Package: bioRad 0.12.0.9000

Adriaan M. Dokter

bioRad: Biological Analysis and Visualization of Weather Radar Data

Extract, visualize and summarize aerial movements of birds and insects from weather radar data. See Dokter, A. M. et al. (2018) "bioRad: biological analysis and visualization of weather radar data" <doi:10.1111/ecog.04028> for a software paper describing package and methodologies.

Authors:Adriaan M. Dokter [aut, cre], Peter Desmet [aut], Bart Kranstauber [aut], Cecilia Nilsson [aut], Alexander Tedeschi [aut], Stijn Van Hoey [aut], Bart Hoekstra [ctb], Pieter Huybrechts [ctb], Hidde Leijnse [ctb], Nicolas Noé [ctb], Raphaël Nussbaumer [ctb], Jurriaan Spaaks [ctb], Lourens Veen [ctb], Liesbeth Verlinden [ctb]

bioRad_0.12.0.9000.tar.gz
bioRad_0.12.0.9000.zip(r-4.7)bioRad_0.12.0.9000.zip(r-4.6)bioRad_0.12.0.9000.zip(r-4.5)
bioRad_0.12.0.9000.tgz(r-4.6-any)bioRad_0.12.0.9000.tgz(r-4.5-any)
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bioRad_0.12.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bioRad/json (API)

# Install 'bioRad' in R:
install.packages('bioRad', repos = c('https://adokter.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/adokter/biorad/issues

Pkgdown/docs site:https://adriaandokter.com

Datasets:

On CRAN:

Conda:

aeroecologyenrameumetnet-operalifewatchmovement-ecologynexradoscibioradarweather-radarwsr-88d

9.45 score 31 stars 1 packages 112 scripts 858 downloads 68 exports 80 dependencies

Last updated from:6e6a8e924e. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK324
source / vignettesOK272
linux-release-x86_64OK323
macos-release-arm64OK258
macos-oldrel-arm64OK214
windows-develOK327
windows-releaseOK308
windows-oldrelOK309
wasm-releaseOK147

Exports:add_paramapply_mistnetas.vpas.vptsattribute_tablebeam_distancebeam_heightbeam_profilebeam_profile_overlapbeam_rangebeam_widthbind_into_vptscalculate_paramcalculate_vpcheck_dockercheck_nightclean_mixturecomposite_ppiconvert_legacydbz_to_etadownload_basemapdownload_pvolfilesdownload_vpfilesdoyeta_to_dbzfilter_precipfilter_vptsget_elevation_anglesget_iris_raw_taskget_odim_object_typeget_paramget_quantityget_scanintegrate_profileintegrate_to_ppiis.paramis.ppiis.pvolis.pvolfileis.scanis.vpis.vpfileis.vpiis.vptslist_vpts_aloftmapnexrad_to_odimnoynyquist_velocityproject_as_ppircsrcs<-read_cajunread_pvolfileread_stdoutread_vpfilesread_vptsregularize_vptsscan_to_rasterscan_to_spatialsd_vvp_thresholdsd_vvp_threshold<-select_vpfilessunrisesunsetupdate_dockervol2bird_versionwrite_pvolfile

Dependencies:askpassassertthatbiocmakebitbit64classclassIntclicliprcpp11crayoncurlDBIdir.expirydotCall64dplyre1071farverfieldsfilelockgenericsggplot2gluegridExtragtablehmshttr2isobandjsonliteKernSmoothlabelinglatticelifecyclelubridatelutzmagrittrmapsMASSopensslpillarpkgconfigprettyunitsprogressproxypurrrR6rappdirsrasterRColorBrewerRcppreadrrhdf5rhdf5filtersRhdf5librlangs2S7scalessfspspamstringistringrsuntoolssysterratibbletidyrtidyselecttimechangetzdbunitsutf8vctrsviridisviridisLitevroomwithrwkxml2

Introduction to bioRad
General package structure and functionality | Figure 2 | Analysis workflow | Step 1: loading and visualizing radar scans | Step 2: processing volumes into vertical profiles | Step 3: visualizing and interpreting individual profiles | Step 4: analyzing and visualizing vertical profiles as time series | Example datasets
Rendered frombioRad.Rmdusingknitr::rmarkdown

Last update: 2026-06-15
Started: 2018-09-22

Introductory exercises with bioRad
Getting started | Basic visualization of radar scans | The structure of polar volumes | Plotting radar scans | Overlaying radar scans on maps | Screening out weather | using correlation coefficient | using MistNet | using depolarization ratio | Vertical profiles | Loading processed vertical profiles | Inspecting single vertical profiles | Plotting vertical profile time series | Vertical and time integration of profiles | Inspecting precipitation signals in profiles | Range bias correction | Processing a polar volume into a profile | Range bias correction and vertical integration on a map | Processing many polar volumes | Accessing radar data | Processing multiple polar volumes | Parallel processing | Further analysis outside bioRad
Rendered fromrad_aero_22.Rmdusingknitr::rmarkdown

Last update: 2026-06-15
Started: 2023-06-07

Correction for range effects
1 Preparations | 2 Beam propagation | 3 Vertical profiles and polar volumes | 4 Spatial estimates of vertically integrated density (VID) | 5 Example: estimating a VID image | 6 Overlap between radiation profile and bird profile | 7 To do
Rendered fromrange_correction.Rmdusingknitr::rmarkdown

Last update: 2024-07-30
Started: 2019-07-24

Readme and manuals

Help Manual

Help pageTopics
Subset a plan position indicator ('ppi')[.ppi
Add scan parameter from a georeferenced raster.add_param add_param.pvol add_param.scan
Apply MistNet segmentation to a polar volumeapply_mistnet
Convert a vertical profile ('vp') or time series of vertical profiles ('vpts') to a data frameas.data.frame.vp as.data.frame.vpts
Convert a dataframe into a vp objectas.vp
Convert a dataframe into a vpts objectas.vpts
Extract a volume coverage pattern table with all attributesattribute_table
Calculate radar beam distancebeam_distance
Calculate radar beam heightbeam_height
Calculate vertical radiation profilebeam_profile
Calculate overlap between a vertical profile ('vp') and the vertical radiation profile emitted by the radarbeam_profile_overlap
Calculate radar beam rangebeam_range
Calculate radar beam widthbeam_width
Bind vertical profiles ('vp') into time series ('vpts')bind_into_vpts bind_into_vpts.list bind_into_vpts.vp bind_into_vpts.vpts
Concatenate vertical profiles ('vp') into a list of vertical profilesc.vp
Calculate a new scan parametercalculate_param calculate_param.ppi calculate_param.pvol calculate_param.scan
Calculate a vertical profile ('vp') from a polar volume ('pvol') filecalculate_vp
Check if it is night at a given time and placecheck_night check_night.default check_night.list check_night.pvol check_night.vp check_night.vpi check_night.vpts
Partition mixtures of animals using assumptions on airspeeds.clean_mixture clean_mixture.default clean_mixture.vp clean_mixture.vpts
Create a composite of multiple plan position indicators ('ppi')composite_ppi
Convert legacy bioRad objectsconvert_legacy convert_legacy.vp convert_legacy.vpts
Convert reflectivity factor (dBZ) to reflectivity (eta)dbz_to_eta
Download polar volume ('pvol') files from the NEXRAD archivedownload_pvolfiles
Download vertical profile ('vp') files from the ENRAM data repositorydownload_vpfiles
Look up day of year (doy) or night of year (noy)doy doy.default doy.pvol doy.vp doy.vpi doy.vpts doy_noy noy noy.default noy.pvol noy.vp noy.vpi noy.vpts
Convert reflectivity (eta) to reflectivity factor (dBZ)eta_to_dbz
Scan ('scan') exampleexample_scan
Vertical profile ('vp') exampleexample_vp
Time series of vertical profiles ('vpts') exampleexample_vpts
Posthoc precipitation filterfilter_precip
Filter a time series of vertical profiles ('vpts').filter_vpts
Get elevation angles of a polar volume ('pvol'), scan ('scan') or parameter ('param')get_elevation_angles get_elevation_angles.param get_elevation_angles.pvol get_elevation_angles.scan
Check the 'task' type of an IRIS RAW fileget_iris_raw_task
Check the 'data' type of an ODIM HDF5 fileget_odim_object_type
Get a parameter ('param') from a scan ('scan')get_param
Get a quantity from a vertical profile ('vp') or time series of vertical profiles ('vpts')get_quantity get_quantity.list get_quantity.vp get_quantity.vpts
Get a scan ('scan') from a polar volume ('pvol')get_scan
Vertically integrate profiles ('vp' or 'vpts') into an integrated profile ('vpi')integrate_profile integrate_profile.list integrate_profile.vp integrate_profile.vpts
Calculate a plan position indicator ('ppi') of vertically integrated density adjusted for range effectsintegrate_to_ppi
Check if a file is a polar volume ('pvol')is.pvolfile
Check if a file is a vertical profile ('vp')is.vpfile
List aloft urls for time series of vertical profiles ('vpts') of radar stationslist_vpts_aloft
Map a plan position indicator ('ppi') on a mapmap map.ppi
Mathematical and arithmetic operations on param's, scan's and pvol'sMath.pvol Math.scan Ops.param Ops.pvol Ops.scan
Convert a NEXRAD polar volume file to an ODIM polar volume filenexrad_to_odim
Calculate Nyquist velocity for a given pulse repetition frequency (PRF)nyquist_velocity
Plot a plan position indicator ('ppi')plot.ppi
Plot a scan ('scan') in polar coordinatesplot.scan
Plot a vertical profile ('vp')plot.vp
Plot an integrated profile ('vpi')plot.vpi
Plot a time series of vertical profiles ('vpts')plot.vpts
Project a scan ('scan') or parameter ('param') to a plan position indicator ('ppi')project_as_ppi project_as_ppi.param project_as_ppi.scan
Get radar cross sectionrcs rcs.list rcs.vp rcs.vpi rcs.vpts
Set radar cross sectionrcs<- rcs<-.list rcs<-.vp rcs<-.vpi rcs<-.vpts
Read a vertical profile ('vp') from UMASS Cajun text fileread_cajun
Read a polar volume ('pvol') from fileread_pvolfile
Read a vertical profile ('vp') or a list of vertical profiles ('vp') from filesread_vpfiles
Read time series of vertical profiles ('vpts') from file(s)read_vpts
Regularize a time series of vertical profiles ('vpts') on a regular time gridregularize_vpts
convert a polar scan into a rasterscan_to_raster
convert a polar scan into a spatial object.scan_to_spatial
Get threshold of the radial velocity standard deviationsd_vvp_threshold sd_vvp_threshold.list sd_vvp_threshold.vp sd_vvp_threshold.vpts
Set threshold of the radial velocity standard deviationsd_vvp_threshold<- sd_vvp_threshold<-.list sd_vvp_threshold<-.vp sd_vvp_threshold<-.vpts
Select vertical profile ('vp') files from computerselect_vpfiles
Inspect a parameter ('param')is.param summary.param
Inspect a plan position indicator ('ppi')dim.ppi is.ppi summary.ppi
Inspect a polar volume ('pvol')dim.pvol is.pvol summary.pvol
Inspect a scan ('scan')dim.scan is.scan summary.scan
Inspect a vertical profile ('vp')dim.vp is.vp summary.vp
Inspect an integrated profile ('vpi')is.vpi summary.vpi
Inspect a time series of vertical profiles ('vpts')dim.vpts is.vpts print.vpts summary.vpts [.vpts
Calculate sunrise or sunset for a time and placesunrise sunrise_sunset sunset
Tidyverse methods for bioRad objectsselect.scan tidyverse
Write a polar volume ('pvol') object to ODIM HDF5 filewrite_pvolfile