bioRad 0.8.1

Addresses minor bugs appearing on CRAN shortly after bioRad 0.8.0 release.

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

All issues included in release 0.8.0 can be found here.

New features

• ENRAM VPTS data exchange format added in package data as vpts_schema.rda (#661)

• 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 (#661)

• 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

bioRad 0.7.3 includes minor bugfixes and improvements. Basemaps used by function map() are now based on OpenStreetMap tiles provided through dependency packages ggspatial and rosm. All issues included in this release can be found here.

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

• Improved the polar volume file fetching mechanism from s3 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

bioRad 0.7.2 includes a bugfix and several minor updates:

• fix a bug in the calculation of flight altitude quantiles (when using argument height_quantile in function integrate_profile()), which caused underestimation of flight altitude quantiles by up to one altitude bin (#627)

• changed default aloft bucket to aloftdata (#622)

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

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

bioRad 0.7.1

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).

bioRad 0.6.2

This release is a bug fix for issue #532, which caused the lowest altitude bin of profiles to be excluded in vertical integration using integrate_profile(). This bug only affects radars for which the antenna height is close to sea level, i.e. within the first bin of the profile (typically 100 or 200 m). It first appeared in bioRad version 0.6.0.

Additional fixes:

• allow linear reflectivity eta to be zero in eta_to_dbz() (#526)

• fix for running calculate_vp() on files on external hard disks or different partitions (#535)

bioRad 0.6.1

No functional changes compared to version 0.6.0. Rebuilding the documentation for compatibility with HTML5 on request of CRAN.

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.

• 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.

New features

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

Bugfixes

• 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)

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

• minor documentation improvements