NEWS.md

bioRad 0.8.1.9000

• Correct units specified in plot label for quantity VIR (#674).

• Discard profiles with misspecified altitude bins in as.vpts() and read_vpts() (#684).

• New argument zoomin for function bioRad::map() to increase basemap resolution (#689).

• Correct type of gap field in vpts objects for profiles stored in ODIM HDF5 format (.h5) (#635, #691).

• Interpret NA values in field DBZH in integrate_to_ppi() as pixels that were not irradiated (#658).

• Fixes a bug that prevented a data.frame to be converted to a vpts object with as.vpts() when profiles are not sorted in datetime and height (#692).

• Bugfix for ignored xlab argument in plot.vpi() and night shading fix for dealing with NA values (#693)

bioRad 0.8.1

bugfixes

• dbz_all field in VPTS CSV files is now correctly mapped to DBZH field (#661).

• Non-standard data fields are now retained in vpts objects produced with as.vpts() (#661).

• Corrected the type of gap field in vpts objects to logical (#635).

bioRad 0.8.0

New features

• ENRAM VPTS data exchange format added in package data as vpts_schema.rda

• VPTS files are now able to be validated with validate_vpts() which uses the schema to check for min/max constraint violations for specific fields, regex and datetime formatting

• speed up integrate_to_ppi() and project_as_ppi() by using native sf functions (#669)

• support for tidyverse select method for polar volume and polar scan objects (#668,#460)

Bugfixes

• Corrected the default refractive index value used in conversion of linear reflectivity (eta) to logarithmic reflectivity (dBZ). The effect is a 7% increase in animal densities in output of functions integrate_to_ppi() and read_cajun() only (#642).

• Fixed the handling of empty numeric vectors when plotting clutter maps (#655)

• Fixed warning when reading VPTS csv containing multiple values in lat, lon, 'rcs' or sd_vvp_threshold (#651)

• Fixed enabling/disabling of single_pol flag in calculate_vp() (#646)

• Updated the s3 source bucket of download_vpfiles() to https://aloftdata.s3-eu-west-1.amazonaws.com (#648)

• Fixed an error in the idw method of composite_ppi() that emerged with the evolution of dependency package sp / deprecation of rgdal (#666)

bioRad 0.7.3

• 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 format to corresponding DBZH data column in bioRad vpts object (#634).

• Improved the polar volume downloads by download_pvolfiles(): 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

• changed default aloft bucket to aloftdata (#622)

• skip tests for calculate_vp() when vol2birdR package is not installed (#624)

• fix a bug in the calculation of flight altitude quantiles (#627), which caused underestimation of flight altitude quantiles by up to one altitude bin.

• updates for compatibility with testthat package 3rd edition ($630)

bioRad 0.7.1

Rebuilds documentation with examples formatted as per CRAN requirements.

bioRad 0.7.0

bioRad 0.7 includes a major backend overhaul that deprecates the use of Docker. All Docker-dependent functionality is now included in the new dependency package vol2birdR package, which needs to be installed as part of bioRad. All bioRad functions remain the same, but several functions will run considerable faster.

New features

• bioRad is now fully available on Windows.

• Simplified installation, including automatic installation of rhdf5 from bioconductor (#464).

• Faster implementations of functions previously dependent on Docker, such as calculate_vp(), apply_mistnet() and read_pvolfile().

• Support for reading VPTS CSV format through updated function read_vpts(). VPTS CSV table schema included to allow offline parsing of VPTS CSV files as a frictionless data package (#551, #590).

• Updated function read_vpts() supports reading vp/vpts data in ODIM HDF and VPTS CSV format (#551, #590).

• New function list_vpts_aloft() produces a list of aloft archive URLs for time series of vertical profiles (vpts). This list of URLs can then be used to bulk download data using any number of external tools (#553).

• New function read_stdout() replaces previous functionality of read_vpts() to read vol2bird stdout format. It also has a new sep argument (#536) to support both fixed-delimited and comma-separated stdout data.

• New function as.vpts converts a data.frame originating from a VPTS CSV file into a vpts object (#555). Inverse operation of as.data.frame.vpts().

• read_pvolfiles() now allows ODIM H5 files with missing source attribute. The functionality is similar to read_vpfiles(), i.e. extracting the NOD, RAD or WMO identifier, otherwise using unknown (2f6935c).

• bind_into_vpts() now works for vp and vpts objects with different heights (#343).

• Faster parallel mistnet runs (adokter/vol2birdR#16).

Bugfixes

• Fix bug in height integration, which excluded the lowest bins for certain low altitude radars (#534).

Deprecations

• Argument local_install in calculate_vp() and apply_mistnet() is now deprecated.

• Functions check_docker() and update_docker() have been deprecated.

• Function vol2bird_version() has been migrated to package vol2birdR and can be accessed by vol2birdR::vol2bird_version().

• Dependency maptools has been replaced with suntools, rgdal has been removed in accordance with the evolution of sp and the imminent archiving of rgdal.

• Function as.data.frame.vpts() has output column names lat, lon, antenna_height renamed to radar_latitude, radar_longitude, radar_height for compatibility with the VPTS CSV data format. The function also outputs an additional column radar_wavelength (#609).

bioRad 0.6.1

Rebuilds the documentation using roxygen2 for compability with HTML5 (a CRAN requirement).

bioRad 0.6.0

Introduces a number of new functions and parameters and includes bugfixes. All issues included in this release can be found here.

New functions

• New function attribute_table() to quickly tabulate scan attributes (#365).

• New function get_iris_raw_task() to returns task from IRIS files (#411).

• New functions is.vpi() and summary() for vpi objects (#380, #405).

• New function write_pvolfile() to write polar volumes to ODIM hdf5 format (#470, #471).

• New function download_pvolfiles() to download NEXRAD polar volume files from Amazon Web Services (#41, #487)

• New functions Math.pvol(), Math.scan(), Ops.pvol(),Ops.scan(),Ops.param(): standard mathematical operations for param, scan and pvol objects.

New features and bugfixes

• apply_mistnet(), nexrad_to_odim() and read_pvolfile() can now use local vol2bird installation (#416, #398).

• beam_profile_overlap() and integrate_to_ppi() bugfix that affected profiles with only NA values (#396).

• calculate_param() now also works on PPIs (#316) + bugfix for lost attributes (#401) and long expressions without name (#399).

• calculate_vp() now sets default range_max to 35km (#206) + has a new optional parameter height_quantile to calculate flight altitude quantiles (#485) + parameters for local mistnet (#418, #488).

• composite_ppi() now composites multiple PPI parameters at once (#390, #393) + bugfix for ylim parameter (#389).

• get_scan() warns when multiple scans with the same elevation are equally close to the requested elevation and add option to return all (#414).

• integrate_profile() now sets default interval_max to 1h (#481) and has a new argument interval_replace. The function can now integrate at altitude resolutions smaller than the altitude bin spacing. New option antenna for alt_min parameter, setting the altitude of the antenna as the minimum altitude (#472). Directional angles are now always mapped to the 0-360 degree domain (#489).

• integrate_to_ppi() and other functions are sped up by avoiding duplicate input argument checking (#358) + radar name now added to output (#425, #443). Bugfix affecting profiles consisting of primarily NA/NaN values (#415), which are now treated as zeros.

• map() bugfix for transparency (#438) and base layer (#468).

• plot.vpi() now has an elev parameter (#412).

• plot.vpts() now supports custom color scales (#444). It can plot speed and direction as colours (#424) + height offset fixed in plots (#198) + bugfix negative zlim values (#402).

• read_cajun() bugfix for incorrect conversion of linear eta to reflectivity (#403).

• read_vpts() bugfix for missing height attribute (#409).

• regularize_vpts()'s fill parameter now allows to specify a time interval over which to perform nearest neighbour interpolation to fill gaps of missing profile data. (#475) + bugfix for max_interval parameter (#480, #484, #475).

• scan_to_spatial() now creates points for cell centers (#430).

Additional features

• The package now accounts for rstart and astart from the ODIM specification (#434).

• Clearly indicate when a speed is ground speed (#462).

• Improved documentation and unit tests for a number of functions thanks to an online bioRad sprint (June 2021).

• GitHub Actions are set up to automatically test changes (#428).

bioRad 0.5.2

This release is primarily a hotfix for R version 4.0 (#375). All issues included in this release can be found here. New features and improvements include:

• regularize_vpts() is now much faster, and chooses more intuitive starting and ending point of the regularized grid, e.g. projecting on half hour grid will have time series start on the nearest half hour (#332).

• regularize_vpts() has new option keep_timestamp, which allows individual profiles to keep there original timestamp instead of the timestamp of the regularized grid.

• sunrise()/sunset() have improved documentation (#180) and new option force_tz (4968019).

• check_night() has new option offset, which allows day/night transition to be shifted by a temporal offset (#338). For example, this is useful when selecting night time profiles that start a specific number of hours after sunset.

• check_night() now works for vpi objects (23def64).

• filter_vpts() allows to select for day and night in vpts using new arguments night, elev and offset, based on functionality of check_night() (#345).

• New functions noy() and doy() to determine which night or day of the year a profile belongs to (#346).

• as.data.frame.vp() now has separate function page and deprecated parameter quantities (#364).

• get_quantity() now has improved documentation and allows to return height (#352).

• dim() now returns dimensions in a different, more logical order for pvol and vpts objects (#355).

• Improved documentation and unit tests for a number of functions thanks to an online bioRad sprint (April 2020).

• Bugfixes (#330, #368).

bioRad 0.5.1

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 dependencies.

• 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

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

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.

• 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).

Newer/faster conversions

• calculate_param() is a new function to calculate parameters from existing parameters, e.g. reflectivity eta from reflectivity factor DBZH (#287).

• scan_to_raster() is a new function to convert a scan into a RasterBrick compatible with package raster (#238).

• scan_to_spatial() is a new function to convert a scan into a SpatialPointsDataFrame compatible with package sp (#238).

• project_as_ppi() is now much faster (e420e5d) and accounts for earth's curvature (820e85f).

New functions describing the radar beam geometry

• beam_distance() and beam_range() are new functions to relate range (i.e. slant range), distance (i.e. down range) and height of the radar beam.

• beam_profile() is a new function to calculate for a set of beam elevations the altitudinal normalized distribution of radiated energy by those beams.

• beam_profile_overlap() is a new function to calculate the distribution overlap (in terms of Bhattacharyya distance) between a vertical profile (vp) and the vertical radiation profile of a set of emitted radar beams (given by beam_profile()).

Additional features

• Custom color scales in map() and plot.ppi (#318).

• nyquist_velocity() is a new function to calculate the unambiguous velocity of Doppler radar from its pulse repetition frequency/frequencies (#208).

• filter_vpts() is a new function simplifying the selection of time ranges and instances in vertical profile time series (vpts) (#241).

• The definition of height-integrated velocity is now corrected (#232, #233, 72be6d1).

• Improved documentation of how mtr can be calculated from vid, u, v (6dce625).

• read_pvolfile() now also reads quantities DBZ, TH, T, because these often occur in European data and are relevant for biological analysis (note that DBZ and T are not ODIM-compliant names) (5db08bd).

• plot.scan() now has correct ordering of rays (#285).

• plot.vpts() now has correctly positioned and rounded speed barbs (#277, #244).

• integrate_profile()'s default unit of interval argument has been changed to seconds (#234).

• project_as_ppi()'s default projection is now on earth's surface (#280).

• height is now the default quantity denoting height above mean sea level. HGHT is deprecated (#273).

• plot.vpts() and plot.vp() plots are shifted up by half the height interval to reflect that height refers to the bottom of the height interval (#277, #198).

• calculate_vp()'s default sd_vvp_threshold parameter value at S-band is now 1 m/s (#93).

• And many small bug fixes and documentation improvements.

bioRad 0.4.0

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

• get_param() added as new function to get parameters from scan (#132).

• download_basemap() now uses Stamen basemaps by default (parameter source), so users do not need to request an API key for the previous default Google Maps (#163).

• download_vpfiles() and select_vpfiles() now use 5 letter radar codes (parameter radars instead of radar and country), allow to skip already downloaded files (parameter overwrite = TRUE) and have improved download and error messages (#176).

• read_pvolfile(), nexrad_to_odim() and calculate_vp() (all Docker dependent) can now read files from directories containing a space (#162).

• Details for deprecated functions mt(), mtr(), cmt() are now displayed with function (#166).

• README reviewed for easier installation and usage (#155).

• Get started vignette is now based on figure and workflow from Dokter et al. (#168).

• Introductory exercises vignette renamed to rad_aero_19.Rmd since it is based on the 3d Radar Aeroecology Training School.

• bioRad now has a code of conduct and contributing guidelines (#145).

bioRad 0.3.0

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.

• Functions (#84), arguments (#112) and objects (#80) have been renamed to be consistent (#51). Deprecated functions will remain functional for now, but we will trigger a warning: we advise to use the new functions names. See the lists for current functions and deprecated functions.

• integrate_profile() replaces the functionality of cmt() (#75) and mt() (#76).

• plot() can now be used for scans (#71), e.g. plot(example_scan).

• Functions are organized in sections on the website (#110).

• Changelog section (this page) has been added to website (#144).

• Package R code is reorganized as one function = one file for easier maintenance (#50).

• First tests are included for some functions.

• Contributors (#90) and citation (#141) have been updated.

• bioRad now has a hex logo (#137). ✨