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)
Rebuilds the documentation using roxygen2 for compability with HTML5
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 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). ✨