + var secondarySelector = 'h' + secondaryLevel; + + return this.findOrFilter($scope, topSelector + ',' + secondarySelector); + }, + + getNavLevel: function(el) { + return parseInt(el.tagName.charAt(1), 10); + }, + + populateNav: function($topContext, topLevel, $headings) { + var $context = $topContext; + var $prevNav; + + var helpers = this; + $headings.each(function(i, el) { + var $newNav = helpers.generateNavItem(el); + var navLevel = helpers.getNavLevel(el); + + // determine the proper $context + if (navLevel === topLevel) { + // use top level + $context = $topContext; + } else if ($prevNav && $context === $topContext) { + // create a new level of the tree and switch to it + $context = helpers.createChildNavList($prevNav); + } // else use the current $context + + $context.append($newNav); + + $prevNav = $newNav; + }); + }, + + parseOps: function(arg) { + var opts; + if (arg.jquery) { + opts = { + $nav: arg + }; + } else { + opts = arg; + } + opts.$scope = opts.$scope || $(document.body); + return opts; + } + }, + + // accepts a jQuery object, or an options object + init: function(opts) { + opts = this.helpers.parseOps(opts); + + // ensure that the data attribute is in place for styling + opts.$nav.attr('data-toggle', 'toc'); + + var $topContext = this.helpers.createChildNavList(opts.$nav); + var topLevel = this.helpers.getTopLevel(opts.$scope); + var $headings = this.helpers.getHeadings(opts.$scope, topLevel); + this.helpers.populateNav($topContext, topLevel, $headings); + } + }; + + $(function() { + $('nav[data-toggle="toc"]').each(function(i, el) { + var $nav = $(el); + Toc.init($nav); + }); + }); +})(); From cc61d3328c9470e42086bb8db7ebf4c7428eed00 Mon Sep 17 00:00:00 2001 From: adokter Date: Wed, 1 Apr 2020 13:33:57 -0400 Subject: [PATCH 14/18] bioRad 0.5.1 --- CRAN-RELEASE | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CRAN-RELEASE b/CRAN-RELEASE index 1d6c835a6..448aed894 100644 --- a/CRAN-RELEASE +++ b/CRAN-RELEASE @@ -1,2 +1,2 @@ -This package was submitted to CRAN on 2020-02-18. -Once it is accepted, delete this file and tag the release (commit 513108933d). +This package was submitted to CRAN on 2020-03-31. +Once it is accepted, delete this file and tag the release (commit ea28c310b7). From 21c7cc6e7731336563013a0b33d4799fa4b09be8 Mon Sep 17 00:00:00 2001 From: adokter Date: Wed, 1 Apr 2020 13:42:16 -0400 Subject: [PATCH 15/18] update news --- NEWS.md | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/NEWS.md b/NEWS.md index 1d98fef0b..78d527663 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,12 +1,22 @@ # bioRad 0.5.1 -Minor bugfixes. All issues included in this release can be found [here](https://github.com/adokter/bioRad/pull/334) +Minor bugfixes. All issues included in this release can be found [here](https://github.com/adokter/bioRad/pull/334). This release primarily fixes a bug that will become effective once R version 4.0 is released. -* extend the functionality of composite_ppi() and improve its documentation (partial fix of #59) +* fixes a conflict due to new raw data format introduced in R version 4.0 (#331) -* fix a bug in the color legend of map() when providing a custom color scale with palette argument (#324) +* corrects incorrect values in reading of correlation coefficient values RHOHV (#328) + +* bugfix in `read_cajun()` which introduced incorrect height column during refactoring in bioRad 0.5.0 release (93ad0a4) + +* bugfix that fixes the mapping by `map()` of composites of composites (ppi's produced after repeated application of `composite_ppi()`) (a5c9048, 043aa73) +* minor bug fixes, and addressing conflicts with CRAN depencies + +* extend the functionality of `composite_ppi()` and improve its documentation (partial fix of #59) + +* fix a bug in the color legend of `map()` when providing a custom color scale with palette argument (#324) + +* minor documentation improvements -* resolve a conflict with upcoming R 0.4 release # bioRad 0.5.0 From 73c74fef79e4a84d379f71b6ebd569cdc199ae33 Mon Sep 17 00:00:00 2001 From: adokter Date: Wed, 1 Apr 2020 14:02:34 -0400 Subject: [PATCH 16/18] rebuild site --- NEWS.md | 5 ++--- docs/news/index.html | 15 ++++++++++----- docs/pkgdown.yml | 2 +- docs/reference/read_pvolfile.html | 2 +- docs/reference/read_vpfiles.html | 2 +- docs/reference/summary.pvol.html | 2 +- docs/reference/sunrise_sunset.html | 2 +- 7 files changed, 17 insertions(+), 13 deletions(-) diff --git a/NEWS.md b/NEWS.md index 78d527663..8fd76f319 100644 --- a/NEWS.md +++ b/NEWS.md @@ -6,9 +6,9 @@ Minor bugfixes. All issues included in this release can be found [here](https:// * corrects incorrect values in reading of correlation coefficient values RHOHV (#328) -* bugfix in `read_cajun()` which introduced incorrect height column during refactoring in bioRad 0.5.0 release (93ad0a4) +* bugfix in `read_cajun()` which introduced incorrect height column during refactoring in bioRad 0.5.0 release ([93ad0a4](https://github.com/adokter/bioRad/commit/93ad0a4)) -* bugfix that fixes the mapping by `map()` of composites of composites (ppi's produced after repeated application of `composite_ppi()`) (a5c9048, 043aa73) +* bugfix that fixes the mapping by `map()` of composites of composites (ppi's produced after repeated application of `composite_ppi()`) ([a5c9048](https://github.com/adokter/bioRad/commit/a5c9048), [043aa73](https://github.com/adokter/bioRad/commit/043aa73)) * minor bug fixes, and addressing conflicts with CRAN depencies * extend the functionality of `composite_ppi()` and improve its documentation (partial fix of #59) @@ -17,7 +17,6 @@ Minor bugfixes. All issues included in this release can be found [here](https:// * minor documentation improvements - # bioRad 0.5.0 New CRAN release. All issues included in this release can be found [here](https://github.com/adokter/bioRad/milestone/6?closed=1). diff --git a/docs/news/index.html b/docs/news/index.html index ed65b2983..f8ad62bd1 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -154,13 +154,18 @@

      Changelog

      -bioRad 0.5.1 Unreleased +bioRad 0.5.1 2020-04-01

      -

      Minor bugfixes. All issues included in this release can be found here

      +

      Minor bugfixes. All issues included in this release can be found here. This release primarily fixes a bug that will become effective once R version 4.0 is released.

        -

      • extend the functionality of composite_ppi() and improve its documentation (partial fix of #59)

        • -

      • fix a bug in the color legend of map() when providing a custom color scale with palette argument (#324)

        • -

      • resolve a conflict with upcoming R 0.4 release

        • +

      • fixes a conflict due to new raw data format introduced in R version 4.0 (#331)

        • +

      • corrects incorrect values in reading of correlation coefficient values RHOHV (#328)

        • +

      • bugfix in read_cajun() which introduced incorrect height column during refactoring in bioRad 0.5.0 release (93ad0a4)

        • +
      • bugfix that fixes the mapping by map() of composites of composites (ppi’s produced after repeated application of composite_ppi()) (a5c9048, 043aa73)
        • +

      • minor bug fixes, and addressing conflicts with CRAN depencies

        • +

      • extend the functionality of composite_ppi() and improve its documentation (partial fix of #59)

        • +

      • fix a bug in the color legend of map() when providing a custom color scale with palette argument (#324)

        • +

      • minor documentation improvements

      diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 11769e4aa..9e6a8b272 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -5,7 +5,7 @@ articles: bioRad: bioRad.html rad_aero_19: rad_aero_19.html range_correction: range_correction.html -last_built: 2020-03-31T21:28Z +last_built: 2020-04-01T17:55Z urls: reference: https://adokter.github.io/bioRad/reference article: https://adokter.github.io/bioRad/articles diff --git a/docs/reference/read_pvolfile.html b/docs/reference/read_pvolfile.html index 9ef54920c..5348b19f6 100644 --- a/docs/reference/read_pvolfile.html +++ b/docs/reference/read_pvolfile.html @@ -256,7 +256,7 @@

      Examp pvolfile <- system.file("extdata", "volume.h5", package = "bioRad") # print the local path of the volume file: -pvolfile

      #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmpJinW0n/temp_libpath1aad377d5d/bioRad/extdata/volume.h5"
      +pvolfile
      #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmpJinW0n/temp_libpath1aa59a1bf7a/bioRad/extdata/volume.h5"
      # load the file: example_pvol <- read_pvolfile(pvolfile) diff --git a/docs/reference/read_vpfiles.html b/docs/reference/read_vpfiles.html index af0c1637a..60be9892b 100644 --- a/docs/reference/read_vpfiles.html +++ b/docs/reference/read_vpfiles.html @@ -184,7 +184,7 @@

      Examp vpfile <- system.file("extdata", "profile.h5", package = "bioRad") # print the local path of the profile file: -vpfile

      #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmpJinW0n/temp_libpath1aad377d5d/bioRad/extdata/profile.h5"
      +vpfile
      #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmpJinW0n/temp_libpath1aa59a1bf7a/bioRad/extdata/profile.h5"
      # load the file: read_vpfiles(vpfile)
      #> Vertical profile (class vp) #> diff --git a/docs/reference/summary.pvol.html b/docs/reference/summary.pvol.html index d6baaa354..d00538b72 100644 --- a/docs/reference/summary.pvol.html +++ b/docs/reference/summary.pvol.html @@ -207,7 +207,7 @@

      Examp pvolfile <- system.file("extdata", "volume.h5", package = "bioRad") # print the local path of the volume file: -pvolfile

      #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmpJinW0n/temp_libpath1aad377d5d/bioRad/extdata/volume.h5"
      +pvolfile
      #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmpJinW0n/temp_libpath1aa59a1bf7a/bioRad/extdata/volume.h5"
      # load the file: example_pvol <- read_pvolfile(pvolfile) diff --git a/docs/reference/sunrise_sunset.html b/docs/reference/sunrise_sunset.html index 1e0aac76c..79602c6b8 100644 --- a/docs/reference/sunrise_sunset.html +++ b/docs/reference/sunrise_sunset.html @@ -206,7 +206,7 @@

      Examp # sunset in the Netherlands sunset("2016-01-01", 5, 53)

      #> [1] "2016-01-01 15:28:31 UTC"
      # civil twilight in Ithaca, NY, today -sunrise(Sys.time(), -76.5, 42.4, elev = -6)
      #> [1] "2020-03-31 06:20:54 EDT"
      +sunrise(Sys.time(), -76.5, 42.4, elev = -6)
      #> [1] "2020-04-01 06:19:08 EDT"
      @@ -162,7 +171,7 @@

      Page not found (404)

      -

      Site built with pkgdown 1.4.1.9000.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/dev/CODE_OF_CONDUCT.html b/docs/dev/CODE_OF_CONDUCT.html index 13f0ac29c..80fdd6aab 100644 --- a/docs/dev/CODE_OF_CONDUCT.html +++ b/docs/dev/CODE_OF_CONDUCT.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,7 +54,6 @@ - @@ -68,7 +71,7 @@ - +
      @@ -121,7 +124,7 @@
      • - + @@ -160,6 +163,12 @@

        Contributor Code of Conduct

      + + @@ -170,7 +179,7 @@

      Contributor Code of Conduct

      -

      Site built with pkgdown 1.4.1.9000.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/dev/CONTRIBUTING.html b/docs/dev/CONTRIBUTING.html index ec589d501..0f5496ca5 100644 --- a/docs/dev/CONTRIBUTING.html +++ b/docs/dev/CONTRIBUTING.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,7 +54,6 @@ - @@ -68,7 +71,7 @@ - +
      @@ -121,7 +124,7 @@
      • - + @@ -233,7 +236,7 @@

      • Write your code.
      • Test your code (bonus points for adding unit tests).
      • Document your code (see function documentation above).
        • -
      • Do an R CMD check using devtools::check() and aim for 0 errors and warnings.
        • +
      • Do an R CMD check using devtools::check() and aim for 0 errors and warnings.

    • Commit and push your changes.
      • @@ -244,6 +247,12 @@

      + + @@ -254,7 +263,7 @@

      -

      Site built with pkgdown 1.4.1.9000.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/dev/LICENSE-text.html b/docs/dev/LICENSE-text.html index d39729e72..b47179c85 100644 --- a/docs/dev/LICENSE-text.html +++ b/docs/dev/LICENSE-text.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,7 +54,6 @@ - @@ -68,7 +71,7 @@ - +
      @@ -121,7 +124,7 @@
      • - + @@ -154,6 +157,12 @@

        License

      + + @@ -164,7 +173,7 @@

      License

      -

      Site built with pkgdown 1.4.1.9000.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/dev/articles/bioRad.html b/docs/dev/articles/bioRad.html index 951214e8e..470be443f 100644 --- a/docs/dev/articles/bioRad.html +++ b/docs/dev/articles/bioRad.html @@ -12,23 +12,23 @@ - - - - - + + + + + + - + - - +
      +
      -

      Introduction to bioRad

      +

      Introduction to bioRad

      Adriaan M. Dokter & Peter Desmet

      @@ -138,7 +138,7 @@

      Figure 2

      -

      Figure 2 from Dokter et al. (2019)

      +Figure 2 from Dokter et al. (2019)

      Figure 2 from Dokter et al. (2019)

      The figure shows the structure and interrelation of bioRad’s main class objects, functions, and plotting methods. (A) objects (rounded box), functions (fixed width font) and their relation (arrows). (B–K) output of the default plot methods for a European radar (left row, Offenthal radar, Germany, 2016-10-04 15:15 UTC–2016-10-05 08:45 UTC) and US radar (right row, KBRO radar, Texas, 2017-05-14 00:09 UTC–2017-05-14 13:25 UTC). The dotted line in (H) and (K) indicates the time slice of (B), (D), (F) and (C), (E), (J) respectively. Grey shading indicates night time (time on the x-axis is in UTC). Altitudes are relative to mean sea level.

      @@ -257,7 +252,7 @@

      -

      Site built with pkgdown 1.4.1.9000.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html index 1382c9768..b03de10e6 100644 --- a/docs/dev/articles/index.html +++ b/docs/dev/articles/index.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,7 +54,6 @@ - @@ -68,7 +71,7 @@ - +
      @@ -121,7 +124,7 @@
      @@ -168,7 +174,7 @@

      All vignettes

      -

      Site built with pkgdown 1.4.1.9000.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/dev/articles/rad_aero_19.html b/docs/dev/articles/rad_aero_19.html index 5627af253..84a3514f0 100644 --- a/docs/dev/articles/rad_aero_19.html +++ b/docs/dev/articles/rad_aero_19.html @@ -12,23 +12,23 @@ - - - - - + + + + + + - + - - +
      +
      -

      Introductory exercises with bioRad

      +

      Introductory exercises with bioRad

      Adriaan M. Dokter

      @@ -125,87 +125,87 @@

      Radar data needed for this practical can be downloaded here.

      Follow bioRad’s install instructions, and install the latest development version to be fully up-to-date.

      Execute each of the code examples provided below in RStudio, and try to complete the exercises.

      -
      # make sure you start with a fresh R session
-# load the bioRad package
-library(bioRad)
-# check the package version
-packageVersion("bioRad")
      +
      # make sure you start with a fresh R session
+# load the bioRad package
+library(bioRad)
+# check the package version
+packageVersion("bioRad")

      Make sure you have the latest version (0.4.0.9243). If you have an older version, download and reinstall as follows:

      -
      library(devtools)
-install_github("adokter/bioRad")
      +
      library(devtools)
+install_github("adokter/bioRad")

      All bioRad’s functions are documented in an extensive function refererence online, as well as in manual pages within R:

      -
      # bring up the package general help page:
-?bioRad
      +
      # bring up the package general help page:
+?bioRad

      Start by making a new directory on your local machine that you will use for this practical:

      -
      # make a new local directory on your machine where to download data for this practical
-# replace the string below with the path of that directory:
-HOME <- "your/personal/working/directory/"
-# check that the directory exists. If the next statement evaluates to FALSE, something went wrong: the directory does not exist or you didn't specify its path correctly
-file.exists(HOME)
-# we will make HOME our work directory, the default folder in which R will look
-# for files, and where it will output newly generated files.
-setwd(HOME)
-# Finally, we set the local time zone to UTC, so all plotted time axes will be in UTC
-Sys.setenv(TZ = "UTC")
      +
      # make a new local directory on your machine where to download data for this practical
+# replace the string below with the path of that directory:
+HOME <- "your/personal/working/directory/"
+# check that the directory exists. If the next statement evaluates to FALSE, something went wrong: the directory does not exist or you didn't specify its path correctly
+file.exists(HOME)
+# we will make HOME our work directory, the default folder in which R will look
+# for files, and where it will output newly generated files.
+setwd(HOME)
+# Finally, we set the local time zone to UTC, so all plotted time axes will be in UTC
+Sys.setenv(TZ = "UTC")

      Your R session is now properly set up.

      To work with US NEXRAD data, bioRad currently requires a working installation of Docker (Linux/Mac) or Docker for Windows (not Docker Toolbox, this is an older implementation of Docker for Windows operating systems that is not supported). If you managed to successfully install Docker, test whether it works:

      -
      # start your local Docker installation
-# we first test whether R can communicate with Docker:
-check_docker()
      +
      # start your local Docker installation
+# we first test whether R can communicate with Docker:
+check_docker()

      The message “running docker image with vol2bird version 0.4.0” indicates everything is working.

      If you did not manage to install Docker, you will be able to continue with all of below exercises, but not be able to load NEXRAD data into R at this time.

      1.2 The structure of polar volumes

      -
      # the bioRad package comes with an example radar volume file, that we will inspect first
-# first locate this example file on our computer:
-my_filename <- system.file("extdata", "volume.h5", package = "bioRad")
-# print the local path of the volume file:
-my_filename
-# load the file into R:
-my_pvol <- read_pvolfile(my_filename)
-## print some information about the polar volume
-my_pvol
-# print information about the polar scans contained in this polar volume:
-my_pvol$scans
      +
      # the bioRad package comes with an example radar volume file, that we will inspect first
+# first locate this example file on our computer:
+my_filename <- system.file("extdata", "volume.h5", package = "bioRad")
+# print the local path of the volume file:
+my_filename
+# load the file into R:
+my_pvol <- read_pvolfile(my_filename)
+## print some information about the polar volume
+my_pvol
+# print information about the polar scans contained in this polar volume:
+my_pvol$scans

      Exercise 1: Load the polar volume file, example_pvol.h5 from the files downloaded in section 1.1. Put it in your working directory and load it into R. What is the minimum and maximum scan elevation contained in the volume? And which scan parameters are available? (See manual page of the read_pvolfile() function for the nomenclature of various available quantities).

      1.3 Plotting radar scans

      -
      # (if you haven't done so already) load the polar volume data from the example_pvol.h5 file you just downloaded
-my_pvol <- read_pvolfile("example_pvol.h5")
-# let's extract the third scan, which was collected at 1.5 degree elevation:
-my_scan <- my_pvol$scans[[3]]
-# print some information about this scan:
-my_scan
-# let's plot the reflectivity factor parameter of the scan in a range - azimuth coordinate system:
-plot(my_scan, param = "DBZH")
      +
      # (if you haven't done so already) load the polar volume data from the example_pvol.h5 file you just downloaded
+my_pvol <- read_pvolfile("example_pvol.h5")
+# let's extract the third scan, which was collected at 1.5 degree elevation:
+my_scan <- my_pvol$scans[[3]]
+# print some information about this scan:
+my_scan
+# let's plot the reflectivity factor parameter of the scan in a range - azimuth coordinate system:
+plot(my_scan, param = "DBZH")

      Usually it is more intuitive to explore radar scans as a PPI (plan position indicator), which is a projection of the scan on a Cartesian (X,Y) or (lat,lon) grid:

      -
      # before we can plot the scan, we need to project it on a Cartesian grid,
-# i.e. we need to make a Plan Position Indicator (PPI)
-my_ppi <- project_as_ppi(my_scan)
-# print some information about this ppi:
-my_ppi
-# you can see we projected it on a 500 meter grid
-# (check the manual of the project_as_ppi function to see how you can
-# change the grid size (argument grid_size) and the maximum distance
-# from the radar up to where to plot data (argument range_max))
-#
-# Now we are ready to plot the ppi, for example let's plot reflectivity factor DBZH:
-plot(my_ppi, param = "DBZH")
      +
      # before we can plot the scan, we need to project it on a Cartesian grid,
+# i.e. we need to make a Plan Position Indicator (PPI)
+my_ppi <- project_as_ppi(my_scan)
+# print some information about this ppi:
+my_ppi
+# you can see we projected it on a 500 meter grid
+# (check the manual of the project_as_ppi function to see how you can
+# change the grid size (argument grid_size) and the maximum distance
+# from the radar up to where to plot data (argument range_max))
+#
+# Now we are ready to plot the ppi, for example let's plot reflectivity factor DBZH:
+plot(my_ppi, param = "DBZH")

      Exercise 2: This case contains convective precipitation, characterized by localized but intense thunderstorms, as well as biological scattering. Make also a ppi plot of the correlation coefficient (RHOHV) and radial velocity (VRADH). Verify how the texture of the radial velocity, and the values of correlation coefficient of the precipitative areas differs from the areas with biological scattering.

      Exercise 3: Based on the radial velocity image, are the biological scatterers birds or insects? Why?

      1.4 Overlaying radar scans on maps

      -
      # It is often informative to plot radar data on a base layer.
-# first download the background image:
-basemap <- download_basemap(my_ppi)
-# then overlay the PPI on the satellite image, restricting the color scale from -20 to 15 dBZ:
-map(my_ppi, map = basemap, param = "DBZH", zlim = c(-20, 15))
      +
      # It is often informative to plot radar data on a base layer.
+# first download the background image:
+basemap <- download_basemap(my_ppi)
+# then overlay the PPI on the satellite image, restricting the color scale from -20 to 15 dBZ:
+map(my_ppi, map = basemap, param = "DBZH", zlim = c(-20, 15))

      bioRad provides several functions to convert radar scans to other common spatial formats in R (cf. package raster and package sp), see scan_to_raster() and scan_to_spatial(), allowing you to process and overlay the radar data further with these spatial analysis toolkits.

      @@ -217,72 +217,72 @@

      2.1 Loading processed vertical profiles

      -
      # Usually we would load processed vertical profiles (vp files) by:
-# my_vplist <- read_vpfiles("./your/directory/with/processed/profiles/goes/here")
-# my_vplist contains after running the command a list of vertical profile (vp) objects
-# To save time, we load these data directly from file
-load("KBRO20170514.RData")
-# print the length of the vplist object. It should contain 95 profiles
-length(my_vplist)
      +
      # Usually we would load processed vertical profiles (vp files) by:
+# my_vplist <- read_vpfiles("./your/directory/with/processed/profiles/goes/here")
+# my_vplist contains after running the command a list of vertical profile (vp) objects
+# To save time, we load these data directly from file
+load("KBRO20170514.RData")
+# print the length of the vplist object. It should contain 95 profiles
+length(my_vplist)

      2.2 Inspecting single vertical profiles

      Now that you have loaded a list of vertical profiles, we can start exploring them. We will start with plotting and inspecting single vertical profiles, i.e. a single profile from the list of vp objects you have just loaded.

      -
      # let's extract a profile from the list, in this example the 41st profile:
-my_vp <- my_vplist[[41]]
-# print some info for this profile to the console
-my_vp
-# test whether this profile was collected at day time:
-check_night(my_vp)
-# plot the vertical profile, in terms of reflectivity factor
-plot(my_vp, quantity = "dbz")
-# plot the vertical profile, in terms of (linear) reflectivity
-plot(my_vp, quantity = "eta")
      +
      # let's extract a profile from the list, in this example the 41st profile:
+my_vp <- my_vplist[[41]]
+# print some info for this profile to the console
+my_vp
+# test whether this profile was collected at day time:
+check_night(my_vp)
+# plot the vertical profile, in terms of reflectivity factor
+plot(my_vp, quantity = "dbz")
+# plot the vertical profile, in terms of (linear) reflectivity
+plot(my_vp, quantity = "eta")

      eta and dbz are closely related, the main difference is that reflectivity factors are logarithmic, and reflectivities linear. You can convert one into the other using eta_to_dbz() and dbz_to_eta() functions, which follow this simple formula:

      eta = (radar-wavelength dependent constant) * 10^(dbz/10)

      The reflectivity factor dBZ is the quantity used by most meteorologist. It has the useful property that at different radar wavelengths (e.g. S-band versus C-band) the same amount of precipitation shows up at similar reflectivity factors. The same holds for insects, as well as any other target that is much smaller than the radar wavelength (S-band = 10 cm, C-band = 5 cm), the so-called Rayleigh-scattering limit.

      In the case of birds we are outside the Rayleigh limit, because birds are of similar size as the radar wavelength. In this limit reflectivity eta is more similar between S-band and C-band. eta is also more directly related to the density of birds, since eta can be expressed as (bird density) x (radar cross section per bird). For these two reasons, for weather radar ornithologists not reflectivity factor dBZ but reflectivity eta is the more conventional unit.

      -
      # let'splot the vertical profile, in terms of bird density
-plot(my_vp, quantity = "dens")
-# print the currently assumed radar cross section (RCS) per bird:
-rcs(my_vp)
      +
      # let'splot the vertical profile, in terms of bird density
+plot(my_vp, quantity = "dens")
+# print the currently assumed radar cross section (RCS) per bird:
+rcs(my_vp)

      Exercise 4: If you change your assumption on the bird’s radar cross section in the previous example, and assume it is 10 times as large, what will be the effect on the bird density profile?

      The radar cross section you assume can be changed as follows:

      -
      # let's change the RCS to 110 cm^2
-rcs(my_vp) <- 110
      +
      # let's change the RCS to 110 cm^2
+rcs(my_vp) <- 110

      Exercise 5: Verify your answers on the previous two questions, by re-plotting the vertical profiles for the bird density quantity.

      2.3 Plotting vertical profile time series

      We will now examine multiple vertical profiles at once that are ordered into a time series, e.g. the vertical profiles obtained from a single radar over a full day.

      -
      # convert the list of vertical profiles into a time series:
-my_vpts <- bind_into_vpts(my_vplist)
-# print summary information
-my_vpts
-# time series objects can be subsetted, just as you may be used to with vectors
-# here we subset the first 50 timesteps:
-my_vpts[1:50]
-# here we extract a single timestep, which gives you back a vertical profile class object:
-my_vpts[100]
-# to extract all the dates of all profiles in the time series:
-my_vpts$datetime
-# to plot the full time series:
-plot(my_vpts)
-# check the help file for the plotting function of profile time series
-# Because profile timeseries are of class 'vpts', it's associated plotting function
-# is called plot.vpts:
-?plot.vpts
      +
      # convert the list of vertical profiles into a time series:
+my_vpts <- bind_into_vpts(my_vplist)
+# print summary information
+my_vpts
+# time series objects can be subsetted, just as you may be used to with vectors
+# here we subset the first 50 timesteps:
+my_vpts[1:50]
+# here we extract a single timestep, which gives you back a vertical profile class object:
+my_vpts[100]
+# to extract all the dates of all profiles in the time series:
+my_vpts$datetime
+# to plot the full time series:
+plot(my_vpts)
+# check the help file for the plotting function of profile time series
+# Because profile timeseries are of class 'vpts', it's associated plotting function
+# is called plot.vpts:
+?plot.vpts

      Let’s make a plot for a subselection of the time series:

      -
      # make a subselection for night time only
-index_night <- check_night(my_vpts)
-# index_night is a logical vector that specifies each profile whether it occurred at night or not:
-index_night
-# now subset our vpts using this selection:
-my_vpts_night <- my_vpts[index_night]
-# plot this smaller time series:
-plot(my_vpts_night)
      +
      # make a subselection for night time only
+index_night <- check_night(my_vpts)
+# index_night is a logical vector that specifies each profile whether it occurred at night or not:
+index_night
+# now subset our vpts using this selection:
+my_vpts_night <- my_vpts[index_night]
+# plot this smaller time series:
+plot(my_vpts_night)

      Exercise 6: Interpret the wind barbs in the profile time series figure: what is the approximate speed and direction at 1500 meter at 6 UTC? In the speed barbs, each half flag represents 2.5 m/s, each full flag 5 m/s, [each pennant (triangle) 25 m/s, not occurring in this case].

      Exercise 7: Extract the vertical profile at 6 UTC from the time series and plot the vertical profile of ground speed (quantity ff). Hint: use function filter_vpts() to extract the 6 UTC profile. Check whether your answer to the previous question was approximately correct.

      @@ -295,31 +295,31 @@

    • Note that the VID quantity doesn’t depend on the speed of the migrants. A common measure that reflects both the density and speed of the migration is migration traffic rate (MTR). This is flux measure that gives you how many migrants are passing the radar station per unit of time and per unit of distance perpendicular to the migratory direction (unit individuals/km/hour).

      • We will be using bioRad’s integrate_profile() function to calculate these quantities:

      -
      # Let's continue with the vpts object created in the previous example.
-# The vertically integrated quantities are calculated as follows:
-my_vpi <- integrate_profile(my_vpts)
-# The my_vpi object you created is a vpi class object, which is an acronym for "vertical profile integrated". It has its own plot method, which by default plots migration traffic rate (MTR):
-plot(my_vpi)
-# you can also plot vertically integrated densities (VID):
-plot(my_vpi, quantity = "vid")
-# the gray and white shading indicates day and night, which is calculated
-# from the date and the radar position. You can also turn this off:
-plot(my_vpi, night_shade = FALSE)
-# plot the cumulative number of birds passing the radar, i.e. migration traffic (mt):
-plot(my_vpi, quantity = "mt")
-# execute `?plot.vpi` to open the help page listing all the options.
-?plot.vpi
      +
      # Let's continue with the vpts object created in the previous example.
+# The vertically integrated quantities are calculated as follows:
+my_vpi <- integrate_profile(my_vpts)
+# The my_vpi object you created is a vpi class object, which is an acronym for "vertical profile integrated". It has its own plot method, which by default plots migration traffic rate (MTR):
+plot(my_vpi)
+# you can also plot vertically integrated densities (VID):
+plot(my_vpi, quantity = "vid")
+# the gray and white shading indicates day and night, which is calculated
+# from the date and the radar position. You can also turn this off:
+plot(my_vpi, night_shade = FALSE)
+# plot the cumulative number of birds passing the radar, i.e. migration traffic (mt):
+plot(my_vpi, quantity = "mt")
+# execute `?plot.vpi` to open the help page listing all the options.
+?plot.vpi

      The following questions only require pen and paper. Assume a night migration event in which the volume density of birds from 0-1 km above ground is 200 birds per cubic kilometer, and from 1-1.5 km 100 birds per cubic kilometer. In the lower layer birds fly at 50 km/hour, and in the upper layer at 100 km/hour. Above 1500 meter there are no birds. Migration continues for exactly three hours after sunset, and then halts abruptly.

      Exercise 8: What is in this case the bird’s vertically integrated density (VID)? Give your answer in units birds/km\(^2\).

      Exercise 9: What is in this case the migration traffic rate across a transect perpendicular to the direction of movement? Give your answer in units birds/km/hour.

      Exercise 10: How many birds have passed a 1km transect perpendicular to the direction of movement in this night? Give your answer in terms of migration traffic (mt) in units birds/km.

      Both MTR, VID and MT depend on the assumed radar cross section (RCS) per bird. If you are unwilling/unable to specify RCS, you can alternatively use two closely related quantities that make no assumptions RCS:

      -
      # instead of vertically integrated density (VID), you can use vertically integrated reflectivity (VIR):
-plot(my_vpi, quantity = "vir")
-# instead of migration traffic rate (MTR), you can use the reflectivity traffic rate (RTR):
-plot(my_vpi, quantity = "rtr")
-# instead of migration traffic (MT), you can use the reflectivity traffic (RT):
-plot(my_vpi, quantity = "rt")
      +
      # instead of vertically integrated density (VID), you can use vertically integrated reflectivity (VIR):
+plot(my_vpi, quantity = "vir")
+# instead of migration traffic rate (MTR), you can use the reflectivity traffic rate (RTR):
+plot(my_vpi, quantity = "rtr")
+# instead of migration traffic (MT), you can use the reflectivity traffic (RT):
+plot(my_vpi, quantity = "rt")

      VIR gives you the total cross-sectional area of air-borne targets per square kilometer of ground surface, whereas RTR gives you the total cross-sectional area of targets flying across a one kilometer line perpendicular to the migratory flow per hour.

      @@ -328,12 +328,12 @@

      Precipitation is known to have a major influence on the timing and intensity of migration, therefore it is a useful skill to be able to inspect profiles for presence of precipitation.

      Also, although automated bird quantification algorithms become more and more reliable, distinguishing precipitation from birds remains challenging for algorithms in specific cases. It is therefore important to have the skills to inspect suspicious profiles. That may help you to identify potential errors of the automated methods, and prevent your from overinterpreting the data.

      An easy way of doing that is plotting the vertical profile of total reflectivity (quantity DBZH), which includes everything: birds, insects and precipitation. Precipitation often has higher reflectivities than birds, and also extends to much higher altitudes.

      -
      # load a time series for the KBGM radar in Binghamton, NY
-load("KBGM20170527-20170602.RData")
-# print the loaded vpts time series for this radar:
-my_vpts
-# plot the bird density over time:
-plot(my_vpts, quantity = "dens")
      +
      # load a time series for the KBGM radar in Binghamton, NY
+load("KBGM20170527-20170602.RData")
+# print the loaded vpts time series for this radar:
+my_vpts
+# plot the bird density over time:
+plot(my_vpts, quantity = "dens")

      Exercise 11: Compare the above plot for bird density (quantity dens) with a profile plot for total reflectivity (quantity DBZH, showing birds and precipitation combined). Compare the two plots to visually identify periods and altitude layers with precipitation.

      @@ -361,55 +361,55 @@

      3.2 Processing a single polar volume with the vol2bird algorithm

      The following steps take you through the process applying the vol2bird algorithm yourself. You need a working installation of Docker (Linux/Mac) or Docker for Windows (not Docker Toolbox, this is an older implementation of Docker for Windows operating systems that is not supported).

      We will generate vertical profiles with the automated algorithm vol2bird (https://github.com/adokter/vol2bird), which is included in the bioRad package.

      -
      # start your local Docker installation
-# we first test whether R can communicate with Docker:
-check_docker()
      +
      # start your local Docker installation
+# we first test whether R can communicate with Docker:
+check_docker()

      If you get a “Hello from Docker!” welcome message, everything is working and you can start processing.

      -
      # download a polar volume file you want to process and put it in your home directory.
-my_file <- "write_your_file_to_be_processed_here"
-# Alternatively, continue with the polar volume that comes with the package:
-my_file <- system.file("extdata", "volume.h5", package = "bioRad")
-# run vol2bird
-# we set autoconf to TRUE, to let vol2bird figure out the optimal settings by itself
-my_vp <- calculate_vp(my_file, autoconf = TRUE)
-# vp is now a 'vp' profile object, that you can examine as in the previous exercises
-# alternatively, you may also store the profile as a hdf5 file, which is what we will do next:
-calculate_vp(my_file, "my_vpfile.h5", autoconf = TRUE)
-# your work directory should now contain a new file 'my_vpfile.h5'
-# check that we can read this file, and retrieve the vertical profile from it:
-vp <- read_vpfiles("my_vpfile.h5")
      +
      # download a polar volume file you want to process and put it in your home directory.
+my_file <- "write_your_file_to_be_processed_here"
+# Alternatively, continue with the polar volume that comes with the package:
+my_file <- system.file("extdata", "volume.h5", package = "bioRad")
+# run vol2bird
+# we set autoconf to TRUE, to let vol2bird figure out the optimal settings by itself
+my_vp <- calculate_vp(my_file, autoconf = TRUE)
+# vp is now a 'vp' profile object, that you can examine as in the previous exercises
+# alternatively, you may also store the profile as a hdf5 file, which is what we will do next:
+calculate_vp(my_file, "my_vpfile.h5", autoconf = TRUE)
+# your work directory should now contain a new file 'my_vpfile.h5'
+# check that we can read this file, and retrieve the vertical profile from it:
+vp <- read_vpfiles("my_vpfile.h5")

      3.3 Processing multiple polar volumes

      This section contains an example for processing a directory of polar volumes into profiles:

      -
      # read the filenames of the polar volumes you want to process
-my_files <- list.files("your/directory/with/volumes/goes/here/", full.names = TRUE)
-# print the filenames
-my_files
-# create output directory for processed profiles
-outputdir <- "~/processed_data"
-dir.create(outputdir)
-# let's loop over the files and generate profiles
-for (file_in in my_files) {
-  # generate the output filename for the input file
-  file_out <- paste(outputdir, "/", basename(file_in), "_vp.h5", sep = "")
-  # generate the profile, and write it as a hdf5 file (for later reference)
-  # we turn autoconfiguration on, so vol2bird chooses the optimal settings for the file automatically
-  vp <- calculate_vp(file_in, file_out, autoconf = TRUE)
-}
      +
      # read the filenames of the polar volumes you want to process
+my_files <- list.files("your/directory/with/volumes/goes/here/", full.names = TRUE)
+# print the filenames
+my_files
+# create output directory for processed profiles
+outputdir <- "~/processed_data"
+dir.create(outputdir)
+# let's loop over the files and generate profiles
+for (file_in in my_files) {
+  # generate the output filename for the input file
+  file_out <- paste(outputdir, "/", basename(file_in), "_vp.h5", sep = "")
+  # generate the profile, and write it as a hdf5 file (for later reference)
+  # we turn autoconfiguration on, so vol2bird chooses the optimal settings for the file automatically
+  vp <- calculate_vp(file_in, file_out, autoconf = TRUE)
+}

      Having generated the profiles, we can read them into R:

      -
      # we assume outputdir contains the path to the directory with processed profiles
-my_vpfiles <- list.files(outputdir, full.names = TRUE)
-# print them
-my_vpfiles
-# read them
-my_vplist <- read_vpfiles(my_vpfiles)
      +
      # we assume outputdir contains the path to the directory with processed profiles
+my_vpfiles <- list.files(outputdir, full.names = TRUE)
+# print them
+my_vpfiles
+# read them
+my_vplist <- read_vpfiles(my_vpfiles)

      You can now continue with visualizing and post-processing as we did earlier:

      -
      # make a time series of profiles:
-my_vpts <- bind_into_vpts(my_vplist)
-# plot them between 0 - 3 km altitude:
-plot(my_vpts, ylim = c(0, 3000))
      +
      # make a time series of profiles:
+my_vpts <- bind_into_vpts(my_vplist)
+# plot them between 0 - 3 km altitude:
+plot(my_vpts, ylim = c(0, 3000))
      @@ -452,7 +445,7 @@

      -

      Site built with pkgdown 1.4.1.9000.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/dev/articles/range_correction.html b/docs/dev/articles/range_correction.html index 83ec5f6d9..dfb3353bf 100644 --- a/docs/dev/articles/range_correction.html +++ b/docs/dev/articles/range_correction.html @@ -12,23 +12,23 @@ - - - - - + + + + + + - + - - +
      +
      -

      Correction for range effects

      +

      Correction for range effects

      Adriaan M. Dokter

      @@ -119,8 +119,8 @@

      Adriaan M. Dokter

      1 Preparations

      Load bioRad

      -
      library(bioRad)
      -
      ## Welcome to bioRad version 0.5.0.9325
      +
      library(bioRad)
      +
      ## Welcome to bioRad version 0.5.1.9000
      ## Docker daemon running, Docker functionality enabled (vol2bird version 0.5.0, MistNet available)
      @@ -135,38 +135,38 @@

      distance: the distance of the target from the radar as measured along the earth’s surface, also known as down range.

      The beam height is changing as a result of earth’s curvature, and beam refraction:

      -
      # define a range grid from 0 to 200 km:
-my_range <- seq(0, 200000, 1000)
-# plot the beam height for each range, for a 0.5 degree elevation beam:
-plot(my_range, beam_height(my_range, elev = .5), xlab = "range [m]", ylab = "beam height [m]")
      +
      # define a range grid from 0 to 200 km:
+my_range <- seq(0, 200000, 1000)
+# plot the beam height for each range, for a 0.5 degree elevation beam:
+plot(my_range, beam_height(my_range, elev = .5), xlab = "range [m]", ylab = "beam height [m]")

      The beam width also broadens with range:

      -
      # plot the beam width, for a beam opening angle of 1 degree (typical for most weather radars):
-plot(my_range, beam_width(my_range, beam_angle = 1), xlab = "range [m]", ylab = "beam width [m]")
      +
      # plot the beam width, for a beam opening angle of 1 degree (typical for most weather radars):
+plot(my_range, beam_width(my_range, beam_angle = 1), xlab = "range [m]", ylab = "beam width [m]")

      We can now combine the relations for beam width and beam height, to calculate the beam profile as a function of height, i.e. the altitudinal normalized distribution of radiated energy by the beam. Let’s plot the radiation profile for a 0.5 and 2 degree beam elevation at 50 km from the radar (the height axis runs from ground level straight up):

      -
      # plot the beam profile, for a 0.5 degree elevation beam at 50 km distance from the radar:
-plot(beam_profile(height = 0:4000, 50000, 0.5), 0:4000, xlab = "normalized radiated energy", ylab = "height [m]", main = "beam elevation: 0.5 deg, distance=50km")
      +
      # plot the beam profile, for a 0.5 degree elevation beam at 50 km distance from the radar:
+plot(beam_profile(height = 0:4000, 50000, 0.5), 0:4000, xlab = "normalized radiated energy", ylab = "height [m]", main = "beam elevation: 0.5 deg, distance=50km")

      -
      # plot the beam profile, for a 2 degree elevation beam at 50 km distance from the radar:
-plot(beam_profile(height = 0:4000, 50000, 2), 0:4000, xlab = "normalized radiated energy", ylab = "height [m]", main = "beam elevation: 2 deg, distance=50km")
      +
      # plot the beam profile, for a 2 degree elevation beam at 50 km distance from the radar:
+plot(beam_profile(height = 0:4000, 50000, 2), 0:4000, xlab = "normalized radiated energy", ylab = "height [m]", main = "beam elevation: 2 deg, distance=50km")

      We can also calculate the normalized radiation profile for the two beams combined:

      -
      # plot the combined beam profile for a 0.5 and 2.0 degree elevation beam at 50 km distance from the radar:
-plot(beam_profile(height = 0:4000, 50000, c(0.5, 2)), 0:4000, xlab = "normalized radiated energy", ylab = "height [m]", main = "beam elevations: 0.5,2 deg, distance=50km")
      +
      # plot the combined beam profile for a 0.5 and 2.0 degree elevation beam at 50 km distance from the radar:
+plot(beam_profile(height = 0:4000, 50000, c(0.5, 2)), 0:4000, xlab = "normalized radiated energy", ylab = "height [m]", main = "beam elevations: 0.5,2 deg, distance=50km")

      3 Vertical profiles and polar volumes

      Let us now assume we have calculated a vertical profile (of birds) for a certain polar volume file. Let’s load an example

      -
      # let's load an example polar volume:
-pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
-example_pvol <- read_pvolfile(file = pvolfile)
-# a vertical profile can also be calculated from the polar volume directly, using
-# calculate_vp(pvolfile)
-# but for now we will use bioRad's example vertical profile already calculated:
-example_vp
      +
      # let's load an example polar volume:
+pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
+example_pvol <- read_pvolfile(file = pvolfile)
+# a vertical profile can also be calculated from the polar volume directly, using
+# calculate_vp(pvolfile)
+# but for now we will use bioRad's example vertical profile already calculated:
+example_vp
      ##                Vertical profile (class vp)
 ## 
 ##        radar:  seang 
@@ -174,10 +174,10 @@ 
      
 ## nominal time:  2015-10-18 18:00:00 
 ## generated by:  vol2bird 0.3.17

      Let’s plot the vertical profile, for the quantity eta (the linear reflectivity):

      -
      plot(example_vp, quantity = "eta")
      +
      plot(example_vp, quantity = "eta")

      Note that eta is directly related to reflectivity factor (DBZH), i.e. a reflectivity factor of 5 dBZ amounts to the following eta at a radar wavelength of 5.3 cm:

      -
      dbz_to_eta(5, wavelength = 5.3)
      +
      dbz_to_eta(5, wavelength = 5.3)
      ## [1] 1060.747
      @@ -208,33 +208,33 @@

      5 Example: estimating a VID image

      Let’s first make a PPI plot of the lowest uncorrected scan:

      -
      # extract the first scan from the polar volume:
-my_scan <- example_pvol$scans[[1]]
-# project it as a PPI on the ground:
-my_ppi <- project_as_ppi(my_scan, range_max = 100000)
-# plot it
-plot(my_ppi)
      +
      # extract the first scan from the polar volume:
+my_scan <- example_pvol$scans[[1]]
+# project it as a PPI on the ground:
+my_ppi <- project_as_ppi(my_scan, range_max = 100000)
+# plot it
+plot(my_ppi)

      Now let’s calculate the range-corrected PPI

      -
      # let's use a 500 metre spatial grid (res), and restrict to 100x100 km area
-my_corrected_ppi <- integrate_to_ppi(example_pvol, example_vp, res = 500, xlim = c(-100000, 100000), ylim = c(-100000, 100000))
-my_corrected_ppi
      +
      # let's use a 500 metre spatial grid (res), and restrict to 100x100 km area
+my_corrected_ppi <- integrate_to_ppi(example_pvol, example_vp, res = 500, xlim = c(-100000, 100000), ylim = c(-100000, 100000))
+my_corrected_ppi
      ##                Plan position indicator (class ppi)
 ## 
 ##   quantities:  VIR VID R overlap eta_sum eta_sum_expected 
 ##         dims:  400 x 400 pixels

      The range corrected PPI has four parameters: VIR, VID, R, overlap. Let’s plot the adjustment factor R:

      -
      # plot the adjustment factor R:
-plot(my_corrected_ppi, param = "R")
      +
      # plot the adjustment factor R:
+plot(my_corrected_ppi, param = "R")

      Let’s also plot the vertically integrated reflectivity:

      -
      plot(my_corrected_ppi, param = "VIR")
      +
      plot(my_corrected_ppi, param = "VIR")

      Or plot the vertically integrated density on a map:

      -
      bm <- download_basemap(my_corrected_ppi)
      +
      bm <- download_basemap(my_corrected_ppi)
      ## Downloading zoom = 8 ...
      ## Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL.
      -
      map(my_corrected_ppi, bm, param = "VIR", alpha = .5)
      +
      map(my_corrected_ppi, bm, param = "VIR", alpha = .5)

      @@ -246,16 +246,16 @@

    • at large distances weak biological echoes may get below the radar’s detection level

      • We can calculate overlap between emitted radiation and the biological profile as follows:

      -
      # calculate overlap between vertical profile of birds
-# and the vertical radiation profile emitted by the radar:
-bpo <- beam_profile_overlap(example_vp, get_elevation_angles(example_pvol), seq(0, 100000, 1000), quantity = "eta")
-# plot the calculated overlap:
-plot(bpo)
      +
      # calculate overlap between vertical profile of birds
+# and the vertical radiation profile emitted by the radar:
+bpo <- beam_profile_overlap(example_vp, get_elevation_angles(example_pvol), seq(0, 100000, 1000), quantity = "eta")
+# plot the calculated overlap:
+plot(bpo)

      The function first normalizes the vertical profile altitudinal distribution. This can be either using profile quantity eta or dens, whichever is preferred (note that dens, the density, is sometimes thresholded to zero based on radial velocity standard deviation, see sd_vvp_threshold(), while eta is not)

      It then calculates the overlap between the normalized vertical profile, and the normalized radiation profile as calculated with beam_profile(), using a metric called the Bhattacharyya distance. This metric is zero when there is no overlap, and 1 when the distributions are identical.

      The range-corrected PPI also contains a field overlap, which contains the same metric but then calculated on the grid of the PPI:

      -
      plot(my_corrected_ppi, param = "overlap")
      +
      plot(my_corrected_ppi, param = "overlap")

      The overlap metric might be used in the future to show only certain section of the PPI, based on their overlap value.

      @@ -270,20 +270,9 @@

      @@ -294,7 +283,7 @@

      -

      Site built with pkgdown 1.4.1.9000.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/dev/authors.html b/docs/dev/authors.html index 1a3cc8214..cc3224917 100644 --- a/docs/dev/authors.html +++ b/docs/dev/authors.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,7 +54,6 @@ - @@ -68,7 +71,7 @@ - +
      @@ -121,7 +124,7 @@
      • - + @@ -211,7 +214,7 @@

        Authors

      -

      Site built with pkgdown 1.4.1.9000.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/dev/bootstrap-toc.css b/docs/dev/bootstrap-toc.css new file mode 100644 index 000000000..5a859415c --- /dev/null +++ b/docs/dev/bootstrap-toc.css @@ -0,0 +1,60 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ + +/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */ + +/* All levels of nav */ +nav[data-toggle='toc'] .nav > li > a { + display: block; + padding: 4px 20px; + font-size: 13px; + font-weight: 500; + color: #767676; +} +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 19px; + color: #563d7c; + text-decoration: none; + background-color: transparent; + border-left: 1px solid #563d7c; +} +nav[data-toggle='toc'] .nav > .active > a, +nav[data-toggle='toc'] .nav > .active:hover > a, +nav[data-toggle='toc'] .nav > .active:focus > a { + padding-left: 18px; + font-weight: bold; + color: #563d7c; + background-color: transparent; + border-left: 2px solid #563d7c; +} + +/* Nav: second level (shown on .active) */ +nav[data-toggle='toc'] .nav .nav { + display: none; /* Hide by default, but at >768px, show it */ + padding-bottom: 10px; +} +nav[data-toggle='toc'] .nav .nav > li > a { + padding-top: 1px; + padding-bottom: 1px; + padding-left: 30px; + font-size: 12px; + font-weight: normal; +} +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 29px; +} +nav[data-toggle='toc'] .nav .nav > .active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 28px; + font-weight: 500; +} + +/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */ +nav[data-toggle='toc'] .nav > .active > ul { + display: block; +} diff --git a/docs/dev/bootstrap-toc.js b/docs/dev/bootstrap-toc.js new file mode 100644 index 000000000..1cdd573b2 --- /dev/null +++ b/docs/dev/bootstrap-toc.js @@ -0,0 +1,159 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ +(function() { + 'use strict'; + + window.Toc = { + helpers: { + // return all matching elements in the set, or their descendants + findOrFilter: function($el, selector) { + // http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/ + // http://stackoverflow.com/a/12731439/358804 + var $descendants = $el.find(selector); + return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])'); + }, + + generateUniqueIdBase: function(el) { + var text = $(el).text(); + var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-'); + return anchor || el.tagName.toLowerCase(); + }, + + generateUniqueId: function(el) { + var anchorBase = this.generateUniqueIdBase(el); + for (var i = 0; ; i++) { + var anchor = anchorBase; + if (i > 0) { + // add suffix + anchor += '-' + i; + } + // check if ID already exists + if (!document.getElementById(anchor)) { + return anchor; + } + } + }, + + generateAnchor: function(el) { + if (el.id) { + return el.id; + } else { + var anchor = this.generateUniqueId(el); + el.id = anchor; + return anchor; + } + }, + + createNavList: function() { + return $('
        '); + }, + + createChildNavList: function($parent) { + var $childList = this.createNavList(); + $parent.append($childList); + return $childList; + }, + + generateNavEl: function(anchor, text) { + var $a = $(''); + $a.attr('href', '#' + anchor); + $a.text(text); + var $li = $('
      • '); + $li.append($a); + return $li; + }, + + generateNavItem: function(headingEl) { + var anchor = this.generateAnchor(headingEl); + var $heading = $(headingEl); + var text = $heading.data('toc-text') || $heading.text(); + return this.generateNavEl(anchor, text); + }, + + // Find the first heading level (`

        `, then `

        `, etc.) that has more than one element. Defaults to 1 (for `

        `). + getTopLevel: function($scope) { + for (var i = 1; i <= 6; i++) { + var $headings = this.findOrFilter($scope, 'h' + i); + if ($headings.length > 1) { + return i; + } + } + + return 1; + }, + + // returns the elements for the top level, and the next below it + getHeadings: function($scope, topLevel) { + var topSelector = 'h' + topLevel; + + var secondaryLevel = topLevel + 1; + var secondarySelector = 'h' + secondaryLevel; + + return this.findOrFilter($scope, topSelector + ',' + secondarySelector); + }, + + getNavLevel: function(el) { + return parseInt(el.tagName.charAt(1), 10); + }, + + populateNav: function($topContext, topLevel, $headings) { + var $context = $topContext; + var $prevNav; + + var helpers = this; + $headings.each(function(i, el) { + var $newNav = helpers.generateNavItem(el); + var navLevel = helpers.getNavLevel(el); + + // determine the proper $context + if (navLevel === topLevel) { + // use top level + $context = $topContext; + } else if ($prevNav && $context === $topContext) { + // create a new level of the tree and switch to it + $context = helpers.createChildNavList($prevNav); + } // else use the current $context + + $context.append($newNav); + + $prevNav = $newNav; + }); + }, + + parseOps: function(arg) { + var opts; + if (arg.jquery) { + opts = { + $nav: arg + }; + } else { + opts = arg; + } + opts.$scope = opts.$scope || $(document.body); + return opts; + } + }, + + // accepts a jQuery object, or an options object + init: function(opts) { + opts = this.helpers.parseOps(opts); + + // ensure that the data attribute is in place for styling + opts.$nav.attr('data-toggle', 'toc'); + + var $topContext = this.helpers.createChildNavList(opts.$nav); + var topLevel = this.helpers.getTopLevel(opts.$scope); + var $headings = this.helpers.getHeadings(opts.$scope, topLevel); + this.helpers.populateNav($topContext, topLevel, $headings); + } + }; + + $(function() { + $('nav[data-toggle="toc"]').each(function(i, el) { + var $nav = $(el); + Toc.init($nav); + }); + }); +})(); diff --git a/docs/dev/docsearch.json b/docs/dev/docsearch.json index 073f8190b..11afd16ab 100644 --- a/docs/dev/docsearch.json +++ b/docs/dev/docsearch.json @@ -74,7 +74,7 @@ "selector": ".contents h2, .contents h3", "default_value": "Context" }, - "text": ".contents p, .contents li, .tempate-article .contents .pre" + "text": ".contents p, .contents li" } }, "selectors_exclude": [ diff --git a/docs/dev/index.html b/docs/dev/index.html index c9ab886c6..8eec1722c 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -12,25 +12,25 @@ - - - - - + + + + + + - - +
        @@ -198,12 +198,12 @@

        Radar data example

        bioRad can read weather radar data (= polar volumes) in the ODIM format and formats supported by the RSL library, such as NEXRAD data. NEXRAD data (US) are available as open data and on AWS.

        Here we read an example polar volume data file with read_pvolfile(), extract the scan/sweep at elevation angle 3 with get_scan(), project the data to a plan position indicator with project_as_ppi() and plot the radial velocity of detected targets with plot():

        -
        library(tidyverse) # To pipe %>% the steps below
-system.file("extdata", "volume.h5", package = "bioRad") %>%
-  read_pvolfile() %>%
-  get_scan(3) %>%
-  project_as_ppi() %>%
-  plot(param = "VRADH") # VRADH = radial velocity in m/s
        +
        library(tidyverse) # To pipe %>% the steps below
+system.file("extdata", "volume.h5", package = "bioRad") %>%
+  read_pvolfile() %>%
+  get_scan(3) %>%
+  project_as_ppi() %>%
+  plot(param = "VRADH") # VRADH = radial velocity in m/s

        Radial velocities towards the radar are negative, while radial velocities away from the radar are positive, so in this plot there is movement from the top right to the bottom left.

        @@ -212,22 +212,22 @@

        Vertical profile data example

        Weather radar data can be processed into vertical profiles of biological targets using calculate_vp(). This type of data is available as open data for over 100 European weather radars.

        Once vertical profile data are loaded into bioRad, these can be bound into time series using bind_into_vpts(). Here we read an example time series, project it on a regular time grid with regularize_vpts() and plot it with plot():

        -
        example_vpts %>%
-  regularize_vpts() %>%
-  plot()
-#> projecting on 300 seconds interval grid...
        +
        example_vpts %>%
+  regularize_vpts() %>%
+  plot()
+#> projecting on 300 seconds interval grid...

        The gray bars in the plot indicate gaps in the data.

        The altitudes in the profile can be integrated with integrate_profile() resulting in a dataframe with rows for datetimes and columns for quantities. Here we plot the quantity migration traffic rate (column mtr) with plot():

        -
        my_vpi <- integrate_profile(example_vpts)
-
-plot(my_vpi, quantity = "mtr") # mtr = migration traffic rate
        +
        my_vpi <- integrate_profile(example_vpts)
+
+plot(my_vpi, quantity = "mtr") # mtr = migration traffic rate

        To know the total number of birds passing over the radar during the full time series, we use the last value of the cumulative migration traffic (column mt):

        -
        my_vpi %>%
-  pull(mt) %>% # Extract column mt as a vector
-  last()
-#> [1] 173023.8
        +
        my_vpi %>%
+  pull(mt) %>% # Extract column mt as a vector
+  last()
+#> [1] 173023.8

        For more exercises, see this tutorial.

        @@ -250,7 +250,7 @@

        Links

        - +
        +

        Dev status

        +
          +
        • CRAN status
          • +
        • DOI
          • +
        +
        + @@ -301,7 +308,7 @@

        Developers

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 0bd58329f..c3c5817b7 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,7 +54,6 @@ - @@ -68,7 +71,7 @@ - +
        @@ -121,7 +124,7 @@
        • - + @@ -145,12 +148,28 @@
          -

          Changelog

          +

          Changelog

          Source: NEWS.md
          +
          +

          +bioRad 0.5.1 2020-04-01 +

          +

          Minor bugfixes. All issues included in this release can be found here. This release primarily fixes a bug that will become effective once R version 4.0 is released.

          +
            +

          • fixes a conflict due to new raw data format introduced in R version 4.0 (#331)

            • +

          • corrects incorrect values in reading of correlation coefficient values RHOHV (#328)

            • +

          • bugfix in read_cajun() which introduced incorrect height column during refactoring in bioRad 0.5.0 release (93ad0a4)

            • +
          • bugfix that fixes the mapping by map() of composites of composites (ppi’s produced after repeated application of composite_ppi()) (a5c9048, 043aa73)
            • +

          • minor bug fixes, and addressing conflicts with CRAN depencies

            • +

          • extend the functionality of composite_ppi() and improve its documentation (partial fix of #59)

            • +

          • fix a bug in the color legend of map() when providing a custom color scale with palette argument (#324)

            • +

          • minor documentation improvements

            • +
          +
          -

          +

          bioRad 0.5.0 2020-02-19

          New CRAN release. All issues included in this release can be found here.

          @@ -204,7 +223,7 @@

          -

          +

          bioRad 0.4.0 2018-12-14

          First release on CRAN! All issues included in this release can be found here.

          @@ -221,7 +240,7 @@

        -

        +

        bioRad 0.3.0 Unreleased

        Release consistent with and in preparation of the bioRad methods paper (https://doi.org/10.1111/ecog.04028). All issues included in this release can be found here.

        @@ -240,14 +259,9 @@

        @@ -259,7 +273,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/pkgdown.css b/docs/dev/pkgdown.css index fa9261632..c01e5923b 100644 --- a/docs/dev/pkgdown.css +++ b/docs/dev/pkgdown.css @@ -17,6 +17,10 @@ html, body { height: 100%; } +body { + position: relative; +} + body > .container { display: flex; height: 100%; @@ -67,6 +71,10 @@ summary { margin-top: calc(-60px + 1em); } +dd { + margin-left: 3em; +} + /* Section anchors ---------------------------------*/ a.anchor { @@ -100,6 +108,52 @@ a.anchor { margin-top: -40px; } +/* Navbar submenu --------------------------*/ + +.dropdown-submenu { + position: relative; +} + +.dropdown-submenu>.dropdown-menu { + top: 0; + left: 100%; + margin-top: -6px; + margin-left: -1px; + border-radius: 0 6px 6px 6px; +} + +.dropdown-submenu:hover>.dropdown-menu { + display: block; +} + +.dropdown-submenu>a:after { + display: block; + content: " "; + float: right; + width: 0; + height: 0; + border-color: transparent; + border-style: solid; + border-width: 5px 0 5px 5px; + border-left-color: #cccccc; + margin-top: 5px; + margin-right: -10px; +} + +.dropdown-submenu:hover>a:after { + border-left-color: #ffffff; +} + +.dropdown-submenu.pull-left { + float: none; +} + +.dropdown-submenu.pull-left>.dropdown-menu { + left: -100%; + margin-left: 10px; + border-radius: 6px 0 6px 6px; +} + /* Sidebar --------------------------*/ #pkgdown-sidebar { @@ -122,6 +176,61 @@ a.anchor { margin-bottom: 0.5em; } +/* bootstrap-toc tweaks ------------------------------------------------------*/ + +/* All levels of nav */ + +nav[data-toggle='toc'] .nav > li > a { + padding: 4px 20px 4px 6px; + font-size: 1.5rem; + font-weight: 400; + color: inherit; +} + +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 5px; + color: inherit; + border-left: 1px solid #878787; +} + +nav[data-toggle='toc'] .nav > .active > a, +nav[data-toggle='toc'] .nav > .active:hover > a, +nav[data-toggle='toc'] .nav > .active:focus > a { + padding-left: 5px; + font-size: 1.5rem; + font-weight: 400; + color: inherit; + border-left: 2px solid #878787; +} + +/* Nav: second level (shown on .active) */ + +nav[data-toggle='toc'] .nav .nav { + display: none; /* Hide by default, but at >768px, show it */ + padding-bottom: 10px; +} + +nav[data-toggle='toc'] .nav .nav > li > a { + padding-left: 16px; + font-size: 1.35rem; +} + +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 15px; +} + +nav[data-toggle='toc'] .nav .nav > .active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 15px; + font-weight: 500; + font-size: 1.35rem; +} + +/* orcid ------------------------------------------------------------------- */ + .orcid { font-size: 16px; color: #A6CE39; diff --git a/docs/dev/pkgdown.js b/docs/dev/pkgdown.js index 087a76227..7e7048fae 100644 --- a/docs/dev/pkgdown.js +++ b/docs/dev/pkgdown.js @@ -9,11 +9,6 @@ $('body').css('padding-top', $('.navbar').height() + 10); }); - $('body').scrollspy({ - target: '#sidebar', - offset: 60 - }); - $('[data-toggle="tooltip"]').tooltip(); var cur_path = paths(location.pathname); diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 3dd836aef..38a083d45 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -1,10 +1,11 @@ -pandoc: '2.9' -pkgdown: 1.4.1.9000 -pkgdown_sha: 48e12e0fc836ec8ca423b44656b97f719cd856c7 +pandoc: '2.5' +pkgdown: 1.5.0 +pkgdown_sha: ~ articles: bioRad: bioRad.html rad_aero_19: rad_aero_19.html range_correction: range_correction.html +last_built: 2020-04-01T18:04Z urls: reference: https://adokter.github.io/bioRad/reference article: https://adokter.github.io/bioRad/articles diff --git a/docs/dev/reference/add_expected_eta_to_scan.html b/docs/dev/reference/add_expected_eta_to_scan.html index 719542e91..ba99e09d6 100644 --- a/docs/dev/reference/add_expected_eta_to_scan.html +++ b/docs/dev/reference/add_expected_eta_to_scan.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -230,13 +233,9 @@

          Details

        @@ -247,7 +246,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/apply_mistnet.html b/docs/dev/reference/apply_mistnet.html index b55249897..810e37ada 100644 --- a/docs/dev/reference/apply_mistnet.html +++ b/docs/dev/reference/apply_mistnet.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -221,14 +224,14 @@

          Details it can estimate a segmentation mask that identifies pixels with weather that should be removed when interested only in biological data.

          MistNet will calculate three class probabilities (from 0 to 1, with 1 corresponding -to a 100% probability) as additional scan parameters to the polar volume:

          +to a 100% probability) as additional scan parameters to the polar volume:

          "BACKGROUND"

          class probability that no signal was detected above the noise level of the radar

          "WEATHER"

          class probability that weather was detected

          "BIOLOGY"

          class probability that biological scatterers were detected

          These class probabilities are only available for the 5 input elevations used as input for the MistNet model. Based on all the class probabilities a final weather segmentation map calculated, -stored as scan parameter CELL, which is available for all elevation scans.

          +stored as scan parameter CELL, which is available for all elevation scans.

          "CELL"

          Final weather segmentation, with values > 1 indicating pixels classified as weather, and values equal to 1 indicating pixels that are located within 5 km distance of a weather pixels

          @@ -252,7 +255,7 @@

          R

          Examples

          - 
          # \dontrun{
+    
          if (FALSE) {
 # download a NEXRAD file, save as KBGM_example
 download.file(paste("https://noaa-nexrad-level2.s3.amazonaws.com/",
   "2019/10/01/KBGM/KBGM20191001_000542_V06",
@@ -270,29 +273,27 @@ 
          Examp
 my_ppi <- project_as_ppi(my_scan, range_max = 100000)
 
 # plot the reflectivity parameter:
-plot(my_ppi, param = "DBZH")
          
+plot(my_ppi, param = "DBZH")
+
 # plot the MistNet class probability [0-1] for weather
-plot(my_ppi, param = "WEATHER")
          
+plot(my_ppi, param = "WEATHER")
+
 # plot the MistNet class probability [0-1] for biology
-plot(my_ppi, param = "BIOLOGY")
          
+plot(my_ppi, param = "BIOLOGY")
+
 # plot the final segmentation result, with values >1 indicating
 # areas classified as weather, and value 1 pixels that fall within an
 # additional 5 km fringe around weather areas.
-plot(my_ppi, param = "CELL")
          
+plot(my_ppi, param = "CELL")
+
 # clean up:
-file.remove("~/KBGM_example")
          #> [1] TRUE
          # }
-
          
+file.remove("~/KBGM_example")
+}

        @@ -303,7 +304,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/as.data.frame.vp.html b/docs/dev/reference/as.data.frame.vp.html index 9e00b0e6c..18b933e4e 100644 --- a/docs/dev/reference/as.data.frame.vp.html +++ b/docs/dev/reference/as.data.frame.vp.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,7 +57,6 @@ on sunrise/sunset, day/night and derived quantities like migration traffic rates." /> - @@ -71,7 +74,7 @@ - +
        @@ -124,7 +127,7 @@
        • - + @@ -364,14 +367,9 @@

          Examp df <- as.data.frame(example_vp, suntime = TRUE, lat = 50, lon = 4)

        @@ -382,7 +380,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/as.data.frame.vpts.html b/docs/dev/reference/as.data.frame.vpts.html index 23064e0ad..c9776dcee 100644 --- a/docs/dev/reference/as.data.frame.vpts.html +++ b/docs/dev/reference/as.data.frame.vpts.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,7 +57,6 @@ data Frame, and optionally adds information on sunrise/sunset, day/night and derived quantities like migration traffic rates." /> - @@ -71,7 +74,7 @@ - +
        @@ -124,7 +127,7 @@
        • - + @@ -292,14 +295,9 @@

          Examp #> 10 519 FALSE 2016-09-01 05:03:05 2016-09-01 18:23:38

        @@ -310,7 +308,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/beam_distance.html b/docs/dev/reference/beam_distance.html index 545a83929..3640af5ac 100644 --- a/docs/dev/reference/beam_distance.html +++ b/docs/dev/reference/beam_distance.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -201,14 +204,9 @@

          Examp beam_distance(100000, 5)

        #> [1] 99495.13
        @@ -219,7 +217,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/beam_height.html b/docs/dev/reference/beam_height.html index 81705044d..40f2f9c81 100644 --- a/docs/dev/reference/beam_height.html +++ b/docs/dev/reference/beam_height.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -215,14 +218,9 @@

          Examp plot(range, beam_height(range, 0.5), ylab = "beam height [m]", xlab = "range [m]")

        @@ -233,7 +231,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/beam_profile.html b/docs/dev/reference/beam_profile.html index 7f10e90a3..00c035bf6 100644 --- a/docs/dev/reference/beam_profile.html +++ b/docs/dev/reference/beam_profile.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -243,14 +246,9 @@

          Examp )

        @@ -261,7 +259,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/beam_profile_overlap.html b/docs/dev/reference/beam_profile_overlap.html index da2ba274e..2e0a98636 100644 --- a/docs/dev/reference/beam_profile_overlap.html +++ b/docs/dev/reference/beam_profile_overlap.html @@ -18,23 +18,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -43,7 +47,7 @@ - + @@ -55,7 +59,6 @@ and the vertical radiation profile of a set of emitted radar beams at various elevation angles as given by beam_profile." /> - @@ -73,7 +76,7 @@ - +
        @@ -126,7 +129,7 @@
        • - + @@ -292,14 +295,9 @@

          Examp plot(bpo)

        @@ -310,7 +308,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/beam_range.html b/docs/dev/reference/beam_range.html index e85e6efce..5d1f73d9d 100644 --- a/docs/dev/reference/beam_range.html +++ b/docs/dev/reference/beam_range.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -200,14 +203,9 @@

          Examp beam_range(100000, 5)

        #> [1] 100508.1
        @@ -218,7 +216,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/beam_width.html b/docs/dev/reference/beam_width.html index 050b07509..4df9fb7b8 100644 --- a/docs/dev/reference/beam_width.html +++ b/docs/dev/reference/beam_width.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -185,13 +188,9 @@

          Examp plot(range, beam_width(range), ylab = "beam width [m]", xlab = "range [m]")

        @@ -202,7 +201,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/bind_into_vpts.html b/docs/dev/reference/bind_into_vpts.html index c09629f33..9732c9fd4 100644 --- a/docs/dev/reference/bind_into_vpts.html +++ b/docs/dev/reference/bind_into_vpts.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,7 +57,6 @@ (vpts), sorted in time. Can also bind multiple vpts of a single radar into one vpts." /> - @@ -71,7 +74,7 @@ - +
        @@ -124,7 +127,7 @@
        • - + @@ -250,14 +253,9 @@

          Examp #> time step (s): 240

        @@ -268,7 +266,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/bioRad-deprecated.html b/docs/dev/reference/bioRad-deprecated.html index 4c160d908..87332e2c9 100644 --- a/docs/dev/reference/bioRad-deprecated.html +++ b/docs/dev/reference/bioRad-deprecated.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,7 +57,6 @@ defunct in the near future. When possible, alternative functions with similar functionality are mentioned." /> - @@ -71,7 +74,7 @@ - +
        @@ -124,7 +127,7 @@
        • - + @@ -365,14 +368,13 @@

          mt

          specified altitude band.

          Deprecated examples

          -# get example time series of vertical profiles:
-data(example_vpts)
-example_vpts
-# total migration traffic in full altitude band:
-mt(example_vpts)
-# total migration traffic in 0-1000 meter band:
-mt(example_vpts, alt.min = 0, alt.max = 1000)
-
          +# get example time series of vertical profiles: +data(example_vpts) +example_vpts +# total migration traffic in full altitude band: +mt(example_vpts) +# total migration traffic in 0-1000 meter band: +mt(example_vpts, alt.min = 0, alt.max = 1000)

          mtr

          @@ -412,15 +414,14 @@

          mtr

          positive or negative, depending on the definition of alpha.

          Deprecated examples

          -# MTR for a single vertical profile:
-mtr(example_vp)
-# MTRs for a time series of vertical profiles:
-data(example_vpts)
-# print migration traffic rates:
-mtr(example_vpts)
-# to plot migration traffic rate data, use integrate_profile:
-plot(integrate_profile(example_vpts), quantity = "mtr")
-
          +# MTR for a single vertical profile: +mtr(example_vp) +# MTRs for a time series of vertical profiles: +data(example_vpts) +# print migration traffic rates: +mtr(example_vpts) +# to plot migration traffic rate data, use integrate_profile: +plot(integrate_profile(example_vpts), quantity = "mtr")

          cmt

          @@ -439,12 +440,11 @@

          cmt

          band.

          Deprecated examples

          -# get example time series of vertical profiles:
-data(example_vpts)
+# get example time series of vertical profiles:
+data(example_vpts)
 
-# print cumulative migration traffic to console:
-cmt(example_vpts)
-
          +# print cumulative migration traffic to console: +cmt(example_vpts)

          night

          @@ -539,46 +539,9 @@

          SCAN

        @@ -589,7 +552,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/bioRad-package.html b/docs/dev/reference/bioRad-package.html index 36a081537..138b4f390 100644 --- a/docs/dev/reference/bioRad-package.html +++ b/docs/dev/reference/bioRad-package.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -54,7 +58,6 @@ insects from weather radar data. See &lt;doi:10.1111/ecog.04028&gt; for a software paper describing package and methodologies." /> - @@ -72,7 +75,7 @@ - +
        @@ -125,7 +128,7 @@
        • - + @@ -187,28 +190,9 @@

          See a

        @@ -219,7 +203,7 @@

        Author

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/c.vp.html b/docs/dev/reference/c.vp.html index 1bf73dd5c..be6963441 100644 --- a/docs/dev/reference/c.vp.html +++ b/docs/dev/reference/c.vp.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -173,12 +176,9 @@

          Value

        @@ -189,7 +189,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/calculate_param.html b/docs/dev/reference/calculate_param.html index cd23a7f1f..2dcafea3f 100644 --- a/docs/dev/reference/calculate_param.html +++ b/docs/dev/reference/calculate_param.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -54,7 +58,6 @@ linear reflectivity eta, depolarization ratio (Kilambi et al. 2018), or for applying clutter corrections (CCORH) to uncorrected reflectivity moments (TH), as in TH+CCORH" /> - @@ -72,7 +75,7 @@ - +
        @@ -125,7 +128,7 @@
        • - + @@ -227,15 +230,9 @@

          Examp #> dims: 480 bins x 360 rays

        @@ -246,7 +243,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/calculate_vp.html b/docs/dev/reference/calculate_vp.html index 1ae0eb1a5..307238ec2 100644 --- a/docs/dev/reference/calculate_vp.html +++ b/docs/dev/reference/calculate_vp.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -405,113 +408,21 @@

          Examp # copy to a home directory with read/write permissions: file.copy(pvolfile, "~/volume.h5")

        #> [1] TRUE
        # calculate the profile: -# \dontrun{ +if (FALSE) { profile <- calculate_vp("~/volume.h5") # print some summary info: -profile
        #> Vertical profile (class vp) -#> -#> radar: seang -#> source: WMO:02606,RAD:SE50,PLC:Angelholm,NOD:seang,ORG:82,CTY:643,CMT:Swedish radar -#> nominal time: 2015-10-18 18:00:00 -#> generated by: vol2bird 0.5.0
        # convert profile to a data.frame: -as.data.frame(profile)
        #> radar datetime ff dbz dens u v -#> 1 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 2 seang 2015-10-18 18:00:00 NaN 2.8776991 61.27740 NaN NaN -#> 3 seang 2015-10-18 18:00:00 14.88610 5.5255389 112.74165 -6.467583 -13.407694 -#> 4 seang 2015-10-18 18:00:00 14.64004 4.6949205 93.11562 -6.711918 -13.010798 -#> 5 seang 2015-10-18 18:00:00 13.30489 0.4530046 35.06153 -6.556170 -11.577423 -#> 6 seang 2015-10-18 18:00:00 10.76581 -1.9438103 20.19061 -5.069613 -9.497456 -#> 7 seang 2015-10-18 18:00:00 10.33567 -1.8632607 20.56858 -5.671824 -8.640401 -#> 8 seang 2015-10-18 18:00:00 12.07231 -2.2290711 18.90703 -7.580208 -9.395803 -#> 9 seang 2015-10-18 18:00:00 10.28255 -2.5026581 17.75271 -3.064733 -9.815207 -#> 10 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 11 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 12 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 13 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 14 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 15 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 16 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 17 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 18 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 19 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> 20 seang 2015-10-18 18:00:00 NA NA NA NA NA -#> gap w n_dbz dd n DBZH height n_dbz_all eta -#> 1 1 NA 0 NA 0 NA 0 0 NA -#> 2 1 NaN 817 NaN 536 4.873434 200 10602 674.0515 -#> 3 0 6.552267 4231 205.7517 2116 8.229273 400 17421 1240.1581 -#> 4 0 -17.817648 4085 207.2880 1866 4.437433 600 8098 1024.2719 -#> 5 0 -12.915339 3897 209.5224 1155 1.342218 800 7801 385.6769 -#> 6 0 30.602781 4369 208.0927 744 -0.492405 1000 7829 222.0967 -#> 7 0 24.725313 2276 213.2821 450 -1.101062 1200 3206 226.2544 -#> 8 0 57.809780 1694 218.8954 198 -1.102251 1400 2851 207.9773 -#> 9 0 36.869717 2045 197.3406 158 10.828478 1600 3213 195.2798 -#> 10 1 NA 0 NA 0 NA 1800 0 NA -#> 11 1 NA 0 NA 0 NA 2000 0 NA -#> 12 1 NA 0 NA 0 NA 2200 0 NA -#> 13 1 NA 0 NA 0 NA 2400 0 NA -#> 14 1 NA 0 NA 0 NA 2600 0 NA -#> 15 1 NA 0 NA 0 NA 2800 0 NA -#> 16 1 NA 0 NA 0 NA 3000 0 NA -#> 17 1 NA 0 NA 0 NA 3200 0 NA -#> 18 1 NA 0 NA 0 NA 3400 0 NA -#> 19 1 NA 0 NA 0 NA 3600 0 NA -#> 20 1 NA 0 NA 0 NA 3800 0 NA -#> sd_vvp n_all lat lon height_antenna day sunrise -#> 1 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 2 3.271695 4351 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 3 3.220699 5304 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 4 3.316308 3144 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 5 3.897997 2043 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 6 4.067675 1380 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 7 4.837257 747 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 8 4.795825 483 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 9 4.506003 315 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 10 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 11 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 12 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 13 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 14 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 15 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 16 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 17 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 18 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 19 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> 20 NA 0 56.3675 12.8517 209 FALSE 2015-10-18 05:50:07 -#> sunset -#> 1 2015-10-18 15:56:28 -#> 2 2015-10-18 15:56:28 -#> 3 2015-10-18 15:56:28 -#> 4 2015-10-18 15:56:28 -#> 5 2015-10-18 15:56:28 -#> 6 2015-10-18 15:56:28 -#> 7 2015-10-18 15:56:28 -#> 8 2015-10-18 15:56:28 -#> 9 2015-10-18 15:56:28 -#> 10 2015-10-18 15:56:28 -#> 11 2015-10-18 15:56:28 -#> 12 2015-10-18 15:56:28 -#> 13 2015-10-18 15:56:28 -#> 14 2015-10-18 15:56:28 -#> 15 2015-10-18 15:56:28 -#> 16 2015-10-18 15:56:28 -#> 17 2015-10-18 15:56:28 -#> 18 2015-10-18 15:56:28 -#> 19 2015-10-18 15:56:28 -#> 20 2015-10-18 15:56:28
        # } +profile +# convert profile to a data.frame: +as.data.frame(profile) +} # clean up: file.remove("~/volume.h5")
        #> [1] TRUE
        @@ -522,7 +433,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/check_date_format.html b/docs/dev/reference/check_date_format.html index 8903ecaff..5d548a672 100644 --- a/docs/dev/reference/check_date_format.html +++ b/docs/dev/reference/check_date_format.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -179,12 +182,9 @@

          Value

        @@ -195,7 +195,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/check_docker.html b/docs/dev/reference/check_docker.html index 7477fd434..00179300d 100644 --- a/docs/dev/reference/check_docker.html +++ b/docs/dev/reference/check_docker.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -175,19 +178,15 @@

          Value

          2 if Docker daemon not running, 3 if Docker daemon not found.

          Examples

          - 
          # \dontrun{
+    
          if (FALSE) {
 # check if Docker is running and vol2bird image is available:
-check_docker()
          #> Running docker image with vol2bird version 0.5.0  (MistNet available) 
          #> [1] 0
          # }
-
          
+check_docker()
+}
        @@ -198,7 +197,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/check_night.html b/docs/dev/reference/check_night.html index adbf242bf..e7781f7ae 100644 --- a/docs/dev/reference/check_night.html +++ b/docs/dev/reference/check_night.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -54,7 +58,6 @@ (pvol, vp, vpts) this information is extracted from the bioRad object directly." /> - @@ -72,7 +75,7 @@ - +
        @@ -125,7 +128,7 @@
        • - + @@ -393,14 +396,9 @@

          Examp #> [1933] FALSE FALSE

        @@ -411,7 +409,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/check_radar_codes.html b/docs/dev/reference/check_radar_codes.html index 30b3f87a7..3d0bfcb5e 100644 --- a/docs/dev/reference/check_radar_codes.html +++ b/docs/dev/reference/check_radar_codes.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -174,12 +177,9 @@

          Value

        @@ -190,7 +190,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/composite_ppi.html b/docs/dev/reference/composite_ppi.html index e34df3a46..ac1b1e259 100644 --- a/docs/dev/reference/composite_ppi.html +++ b/docs/dev/reference/composite_ppi.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,7 +57,6 @@ ppi. Can be used to make a composite of ppi's from multiple radars." /> - @@ -71,7 +74,7 @@ - +
        @@ -124,7 +127,7 @@
        • - + @@ -243,7 +246,7 @@

          Details

          Either multiple ppi's of different scan elevation of the same radar may be combined, or ppi's of different radars can be composited.

          Argument method determines how values of different ppi's at the same -geographic location are combined.

          +geographic location are combined.

          "mean"

          Compute the average value

          "max"

          Compute the maximum value. If ppi's are of the same radar and the same polar volume, this computes a max product, showing the maximum @@ -273,22 +276,18 @@

          Examp # across the available scans at each geographic location my_composite <- composite_ppi(my_ppis, method="max") -# \dontrun{ +if (FALSE) { # download basemap -bm <- download_basemap(my_composite)

        #> Downloading zoom = 9 ...
        #> Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL.
        +bm <- download_basemap(my_composite) + # plot the calculated max product on the basemap -map(my_composite, bm)
        # } -
        +map(my_composite, bm) +} @@ -299,7 +298,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/dbz_to_eta.html b/docs/dev/reference/dbz_to_eta.html index d41b6d940..3652ca217 100644 --- a/docs/dev/reference/dbz_to_eta.html +++ b/docs/dev/reference/dbz_to_eta.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -189,13 +192,9 @@

          Examp dbz_to_eta(7, 5) / 11 # C-band

        #> [1] 192.949
        dbz_to_eta(7, 10) / 11 # S-band
        #> [1] 12.05931
        @@ -206,7 +205,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/download_basemap.html b/docs/dev/reference/download_basemap.html index b162f2175..79c8313bf 100644 --- a/docs/dev/reference/download_basemap.html +++ b/docs/dev/reference/download_basemap.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -212,7 +215,7 @@

          Details enable billing and provide an API key to ggmap. See the ggmap README for details.

          To use maptype, install the development version of ggmap (>3.0.0) with -devtools::install_github("dkahle/ggmap").

          +devtools::install_github("dkahle/ggmap").

          Examples

          # load an example scan:
@@ -226,28 +229,29 @@ 
          Examp
 #>            dims:  480 bins x 360 rays
          
 # make ppi for the scan
 ppi <- project_as_ppi(example_scan)
-# \dontrun{
+if (FALSE) {
 # grab a basemap that matches the extent of the ppi:
-basemap <- download_basemap(ppi)
          #> Downloading zoom = 9 ...
          #> Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL.
          
+basemap <- download_basemap(ppi)
+
 # map the reflectivity quantity of the ppi onto the basemap:
-map(ppi, map = basemap, param = "DBZH")
          
+map(ppi, map = basemap, param = "DBZH")
+
 # increase the transparancy of the basemap:
-basemap <- download_basemap(ppi, alpha = 0.3)
          #> Downloading zoom = 9 ...
          #> Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL.
          map(ppi, map = basemap, param = "DBZH")
          
+basemap <- download_basemap(ppi, alpha = 0.3)
+map(ppi, map = basemap, param = "DBZH")
+
 # download a different type of basemap, e.g. a gray-scale image:
 # see get_map() in ggmap library for full documentation of options
-basemap <- download_basemap(ppi, maptype = "toner-lite")
          #> Downloading zoom = 9 ...
          #> Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL.
          
+basemap <- download_basemap(ppi, maptype = "toner-lite")
+
 # map the radial velocities onto the line image:
-map(ppi, map = basemap, param = "VRADH")
          # }
-
          +map(ppi, map = basemap, param = "VRADH") +}
        @@ -258,7 +262,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/download_vpfiles.html b/docs/dev/reference/download_vpfiles.html index c69043d32..01a4212e2 100644 --- a/docs/dev/reference/download_vpfiles.html +++ b/docs/dev/reference/download_vpfiles.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,7 +57,6 @@ ENRAM data repository, where these are stored as monthly zips per radar." /> - @@ -71,7 +74,7 @@ - +
        @@ -124,7 +127,7 @@
        • - + @@ -202,7 +205,7 @@

          Examp 
          # Download data from radars "bejab" and "bewid", even if previously
 # downloaded (overwrite = TRUE). Will successfully download 2016-10 files,
 # but show 404 error for 2016-11 files (as these are not available).
-# \dontrun{
+if (FALSE) {
 dir.create("~/bioRad_tmp_files")
 download_vpfiles(
   date_min = "2016-10-01",
@@ -210,17 +213,15 @@ 
          Examp
   radar = c("bejab", "bewid"),
   directory = "~/bioRad_tmp_files",
   overwrite = TRUE
-)
          #> Downloading data from https://lw-enram.s3-eu-west-1.amazonaws.com
          #> bejab201610.zip: successfully downloaded
          #> bewid201610.zip: successfully downloaded
          #> bejab201611.zip: http error 404
          #> bewid201611.zip: http error 404
          # clean up:
+)
+# clean up:
 unlink("~/bioRad_tmp_files", recursive = T)
-# }
          +}

        @@ -231,7 +232,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/eta_to_dbz.html b/docs/dev/reference/eta_to_dbz.html index ce20895eb..256d8f5a8 100644 --- a/docs/dev/reference/eta_to_dbz.html +++ b/docs/dev/reference/eta_to_dbz.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -190,13 +193,9 @@

          Examp eta_to_dbz(1000 * 11, 5) # C-band

        #> [1] 14.14557
        eta_to_dbz(1000 * 11, 10) # S-band
        #> [1] 26.18677
        @@ -207,7 +206,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/example_scan.html b/docs/dev/reference/example_scan.html index 8ce5eeb23..8008454e0 100644 --- a/docs/dev/reference/example_scan.html +++ b/docs/dev/reference/example_scan.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -175,17 +178,14 @@

          Examp pvolfile <- system.file("extdata", "volume.h5", package = "bioRad") pvol <- read_pvolfile(pvolfile) example_scan <- pvol$scans[[1]] -# \dontrun{ +if (FALSE) { # save(example_scan, file = "data/example_scan.rda") -# }

        +} @@ -196,7 +196,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/example_vp.html b/docs/dev/reference/example_vp.html index 0a17aad5f..f17a12954 100644 --- a/docs/dev/reference/example_vp.html +++ b/docs/dev/reference/example_vp.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,7 +57,6 @@ example_vp. Can be created with calculate_vp or read from file with read_vpfiles." /> - @@ -71,7 +74,7 @@ - +
        @@ -124,7 +127,7 @@
        • - + @@ -177,17 +180,14 @@

          Examp # example_vp was created with: vpfile <- system.file("extdata", "profile.h5", package = "bioRad") example_vp <- read_vpfiles(vpfile) -# \dontrun{ +if (FALSE) { # save(example_vp, file = "data/example_vp.rda") -# }

        +} @@ -198,7 +198,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/example_vpts.html b/docs/dev/reference/example_vpts.html index f85d7a123..93ab0e063 100644 --- a/docs/dev/reference/example_vpts.html +++ b/docs/dev/reference/example_vpts.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -173,24 +176,22 @@

          Examp #> time range (UTC): 2016-09-01 00:02:00 - 2016-09-10 11:56:00 #> time step (s): min: 180 max: 16320

        # example_vpts was created with: -# \dontrun{ +if (FALSE) { vptsfile <- system.file("extdata", "vpts.txt.zip", package = "bioRad") unzip(vptsfile, exdir = (dirname(vptsfile)), junkpaths = T) vptsfile <- substr(vptsfile, 1, nchar(vptsfile) - 4) example_vpts <- read_vpts(vptsfile, radar = "KBGM", wavelength = "S") -rcs(example_vpts) <- 11
        #> Warning: Threshold for sd_vvp not set, defaulting to 2 m/s
        sd_vvp_threshold(example_vpts) <- 2 +rcs(example_vpts) <- 11 +sd_vvp_threshold(example_vpts) <- 2 example_vpts$attributes$where$lat <- 42.2 example_vpts$attributes$where$lon <- -75.98 # save(example_vpts, file = "data/example_vpts.rda", compress = "xz") -# }
        +} @@ -201,7 +202,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/filter_vpts.html b/docs/dev/reference/filter_vpts.html index 476ef012b..3a6e46a9c 100644 --- a/docs/dev/reference/filter_vpts.html +++ b/docs/dev/reference/filter_vpts.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -166,11 +169,11 @@

          Arg min -

          Minimum datetime to be included. POSIXct value or charater string convertable to POSIXct.

          +

          Minimum datetime to be included. POSIXct value or character string convertable to POSIXct.

          max -

          Maximum datetime to be included. POSIXct value or charater string convertable to POSIXct.

          +

          Maximum datetime to be included. POSIXct value or character string convertable to POSIXct.

          nearest @@ -219,14 +222,9 @@

          Examp #> time step (s): min: 540 max: 600

        @@ -237,7 +235,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/gaussian_beam_profile.html b/docs/dev/reference/gaussian_beam_profile.html index 8950dc835..df53c2971 100644 --- a/docs/dev/reference/gaussian_beam_profile.html +++ b/docs/dev/reference/gaussian_beam_profile.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -222,13 +225,9 @@

          Details

        @@ -239,7 +238,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/get_elevation_angles.html b/docs/dev/reference/get_elevation_angles.html index 3ea5069cc..99e154566 100644 --- a/docs/dev/reference/get_elevation_angles.html +++ b/docs/dev/reference/get_elevation_angles.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -203,14 +206,9 @@

          Examp get_elevation_angles(scan)

        #> [1] 0.5
        @@ -221,7 +219,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/get_odim_object_type.html b/docs/dev/reference/get_odim_object_type.html index 327e15701..443d80dad 100644 --- a/docs/dev/reference/get_odim_object_type.html +++ b/docs/dev/reference/get_odim_object_type.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -179,13 +182,9 @@

          Examp get_odim_object_type(pvolfile) # > "PVOL"

        #> [1] "PVOL"
        @@ -196,7 +195,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/get_param.html b/docs/dev/reference/get_param.html index 77898a9e9..9c967c4e9 100644 --- a/docs/dev/reference/get_param.html +++ b/docs/dev/reference/get_param.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -189,13 +192,9 @@

          Examp #> dims: 480 bins x 360 rays

        @@ -206,7 +205,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/get_quantity.html b/docs/dev/reference/get_quantity.html index dc0a04b1a..aa5875e08 100644 --- a/docs/dev/reference/get_quantity.html +++ b/docs/dev/reference/get_quantity.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -227,14 +230,9 @@

          Examp #> 0.0000000

        @@ -245,7 +243,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/get_scan.html b/docs/dev/reference/get_scan.html index b7c030603..8048377f7 100644 --- a/docs/dev/reference/get_scan.html +++ b/docs/dev/reference/get_scan.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -196,14 +199,9 @@

          Examp #> dims: 480 bins x 360 rays

        @@ -214,7 +212,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index e51790a4d..a5c90af01 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,7 +54,6 @@ - @@ -68,7 +71,7 @@ - +
        @@ -121,7 +124,7 @@
        @@ -680,7 +727,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/integrate_profile.html b/docs/dev/reference/integrate_profile.html index 8dfe3c2fa..15404ce40 100644 --- a/docs/dev/reference/integrate_profile.html +++ b/docs/dev/reference/integrate_profile.html @@ -18,23 +18,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -43,7 +47,7 @@ - + @@ -55,7 +59,6 @@ traffic rate, and a vertical averaging of ground speed and direction weighted by density." /> - @@ -73,7 +76,7 @@ - +
        @@ -126,7 +129,7 @@
        • - + @@ -228,7 +231,7 @@

          Details

          Available quantities

          The function generates a specially classed data frame with the following -quantities:

          +quantities:

          datetime

          POSIXct date of each profile in UTC

          vid

          Vertically Integrated Density in individuals/km^2. vid is a surface density, whereas dens in vp @@ -360,15 +363,9 @@

          Examp plot(integrate_profile(example_vpts), quantity = "mt")

        @@ -379,7 +376,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/integrate_to_ppi.html b/docs/dev/reference/integrate_to_ppi.html index cbbde8c0b..52aecfcd4 100644 --- a/docs/dev/reference/integrate_to_ppi.html +++ b/docs/dev/reference/integrate_to_ppi.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -58,7 +62,6 @@ (overshooting) at larger distances from the radar. The methodology is described in detail in Kranstauber et al. (2020)." /> - @@ -76,7 +79,7 @@ - +
        @@ -129,7 +132,7 @@
        • - + @@ -360,15 +363,18 @@

          Examp # plot the vertically integrated reflectivity (VIR) using a 0-2000 cm^2/km^2 color scale: plot(my_ppi, zlim = c(0, 2000))

        -# \dontrun{ +if (FALSE) { # calculate the range-corrected ppi on finer 2000m x 2000m pixel raster: my_ppi <- integrate_to_ppi(example_pvol, example_vp, res = 2000) # plot the vertically integrated density (VID) using a 0-200 birds/km^2 color scale: -plot(my_ppi, param = "VID", zlim = c(0, 200))
        +plot(my_ppi, param = "VID", zlim = c(0, 200)) + # to overlay ppi objects on a background map, first # download a basemap, and map the ppi: -bm <- download_basemap(my_ppi)
        #> Downloading zoom = 7 ...
        #> Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL.
        map(my_ppi, bm)
        +bm <- download_basemap(my_ppi) +map(my_ppi, bm) + # the ppi can also be projected on a user-defined raster, as follows: # first define the raster: template_raster <- raster::raster(raster::extent(12, 13, 56, 57), crs = sp::CRS("+proj=longlat")) @@ -377,35 +383,21 @@

        Examp my_ppi <- integrate_to_ppi(example_pvol, example_vp, raster = template_raster) # extract the raster data from the ppi object: -raster::brick(my_ppi$data)

        #> class : RasterBrick -#> dimensions : 10, 10, 100, 6 (nrow, ncol, ncell, nlayers) -#> resolution : 0.1, 0.1 (x, y) -#> extent : 12, 13, 56, 57 (xmin, xmax, ymin, ymax) -#> crs : +proj=longlat +ellps=WGS84 -#> source : memory -#> names : VIR, VID, R, overlap, eta_sum, eta_sum_expected -#> min values : 0.00000000, 0.00000000, 0.00000000, 0.06252018, 0.00000000, 406.96716161 -#> max values : 6.052578e+04, 5.480034e+03, 6.151489e+01, 9.070487e-01, 6.468812e+04, 3.196694e+03 -#>
        +raster::brick(my_ppi$data) + # calculate the range-corrected ppi on an even finer 500m x 500m pixel raster, # cropping the area up to 50000 meter from the radar. my_ppi <- integrate_to_ppi(example_pvol, example_vp, res = 500, xlim = c(-50000, 50000), ylim = c(-50000, 50000) ) -plot(my_ppi, param = "VID", zlim = c(0, 200))
        # } -
        +plot(my_ppi, param = "VID", zlim = c(0, 200)) +} @@ -416,7 +408,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/is.nan.data.frame.html b/docs/dev/reference/is.nan.data.frame.html index 4b69232ee..7a480a9d8 100644 --- a/docs/dev/reference/is.nan.data.frame.html +++ b/docs/dev/reference/is.nan.data.frame.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,7 +57,6 @@ is.nan() function, which only works on vectors, by allowing data frames as input." /> - @@ -71,7 +74,7 @@ - +
        @@ -124,7 +127,7 @@
        • - + @@ -179,12 +182,9 @@

          Value

        @@ -195,7 +195,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/is.pvolfile.html b/docs/dev/reference/is.pvolfile.html index 45d2789db..548b8900e 100644 --- a/docs/dev/reference/is.pvolfile.html +++ b/docs/dev/reference/is.pvolfile.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -190,14 +193,9 @@

          Examp is.pvolfile(pvolfile) # > TRUE

        #> [1] TRUE
        @@ -208,7 +206,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/is.vpfile.html b/docs/dev/reference/is.vpfile.html index e18ee90ca..cf49d42e1 100644 --- a/docs/dev/reference/is.vpfile.html +++ b/docs/dev/reference/is.vpfile.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -181,13 +184,9 @@

          Examp is.vpfile(profile) # > TRUE

        #> [1] TRUE
        @@ -198,7 +197,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/map.html b/docs/dev/reference/map.html index 292e6443c..ff34dd42b 100644 --- a/docs/dev/reference/map.html +++ b/docs/dev/reference/map.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -259,7 +262,7 @@

          Value

          Details

          Available scan parameters for mapping can by printed to screen by -summary(x). Commonly available parameters are:

          +summary(x). Commonly available parameters are:

          "DBZH", "DBZ"

          (Logged) reflectivity factor [dBZ]

          "TH", "T"

          (Logged) uncorrected reflectivity factor [dBZ]

          "VRADH", "VRAD"

          Radial velocity [m/s]. Radial @@ -285,36 +288,38 @@

          Examp data(example_scan) # make ppi's for all scan parameters in the scan ppi <- project_as_ppi(example_scan) -# \dontrun{ +if (FALSE) { # grab a basemap that matches the extent of the ppi: # using a gray-scale basemap: -basemap <- download_basemap(ppi, maptype = "toner-lite")

        #> Downloading zoom = 9 ...
        #> Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL.
        +basemap <- download_basemap(ppi, maptype = "toner-lite") + # map the radial velocity scan parameter onto the basemap: -map(ppi, map = basemap, param = "VRADH")
        +map(ppi, map = basemap, param = "VRADH") + # extend the plotting range of velocities, from -50 to 50 m/s: -map(ppi, map = basemap, param = "VRADH", zlim = c(-50, 50))
        +map(ppi, map = basemap, param = "VRADH", zlim = c(-50, 50)) + # map the reflectivity on a terrain basemap: -basemap <- download_basemap(ppi, maptype = "terrain")
        #> Downloading zoom = 9 ...
        #> Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL.
        map(ppi, map = basemap, param = "DBZH")
        +basemap <- download_basemap(ppi, maptype = "terrain") +map(ppi, map = basemap, param = "DBZH") + # change the color palette, e.g. Viridis colors: -map(ppi, map = basemap, param = "DBZH", palette = viridis::viridis(100), zlim=c(-10,10))
        +map(ppi, map = basemap, param = "DBZH", palette = viridis::viridis(100), zlim=c(-10,10)) + # give the data more transparency: -map(ppi, map = basemap, param = "DBZH", alpha = 0.3)
        +map(ppi, map = basemap, param = "DBZH", alpha = 0.3) + # change the appearance of the symbol indicating the radar location: -map(ppi, map = basemap, radar_size = 5, radar_color = "blue")
        +map(ppi, map = basemap, radar_size = 5, radar_color = "blue") + # crop the map: -map(ppi, map = basemap, xlim = c(12.4, 13.2), ylim = c(56, 56.5))
        #> Warning: Removed 1 rows containing missing values (geom_rect).
        # } -
        +map(ppi, map = basemap, xlim = c(12.4, 13.2), ylim = c(56, 56.5)) +} @@ -325,7 +330,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/match_filenames.html b/docs/dev/reference/match_filenames.html index bb2f83e09..517296e06 100644 --- a/docs/dev/reference/match_filenames.html +++ b/docs/dev/reference/match_filenames.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -54,7 +58,6 @@ function basically wraps a grep to make it work on vectors by combining the vector of regex options as possible options." /> - @@ -72,7 +75,7 @@ - +
        @@ -125,7 +128,7 @@
        • - + @@ -184,12 +187,9 @@

          Value

        @@ -200,7 +200,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/nexrad_to_odim.html b/docs/dev/reference/nexrad_to_odim.html index ff2ff6f63..81ca2b875 100644 --- a/docs/dev/reference/nexrad_to_odim.html +++ b/docs/dev/reference/nexrad_to_odim.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -191,7 +194,7 @@

          Value

          TRUE on success

          Examples

          - 
          # \dontrun{
+    
          if (FALSE) {
 # download a NEXRAD file, save as KBGM_example
 download.file(paste("https://noaa-nexrad-level2.s3.amazonaws.com/",
   "2019/10/01/KBGM/KBGM20191001_000542_V06",
@@ -199,21 +202,19 @@ 
          Examp
 ), "~/KBGM_example")
 
 # convert to ODIM format
-nexrad_to_odim("~/KBGM_example", "~/KBGM_example.h5")
          #> [1] TRUE
          
+nexrad_to_odim("~/KBGM_example", "~/KBGM_example.h5")
+
 # verify that we have generated a polar volume in ODIM hdf5 format
-get_odim_object_type("~/KBGM_example.h5")
          #> [1] "PVOL"
          
+get_odim_object_type("~/KBGM_example.h5")
+
 # clean up
-file.remove("~/KBGM_example", "~/KBGM_example.h5")
          #> [1] TRUE TRUE
          # }
-
          
+file.remove("~/KBGM_example", "~/KBGM_example.h5")
+}
        @@ -224,7 +225,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/nyquist_velocity.html b/docs/dev/reference/nyquist_velocity.html index 858c184bf..0556042bb 100644 --- a/docs/dev/reference/nyquist_velocity.html +++ b/docs/dev/reference/nyquist_velocity.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,7 +57,6 @@ and wavelength. When specifying two PRFs, the extended Nyquist velocity is given for a radar using the dual-PRF technique." /> - @@ -71,7 +74,7 @@ - +
        @@ -124,7 +127,7 @@
        • - + @@ -190,13 +193,9 @@

          Examp nyquist_velocity(5.3, 2000, 1500)

        #> [1] 79.5
        @@ -207,7 +206,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/plot.ppi.html b/docs/dev/reference/plot.ppi.html index c6adca178..79d240afd 100644 --- a/docs/dev/reference/plot.ppi.html +++ b/docs/dev/reference/plot.ppi.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -209,7 +212,7 @@

          Arg

          Details

          Available scan paramaters for plotting can by printed to screen -by summary(x). Commonly available parameters are:

          +by summary(x). Commonly available parameters are:

          "DBZH", "DBZ"

          (Logged) reflectivity factor [dBZ]

          "TH", "T"

          (Logged) uncorrected reflectivity factor [dBZ]

          "VRADH", "VRAD"

          Radial velocity [m/s]. Radial @@ -248,13 +251,9 @@

          Examp #> will replace the existing scale.

        @@ -265,7 +264,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/plot.scan.html b/docs/dev/reference/plot.scan.html index b720aaac8..38af00de3 100644 --- a/docs/dev/reference/plot.scan.html +++ b/docs/dev/reference/plot.scan.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -204,7 +207,7 @@

          Arg

          Details

          Available scan parameters for plotting can by printed to screen -by summary(x). Commonly available parameters are:

          +by summary(x). Commonly available parameters are:

          "DBZH", "DBZ"

          (Logged) reflectivity factor [dBZ]

          "TH", "T"

          (Logged) uncorrected reflectivity factor [dBZ]

          "VRADH", "VRAD"

          Radial velocity [m/s]. Radial @@ -232,22 +235,18 @@

          Examp #> dims: 480 bins x 360 rays

        # make ppi for the scan # plot the reflectivity param: -plot(example_scan, param = "DBZH")
        # \dontrun{ +plot(example_scan, param = "DBZH")
        if (FALSE) { # change the range of reflectivities to plot, from -10 to 10 dBZ: -plot(example_scan, param = "DBZH", zlim = c(-10, 10))
        +plot(example_scan, param = "DBZH", zlim = c(-10, 10)) + # change the scale name and colour scheme, using viridis colors: -plot(example_scan, param = "DBZH", zlim = c(-10, 10)) + viridis::scale_fill_viridis(name = "dBZ")
        #> Scale for 'fill' is already present. Adding another scale for 'fill', which -#> will replace the existing scale.
        # } -
        +plot(example_scan, param = "DBZH", zlim = c(-10, 10)) + viridis::scale_fill_viridis(name = "dBZ") +} @@ -258,7 +257,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/plot.vp.html b/docs/dev/reference/plot.vp.html index 801a4045a..006c30cbe 100644 --- a/docs/dev/reference/plot.vp.html +++ b/docs/dev/reference/plot.vp.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -233,12 +236,9 @@

          Examp plot(example_vp, quantity = "DBZH")

        @@ -249,7 +249,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/plot.vpi.html b/docs/dev/reference/plot.vpi.html index 15724c803..4f5e36c3e 100644 --- a/docs/dev/reference/plot.vpi.html +++ b/docs/dev/reference/plot.vpi.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -242,7 +245,7 @@

          Arg

          Details

          The integrated profiles can be visualized in various related quantities, as specified by -argument quantity:

          +argument quantity:

          "vid"

          Vertically Integrated Density, i.e. the aerial surface density of individuals. This quantity is dependent on the assumed radar cross section per individual (RCS)

          @@ -272,13 +275,9 @@

          Examp plot(vpi, quantity = "vid", night_shade = FALSE)

        @@ -289,7 +288,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/plot.vpts.html b/docs/dev/reference/plot.vpts.html index 003b3cfbc..5d44758a1 100644 --- a/docs/dev/reference/plot.vpts.html +++ b/docs/dev/reference/plot.vpts.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -260,7 +263,7 @@

          Arg

          Details

          Profile can be visualized in three related quantities, as specified -by argument quantity:

          +by argument quantity:

          "dens"

          the aerial density of individuals. This quantity is dependent on the assumed radar cross section (RCS) in the x$attributes$how$rcs_bird attribute

          @@ -287,13 +290,9 @@

          Examp plot(ts[1:500], ylim = c(0, 3000), quantity = "DBZH")

        #> Warning: Irregular time-series: missing profiles will not be visible.Use 'regularize_vpts' to make time series regular.
        @@ -304,7 +303,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/print.param.html b/docs/dev/reference/print.param.html index ae859a1ce..0ab8d6910 100644 --- a/docs/dev/reference/print.param.html +++ b/docs/dev/reference/print.param.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -170,11 +173,9 @@

          Arg

        @@ -185,7 +186,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/print.ppi.html b/docs/dev/reference/print.ppi.html index 2b6996ba8..1755db9aa 100644 --- a/docs/dev/reference/print.ppi.html +++ b/docs/dev/reference/print.ppi.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -170,11 +173,9 @@

          Arg

        @@ -185,7 +186,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/print.pvol.html b/docs/dev/reference/print.pvol.html index 0bf149e0d..a0c813bb5 100644 --- a/docs/dev/reference/print.pvol.html +++ b/docs/dev/reference/print.pvol.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -170,11 +173,9 @@

          Arg

        @@ -185,7 +186,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/print.scan.html b/docs/dev/reference/print.scan.html index 464ef3f68..5b2938212 100644 --- a/docs/dev/reference/print.scan.html +++ b/docs/dev/reference/print.scan.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -170,11 +173,9 @@

          Arg

        @@ -185,7 +186,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/print.vp.html b/docs/dev/reference/print.vp.html index ab29d2fba..632c4a9f2 100644 --- a/docs/dev/reference/print.vp.html +++ b/docs/dev/reference/print.vp.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -171,11 +174,9 @@

          Arg

        @@ -186,7 +187,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/print.vpts.html b/docs/dev/reference/print.vpts.html index e448c6020..7814f8e04 100644 --- a/docs/dev/reference/print.vpts.html +++ b/docs/dev/reference/print.vpts.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -171,11 +174,9 @@

          Arg

        @@ -186,7 +187,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/proj_to_wgs.html b/docs/dev/reference/proj_to_wgs.html index 51dea7647..4bd2dc733 100644 --- a/docs/dev/reference/proj_to_wgs.html +++ b/docs/dev/reference/proj_to_wgs.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -180,12 +183,9 @@

          Value

        @@ -196,7 +196,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/project_as_ppi.html b/docs/dev/reference/project_as_ppi.html index 2efaf8fa3..861b4b5eb 100644 --- a/docs/dev/reference/project_as_ppi.html +++ b/docs/dev/reference/project_as_ppi.html @@ -18,23 +18,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -43,7 +47,7 @@ - + @@ -53,7 +57,6 @@ position indicator (ppi) — project_as_ppi" /> - @@ -71,7 +74,7 @@ - +
        @@ -124,7 +127,7 @@
        • - + @@ -298,15 +301,9 @@

          Examp plot(ppi)

        @@ -317,7 +314,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/rcs-set.html b/docs/dev/reference/rcs-set.html index ba1242c67..0ebee1f67 100644 --- a/docs/dev/reference/rcs-set.html +++ b/docs/dev/reference/rcs-set.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -206,13 +209,9 @@

          Examp rcs(example_vpts)

        #> [1] 11
        @@ -223,7 +222,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/rcs.html b/docs/dev/reference/rcs.html index df6e9bd52..c0ec426c7 100644 --- a/docs/dev/reference/rcs.html +++ b/docs/dev/reference/rcs.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -212,15 +215,9 @@

          Examp rcs(example_vpts) <- 11

        @@ -231,7 +228,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/read_cajun.html b/docs/dev/reference/read_cajun.html index 297b7fcfd..18dffe282 100644 --- a/docs/dev/reference/read_cajun.html +++ b/docs/dev/reference/read_cajun.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -183,12 +186,9 @@

          Value

        @@ -199,7 +199,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/read_pvolfile.html b/docs/dev/reference/read_pvolfile.html index 849861aa0..9b84487dc 100644 --- a/docs/dev/reference/read_pvolfile.html +++ b/docs/dev/reference/read_pvolfile.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -233,7 +236,7 @@

          Details

          Scan parameters are named according to the OPERA data information model (ODIM), see Table 16 in the ODIM specification. -Commonly available parameters are:

          +Commonly available parameters are:

          "DBZH", "DBZ"

          (Logged) reflectivity factor [dBZ]

          "TH", "T"

          (Logged) uncorrected reflectivity factor [dBZ]

          "VRADH", "VRAD"

          Radial velocity [m/s]. Radial @@ -253,7 +256,7 @@

          Examp pvolfile <- system.file("extdata", "volume.h5", package = "bioRad") # print the local path of the volume file: -pvolfile

        #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmpZAoJBf/temp_libpath117f5846b493/bioRad/extdata/volume.h5"
        +pvolfile
        #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmphJXQg6/temp_libpath1693e32793fa4/bioRad/extdata/volume.h5"
        # load the file: example_pvol <- read_pvolfile(pvolfile) @@ -298,14 +301,9 @@

        Examp #> dims: 480 bins x 360 rays

        @@ -316,7 +314,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/read_vp.html b/docs/dev/reference/read_vp.html index c15e36c9a..bdef03dd8 100644 --- a/docs/dev/reference/read_vp.html +++ b/docs/dev/reference/read_vp.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -173,12 +176,9 @@

          Value

        @@ -189,7 +189,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/read_vpfiles.html b/docs/dev/reference/read_vpfiles.html index 70dca3588..19d3ec29f 100644 --- a/docs/dev/reference/read_vpfiles.html +++ b/docs/dev/reference/read_vpfiles.html @@ -18,23 +18,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -43,7 +47,7 @@ - + @@ -54,7 +58,6 @@ - @@ -72,7 +75,7 @@ - +
        @@ -125,7 +128,7 @@
        • - + @@ -181,7 +184,7 @@

          Examp vpfile <- system.file("extdata", "profile.h5", package = "bioRad") # print the local path of the profile file: -vpfile

        #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmpZAoJBf/temp_libpath117f5846b493/bioRad/extdata/profile.h5"
        +vpfile
        #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmphJXQg6/temp_libpath1693e32793fa4/bioRad/extdata/profile.h5"
        # load the file: read_vpfiles(vpfile)
        #> Vertical profile (class vp) #> @@ -189,21 +192,15 @@

        Examp #> source: WMO:02606,RAD:SE50,PLC:Ängelholm,NOD:seang,ORG:82,CTY:643,CMT:Swedish radar #> nominal time: 2015-10-18 18:00:00 #> generated by: vol2bird 0.3.17

        -# load multiple files at once: -# \dontrun{ -# read_vpfiles(c("my/path/profile1.h5", "my/path/profile2.h5", ...)) -# } - -
        +# load multiple files at once: +if (FALSE) { +# read_vpfiles(c("my/path/profile1.h5", "my/path/profile2.h5", ...)) +} @@ -214,7 +211,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/read_vpts.html b/docs/dev/reference/read_vpts.html index fff012238..67a7e4275 100644 --- a/docs/dev/reference/read_vpts.html +++ b/docs/dev/reference/read_vpts.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -207,13 +210,9 @@

          Examp #> time step (s): min: 540 max: 600

        @@ -224,7 +223,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/regularize_vpts.html b/docs/dev/reference/regularize_vpts.html index e71324944..9a0bde9a8 100644 --- a/docs/dev/reference/regularize_vpts.html +++ b/docs/dev/reference/regularize_vpts.html @@ -18,23 +18,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -43,7 +47,7 @@ - + @@ -53,7 +57,6 @@ regular time grid — regularize_vpts" /> - @@ -71,7 +74,7 @@ - +
        @@ -124,7 +127,7 @@
        • - + @@ -231,14 +234,9 @@

          Examp tsRegular <- regularize_vpts(ts, interval = 300)

        @@ -249,7 +247,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/scan_to_raster.html b/docs/dev/reference/scan_to_raster.html index accfcb39e..07029ffc2 100644 --- a/docs/dev/reference/scan_to_raster.html +++ b/docs/dev/reference/scan_to_raster.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -283,14 +286,9 @@

          Examp #>

        @@ -301,7 +299,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/scan_to_spatial.html b/docs/dev/reference/scan_to_spatial.html index 631c09ddf..a26b7901f 100644 --- a/docs/dev/reference/scan_to_spatial.html +++ b/docs/dev/reference/scan_to_spatial.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -209,14 +212,9 @@

          Examp #> max values : 359, 240000, 239848.089357779, 5695.96400438249, 23.6928958296776, 55, 7.90588282048702, 0.99959997474798, 178.588244199753

        @@ -227,7 +225,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/sd_vvp_threshold-set.html b/docs/dev/reference/sd_vvp_threshold-set.html index 08203e68a..edcc67731 100644 --- a/docs/dev/reference/sd_vvp_threshold-set.html +++ b/docs/dev/reference/sd_vvp_threshold-set.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -54,7 +58,6 @@ individuals. This method updates the migration densities in x$data$dens" /> - @@ -72,7 +75,7 @@ - +
        @@ -125,7 +128,7 @@
        #> [1] 2
        @@ -224,7 +223,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/sd_vvp_threshold.html b/docs/dev/reference/sd_vvp_threshold.html index 998bbee65..2a3b77b37 100644 --- a/docs/dev/reference/sd_vvp_threshold.html +++ b/docs/dev/reference/sd_vvp_threshold.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -212,15 +215,9 @@

          Examp sd_vvp_threshold(example_vp) <- 2

        @@ -231,7 +228,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/select_vpfiles.html b/docs/dev/reference/select_vpfiles.html index 5d145b948..f3fb34ae8 100644 --- a/docs/dev/reference/select_vpfiles.html +++ b/docs/dev/reference/select_vpfiles.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -54,7 +58,6 @@ file name (not directory structure), which should be of format radar_vp_yyyymmdd*.*, such as bewid_vp_20171123T1900Z_0x5.h5." /> - @@ -72,7 +75,7 @@ - +
        @@ -125,7 +128,7 @@
        • - + @@ -205,13 +208,9 @@

          Examp )

        #> character(0)
        @@ -222,7 +221,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/sub-.ppi.html b/docs/dev/reference/sub-.ppi.html index 04b56ea1b..54c70db27 100644 --- a/docs/dev/reference/sub-.ppi.html +++ b/docs/dev/reference/sub-.ppi.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -196,12 +199,9 @@

          Examp #>

        @@ -212,7 +212,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/sub-.vpts.html b/docs/dev/reference/sub-.vpts.html index 8ab972f13..9c469db04 100644 --- a/docs/dev/reference/sub-.vpts.html +++ b/docs/dev/reference/sub-.vpts.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -199,12 +202,9 @@

          Examp #> time step (s): min: 240 max: 420

        @@ -215,7 +215,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/summary.param.html b/docs/dev/reference/summary.param.html index 75a0c78df..c7d0660b4 100644 --- a/docs/dev/reference/summary.param.html +++ b/docs/dev/reference/summary.param.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -186,7 +189,7 @@

          Value

          Details

          An object of class scan is a simple matrix, with the following -specific attributes:

          +specific attributes:

          radar

          character string with the radar identifier

          datetime

          nominal time of the volume to which this scan belongs [UTC]

          @@ -199,7 +202,7 @@

          Details

          Scan parameters are named according to the OPERA data information model (ODIM), see Table 16 in the ODIM specification. -Commonly available parameters are:

          +Commonly available parameters are:

          "DBZH", "DBZ"

          (Logged) reflectivity factor [dBZ]

          "VRADH", "VRAD"

          Radial velocity [m/s]. Radial velocities towards the radar are negative, while radial velocities away @@ -229,14 +232,9 @@

          Examp #> dims: 480 bins x 360 rays

        @@ -247,7 +245,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/summary.ppi.html b/docs/dev/reference/summary.ppi.html index e4d627fea..cd6b00ea3 100644 --- a/docs/dev/reference/summary.ppi.html +++ b/docs/dev/reference/summary.ppi.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -192,10 +195,10 @@

          Details

          ppi objects are generated from elevation scans (scan objects) with project_as_ppi or from polar volumes with integrate_to_ppi, producing projections of the radar data onto the earth's surface.

          -

          An object of class ppi is a list containing:

          +

          An object of class ppi is a list containing:

          data

          an object of class SpatialGridDataFrame containing the georeferenced data. Commonly available parameters are: -

          +
          "DBZH", "DBZ"

          (Logged) reflectivity factor [dBZ]

          "TH", "T"

          (Logged) uncorrected reflectivity factor [dBZ]

          "VRADH", "VRAD"

          Radial velocity [m/s]. Radial @@ -207,7 +210,7 @@

          Details
          "PHIDP"

          Differential phase [degrees]

          "ZDR"

          (Logged) differential reflectivity [dB]

          geo

          geographic data, a list with: -

          +
          lat

          latitude of the radar [decimal degrees]

          lon

          longitude of the radar [decimal degrees]

          height

          height of the radar @@ -240,14 +243,9 @@

          Examp dim(example_ppi)

        #> [1] 5 200 200
        @@ -258,7 +256,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/summary.pvol.html b/docs/dev/reference/summary.pvol.html index 51ac42e8e..7d778228e 100644 --- a/docs/dev/reference/summary.pvol.html +++ b/docs/dev/reference/summary.pvol.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -183,14 +186,14 @@

          Value

          class pvol

          Details

          -

          An object of class pvol is a list containing:

          +

          An object of class pvol is a list containing:

          radar

          character string with the radar identifier

          datetime

          nominal time of the volume [UTC]

          scans

          a list with scan objects of class 'scan'

          attributes

          list with the volume's \what, \where and \how attributes

          geo

          geographic data, a list with: -

          +
          lat

          latitude of the radar [decimal degrees]

          lon

          longitude of the radar [decimal degrees]

          height

          height of the radar @@ -204,7 +207,7 @@

          Examp pvolfile <- system.file("extdata", "volume.h5", package = "bioRad") # print the local path of the volume file: -pvolfile

        #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmpZAoJBf/temp_libpath117f5846b493/bioRad/extdata/volume.h5"
        +pvolfile
        #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmphJXQg6/temp_libpath1693e32793fa4/bioRad/extdata/volume.h5"
        # load the file: example_pvol <- read_pvolfile(pvolfile) @@ -251,14 +254,9 @@

        Examp #> dims: 480 bins x 360 rays

        is.pvol("this is not a polar volume but a string") # > FALSE
        #> [1] FALSE
        @@ -269,7 +267,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/summary.scan.html b/docs/dev/reference/summary.scan.html index 05260748d..3418f0abf 100644 --- a/docs/dev/reference/summary.scan.html +++ b/docs/dev/reference/summary.scan.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -187,7 +190,7 @@

          Value

          For dim.scan: dimensions of the scan.

          Details

          -

          A object of class scan is a list containing:

          +

          A object of class scan is a list containing:

          radar

          character string with the radar identifier

          datetime

          nominal time of the volume to which this scan belongs [UTC]

          @@ -195,7 +198,7 @@

          Details
          attributes

          list with the scan's \what, \where and \how attributes

          geo

          geographic data, a list with: -

          +
          lat

          latitude of the radar [decimal degrees]

          lon

          longitude of the radar [decimal degrees]

          height

          height of the radar @@ -256,14 +259,9 @@

          Examp #> dims: 480 bins x 360 rays

        is.scan("this is not a polar scan but a string") # > FALSE
        #> [1] FALSE
        @@ -274,7 +272,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/summary.vp.html b/docs/dev/reference/summary.vp.html index 8e013c213..cfb6868ff 100644 --- a/docs/dev/reference/summary.vp.html +++ b/docs/dev/reference/summary.vp.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -193,11 +196,11 @@

          Details

          Data contained in this class object should be accessed with the get_quantity function. Information stored under attributes (see below) can be accessed directly.

          -

          A vp object is a list containing

          +

          A vp object is a list containing

          radar

          the radar identifier

          datetime

          the nominal time of the profile

          data

          the profile data, a list containing: -

          +
          height

          height above mean sea level [m]. Alt. bin from height to height+interval)

          u

          speed component west to east [m/s]

          v

          speed component north to south [m/s]

          @@ -249,14 +252,9 @@

          Examp dim(example_vp)

        #> [1] 25 16
        @@ -267,7 +265,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/summary.vpts.html b/docs/dev/reference/summary.vpts.html index b8bdc92f8..c80b1fed3 100644 --- a/docs/dev/reference/summary.vpts.html +++ b/docs/dev/reference/summary.vpts.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -204,7 +207,7 @@

          Details

          Data contained in this class object should be accessed with the get_quantity function. Information stored under attributes (see below) can be accessed directly.

          -

          An object of class vpts is a list containing

          +

          An object of class vpts is a list containing

          radar

          string containing the radar identifier

          datetime

          the N nominal times of the profiles (named dates in bioRad versions < 0.4.0)

          height

          the M heights of the layers in the profile

          @@ -240,14 +243,9 @@

          Examp dim(example_vpts)

        #> [1] 25 1934 15
        @@ -258,7 +256,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/sunrise_sunset.html b/docs/dev/reference/sunrise_sunset.html index 902a7fe1e..efa1e2fa0 100644 --- a/docs/dev/reference/sunrise_sunset.html +++ b/docs/dev/reference/sunrise_sunset.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -203,17 +206,12 @@

          Examp # sunset in the Netherlands sunset("2016-01-01", 5, 53)

        #> [1] "2016-01-01 15:28:31 UTC"
        # civil twilight in Ithaca, NY, today -sunrise(Sys.time(), -76.5, 42.4, elev = -6)
        #> [1] "2020-02-20 06:27:26 EST"
        +sunrise(Sys.time(), -76.5, 42.4, elev = -6)
        #> [1] "2020-04-01 06:19:08 EDT"
        @@ -224,7 +222,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/update_docker.html b/docs/dev/reference/update_docker.html index 93f5c12e8..6d9212816 100644 --- a/docs/dev/reference/update_docker.html +++ b/docs/dev/reference/update_docker.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -182,20 +185,15 @@

          Details run update_docker(mistnet = TRUE)

          Examples

          - 
          # \dontrun{
+    
          if (FALSE) {
 # update the vol2bird docker image:
-update_docker()
          #> Succesfully installed Docker image with vol2bird version 0.5.0 , including MistNet. 
          #> [1] "2020-02-11 19:37:40 UTC"
          # }
-
          
+update_docker()
+}
        @@ -206,7 +204,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/vol2bird_version.html b/docs/dev/reference/vol2bird_version.html index 6385967a3..f7507d23a 100644 --- a/docs/dev/reference/vol2bird_version.html +++ b/docs/dev/reference/vol2bird_version.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,7 +57,6 @@ correctly on the local system and returns the version of the installed vol2bird algorithm in the Docker container." /> - @@ -71,7 +74,7 @@ - +
        @@ -124,7 +127,7 @@
        • - + @@ -182,20 +185,15 @@

          Details the version of this local installation.

          Examples

          - 
          # \dontrun{
+    
          if (FALSE) {
 # check installed vol2bird version:
-vol2bird_version()
          #> [1] ‘0.5.0’
          # }
-
          
+vol2bird_version()
+}
        @@ -206,7 +204,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/vplist_to_vpts.html b/docs/dev/reference/vplist_to_vpts.html index 9e746193d..7b8e23bbb 100644 --- a/docs/dev/reference/vplist_to_vpts.html +++ b/docs/dev/reference/vplist_to_vpts.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,7 +56,6 @@ - @@ -70,7 +73,7 @@ - +
        @@ -123,7 +126,7 @@
        • - + @@ -182,18 +185,15 @@

          Value

          multiple radars, containing vpts objects for each radar.

          Examples

          - 
          # \dontrun{
-vps <- read_vpfiles(c("my/path/profile1.h5", "my/path/profile2.h5", ...))
          #> Error in read_vpfiles(c("my/path/profile1.h5", "my/path/profile2.h5",     ...)): '...' used in an incorrect context
          ts <- bind_into_vpts(vps)
          #> Error in bind_into_vpts(vps): object 'vps' not found
          # }
-
          + 
          if (FALSE) {
+vps <- read_vpfiles(c("my/path/profile1.h5", "my/path/profile2.h5", ...))
+ts <- bind_into_vpts(vps)
+}
        @@ -204,7 +204,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        diff --git a/docs/dev/reference/wgs_to_proj.html b/docs/dev/reference/wgs_to_proj.html index 35ac59634..f1ed134f4 100644 --- a/docs/dev/reference/wgs_to_proj.html +++ b/docs/dev/reference/wgs_to_proj.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,7 +55,6 @@ - @@ -69,7 +72,7 @@ - +
        @@ -122,7 +125,7 @@
        • - + @@ -180,12 +183,9 @@

          Value

        @@ -196,7 +196,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.9000.

        +

        Site built with pkgdown 1.5.0.

        From b7e6195ebbd6dec15195fc5441294c30a8f8778d Mon Sep 17 00:00:00 2001 From: adokter Date: Wed, 1 Apr 2020 14:14:55 -0400 Subject: [PATCH 18/18] build site --- docs/index.html | 3 ++- docs/news/index.html | 2 +- docs/pkgdown.yml | 2 +- docs/reference/integrate_to_ppi.html | 2 +- docs/reference/read_pvolfile.html | 2 +- docs/reference/read_vpfiles.html | 2 +- docs/reference/summary.pvol.html | 2 +- 7 files changed, 8 insertions(+), 7 deletions(-) diff --git a/docs/index.html b/docs/index.html index 5deb96311..c5afa4bdb 100644 --- a/docs/index.html +++ b/docs/index.html @@ -136,7 +136,8 @@

        You can install the released version of bioRad from CRAN with:

        Alternatively, you can install the latest development version from GitHub with:

        -
        devtools::install_github("adokter/bioRad")
        +
        # install.packages("devtools")
+devtools::install_github("adokter/bioRad")

        Then load the package with:

        library(bioRad)
 #> Welcome to bioRad version 0.5.1
diff --git a/docs/news/index.html b/docs/news/index.html
index f8ad62bd1..3c79281a2 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -177,7 +177,7 @@ 
        
 
        
 New features
        
 
          
-
        • integrate_to_ppi() is a new function to estimate spatial images of vertically integrated density and reflectivity. This function produces an ppi image showing the density of animals on the earth’s surface, corrected for the changing overlap between the radar beams and animal layer with distance from the radar. See Kranstauber et al. 2020 for methodology and this vignette for examples.
          • 
+
        • integrate_to_ppi() is a new function to estimate spatial images of vertically integrated density and reflectivity. This function produces an ppi image showing the density of animals on the earth’s surface, corrected for the changing overlap between the radar beams and animal layer with distance from the radar. See Kranstauber et al. 2020 for methodology and this vignette for examples.
          • 
 
        • apply_mistnet() is a new function to apply the convolution neural network “MistNet” on pvolfiles to separate biological and meteorological signals (see Lin et al. 2019). Results can be readily visualized with plot.ppi() and plot.scan(). MistNet is now also a segmentation option in calculate_vp() (#262).
          • 
 
        • read_pvolfile() and calculate_vp() now read Vaisala IRIS RAW format directly, helpful for countries like 🇨🇦🇫🇮🇨🇴🇵🇹 (#222). bioRad now also reads files containing single elevation scans and calculate_vp() can calculate profiles from multiple files containing single elevation scans (#221).
          • 
 
        
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 9e6a8b272..5eb0cdce3 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -5,7 +5,7 @@ articles:
   bioRad: bioRad.html
   rad_aero_19: rad_aero_19.html
   range_correction: range_correction.html
-last_built: 2020-04-01T17:55Z
+last_built: 2020-04-01T18:13Z
 urls:
   reference: https://adokter.github.io/bioRad/reference
   article: https://adokter.github.io/bioRad/articles
diff --git a/docs/reference/integrate_to_ppi.html b/docs/reference/integrate_to_ppi.html
index 44d5639c3..4212f4d4f 100644
--- a/docs/reference/integrate_to_ppi.html
+++ b/docs/reference/integrate_to_ppi.html
@@ -340,7 +340,7 @@ 
        R
 
      • Kranstauber B, Bouten W, Leijnse H, Wijers B, Verlinden L,
   Shamoun-Baranes J, Dokter AM (2020) High-Resolution Spatial Distribution of
   Bird Movements Estimated from a Weather Radar Network. Remote Sensing 12 (4), 635.
-  https://www.mdpi.com/2072-4292/12/4/635
        • 
+  https://doi.org/10.3390/rs12040635
        
 
      • Buler JJ & Diehl RH (2009) Quantifying bird density during migratory
   stopover using weather surveillance radar. IEEE Transactions on Geoscience
   and Remote Sensing 47: 2741-2751.
diff --git a/docs/reference/read_pvolfile.html b/docs/reference/read_pvolfile.html
index 5348b19f6..d802448ed 100644
--- a/docs/reference/read_pvolfile.html
+++ b/docs/reference/read_pvolfile.html
@@ -256,7 +256,7 @@ 
        Examp
 pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
 
 # print the local path of the volume file:
-pvolfile
        • #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmpJinW0n/temp_libpath1aa59a1bf7a/bioRad/extdata/volume.h5"
        +pvolfile
        #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmpALK0nH/temp_libpath16c501fd7b223/bioRad/extdata/volume.h5"
        # load the file: example_pvol <- read_pvolfile(pvolfile) diff --git a/docs/reference/read_vpfiles.html b/docs/reference/read_vpfiles.html index 60be9892b..60ec40fed 100644 --- a/docs/reference/read_vpfiles.html +++ b/docs/reference/read_vpfiles.html @@ -184,7 +184,7 @@

        Examp vpfile <- system.file("extdata", "profile.h5", package = "bioRad") # print the local path of the profile file: -vpfile

        #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmpJinW0n/temp_libpath1aa59a1bf7a/bioRad/extdata/profile.h5"
        +vpfile
        #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmpALK0nH/temp_libpath16c501fd7b223/bioRad/extdata/profile.h5"
        # load the file: read_vpfiles(vpfile)
        #> Vertical profile (class vp) #> diff --git a/docs/reference/summary.pvol.html b/docs/reference/summary.pvol.html index d00538b72..54f76ceda 100644 --- a/docs/reference/summary.pvol.html +++ b/docs/reference/summary.pvol.html @@ -207,7 +207,7 @@

        Examp pvolfile <- system.file("extdata", "volume.h5", package = "bioRad") # print the local path of the volume file: -pvolfile

        #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmpJinW0n/temp_libpath1aa59a1bf7a/bioRad/extdata/volume.h5"
        +pvolfile
        #> [1] "/private/var/folders/hq/tlbyscp93lq2js72t62dkbrh2z_dgv/T/RtmpALK0nH/temp_libpath16c501fd7b223/bioRad/extdata/volume.h5"
        # load the file: example_pvol <- read_pvolfile(pvolfile)