Merge branch 'master' into bugfix/dbzh

.Rbuildignore

@@ -17,4 +17,4 @@ inst/extdata/vpts.txt.zip
 ^CRAN-SUBMISSION$
 ^doc$
 ^Meta$
-rosm.cache
+^rosm\.cache$

DESCRIPTION

@@ -53,9 +53,11 @@ Imports:
     viridisLite
 Suggests:
     aws.s3,
-    ggmap (>= 3.0.0),
+    ggspatial,
     knitr,
+    prettymapr,
     rmarkdown,
+    rosm,
     sf,
     testthat (>= 3.0.0),
     tidyselect,

NEWS.md

@@ -1,3 +1,19 @@
+# bioRad 0.7.3
+
+## New features
+
+* Replaced the `ggmap` package with `ggspatial` for map visualizations. This change was made as `ggmap` no longer provides reliable open-source basemaps without the necessity to register for an API key (#638).
+
+## Bugfixes
+
+* Corrected incorrect mapping of to `dbz_all` data column in [VPTS CSV](https://aloftdata.eu/vpts-csv/) format to corresponding `DBZH` data column in bioRad vpts object (#634).
+
+* Improved the VPTS file fetching mechanism from s3: now skips a day if there are issues with fetching instead of aborting the entire download (#636)
+
+## Deprecations
+
+* `download_basemap()` has been deprecated, function `map()` now automatically downloads a basemap (#638).
+
 # bioRad 0.7.2
 
 ## Bugfixes
@@ -48,6 +64,8 @@ bioRad 0.7 includes a major backend overhaul that deprecates the use of Docker.
 
 ## Deprecations
 
+
+
 * Argument `local_install` in `calculate_vp()` and `apply_mistnet()` is now deprecated.
 
 * Functions `check_docker()` and `update_docker()` have been deprecated.

R/bioRad-deprecated.R

@@ -40,4 +40,14 @@ vol2bird_version <- function(...) {
   warning("vol2bird_version has been moved to package vol2birdR")
   vol2birdR::vol2bird_version()
 }
-
+#' @section download_basemap:
+#' This function has been deprecated 
+#' ggmap has been replaced by ggspatial which no longer requires a pre-downloaded raster basemap
+#'
+#' @rdname bioRad-deprecated
+#' @export
+#' @return No return value, called for warning message side effect only
+download_basemap <- function(...) {
+  warning("download_basemap has been deprecated; ?bioRad::map for details")
+  return("cartolight")
+}

R/color_scale.R

@@ -1,3 +1,33 @@
+# Color scale used in map plots:
+colors_dbz <- c(
+  "lightblue", "darkblue",
+  "green", "yellow", "red",
+  "magenta"
+)
+colors_vrad <- c("blue", "white", "red")
+
+# Color scale used in vertical profile plots:
+r_points <- c(1, 63, 82, 94, 146, 177, 192, 209, 256)
+r_values <- c(255, 255, 163, 255, 255, 81, 81, 0, 0)
+g_points <- c(1, 65, 80, 111, 143, 256)
+g_values <- c(255, 255, 163, 163, 0, 0)
+b_points <- c(1, 80, 97, 111, 128, 160, 207, 256)
+b_values <- c(255, 0, 0, 82, 0, 0, 255, 0)
+vpts_default_palette <- grDevices::rgb(approx(
+  r_points, r_values,
+  seq(1, 255, length.out = 255)
+)$y,
+approx(
+  g_points, g_values,
+  seq(1, 255, length.out = 255)
+)$y,
+approx(
+  b_points, b_values,
+  seq(1, 255, length.out = 255)
+)$y,
+maxColorValue = 255
+)
+
 color_scale <- function(param, zlim, na.value = "transparent") {
   if (param %in% c("VRADH", "VRADV", "VRAD")) {
     colorscale <- ggplot2::scale_colour_gradient2(
@@ -118,35 +148,6 @@ add_color_transparency <- function(color, alpha = 1) {
   }
 }
 
-# Color scale used in map plots:
-colors_dbz <- c(
-  "lightblue", "darkblue",
-  "green", "yellow", "red",
-  "magenta"
-)
-colors_vrad <- c("blue", "white", "red")
-
-# Color scale used in vertical profile plots:
-r_points <- c(1, 63, 82, 94, 146, 177, 192, 209, 256)
-r_values <- c(255, 255, 163, 255, 255, 81, 81, 0, 0)
-g_points <- c(1, 65, 80, 111, 143, 256)
-g_values <- c(255, 255, 163, 163, 0, 0)
-b_points <- c(1, 80, 97, 111, 128, 160, 207, 256)
-b_values <- c(255, 0, 0, 82, 0, 0, 255, 0)
-vpts_default_palette <- grDevices::rgb(approx(
-  r_points, r_values,
-  seq(1, 255, length.out = 255)
-)$y,
-approx(
-  g_points, g_values,
-  seq(1, 255, length.out = 255)
-)$y,
-approx(
-  b_points, b_values,
-  seq(1, 255, length.out = 255)
-)$y,
-maxColorValue = 255
-)
 
 get_zlim <- function(param, zlim) {
   if (param %in% c("DBZH", "DBZV", "DBZ")) {

R/composite_ppi.R

@@ -74,11 +74,8 @@
 #' # across the available scans at each geographic location
 #' composite <- composite_ppi(ppis, method = "max", res=1000)
 #'
-#' # Download basemap
-#' bm <- download_basemap(composite)
-#'
 #' # Plot the calculated max product on the basemap
-#' map(composite, bm)
+#' map(composite)
 #' }
 composite_ppi <-
   function(x,

R/download_pvolfiles.R

@@ -97,15 +97,19 @@ download_pvolfiles <- function(date_min, date_max, radar,
     if (nrow(bucket_df) == 0) {
       # Check if date is correct
       prefix_tmp <- paste(gsub("-", "/", dates[i_d]), sep = "/")
-      assertthat::assert_that(assertthat::not_empty(
+      msg <- assertthat::validate_that(assertthat::not_empty(
         aws.s3::get_bucket_df(bucket = bucket, prefix = prefix_tmp, max = 1)
       ),
       msg = paste0(
         "No data availble on the ", dates[i_d],
         ". Please check data availability for this date."
       )
       )
-      assertthat::assert_that(assertthat::not_empty(
+      if(msg != TRUE){
+        warning(msg)
+        next
+      }
+      msg <- assertthat::validate_that(assertthat::not_empty(
         aws.s3::get_bucket_df(bucket = bucket, prefix = prefix, max = 1)
       ),
       msg = paste0(
@@ -114,6 +118,10 @@ download_pvolfiles <- function(date_min, date_max, radar,
         " https://noaa-nexrad-level2.s3.amazonaws.com/index.html"
       )
       )
+      if(msg != TRUE){
+        warning(msg)
+        next
+      }
     }
 
     # filter bucket with exact date
@@ -130,12 +138,17 @@ download_pvolfiles <- function(date_min, date_max, radar,
     # throw out occasional NA keys, see e.g. 2015/03/01/KEPZ/
     bucket_df %>% dplyr::filter(!is.na(.data$Key)) -> bucket_df
 
-    assertthat::assert_that(nrow(bucket_df) > 0,
+    msg <- assertthat::validate_that(nrow(bucket_df) > 0,
       msg = paste0(
         "No data available for ", radar, " on the ", dates[i_d],
         "within the selected datetime range. Check radar code and data availability on",
         " https://noaa-nexrad-level2.s3.amazonaws.com/index.html"
       ))
+    if(msg != TRUE){
+      warning(msg)
+      next
+    }
+
 
     # create progress bar
     message(paste0("\nDownloading pvol for ", prefix))

R/integrate_to_ppi.R

@@ -119,8 +119,7 @@
 #' plot(ppi, param = "VID", zlim = c(0, 200))
 #'
 #' # Download a basemap and map the ppi
-#' bm <- download_basemap(ppi)
-#' map(ppi, bm)
+#' map(ppi)
 #'
 #' # The ppi can also be projected on a user-defined raster, as follows:
 #'