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dbz_all field in VPTS CSV files is now correctly mapped to DBZH field
non-standard data fields are now retained in vpts objects produced with as.vpts()
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)
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)
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).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)
download_basemap() has been deprecated, function
map() now automatically downloads a basemap (#638).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)
Rebuilds documentation with examples formatted as per CRAN requirements.
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.
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 (https://github.com/adokter/vol2birdR/issues/16).
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).
Rebuilds the documentation using roxygen2 for compability with HTML5 (a CRAN requirement).
Introduces a number of new functions and parameters and includes bugfixes. All issues included in this release can be found here.
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.
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).
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).
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).
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.
New CRAN release. All issues included in this release can be found here.
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).
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).
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()).
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.
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).
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). ✨
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.