bioRad

R package for analysis and visualisation of biological signals in weather radar data.
https://github.com/adokter/bioRad

Category: Biosphere
Sub Category: Avian Monitoring and Analysis

Keywords

aeroecology enram eumetnet-opera lifewatch movement-ecology nexrad oscibio package r radar weather-radar wsr-88d

Keywords from Contributors

birds ecology biodiversity gbif invasive-species jekyll simulator geolocation climate camera-traps

Last synced: 30 minutes ago
JSON representation

Repository metadata

R package for analysis and visualisation of biological signals in weather radar data

• Host: GitHub
• URL: https://github.com/adokter/bioRad
• Owner: adokter
• License: other
• Created: 2016-05-24T15:49:06.000Z (almost 9 years ago)
• Default Branch: master
• Last Pushed: 2025-04-09T15:35:37.000Z (18 days ago)
• Last Synced: 2025-04-10T14:52:30.512Z (17 days ago)
• Topics: aeroecology, enram, eumetnet-opera, lifewatch, movement-ecology, nexrad, oscibio, package, r, radar, weather-radar, wsr-88d
• Language: R
• Homepage: http://adokter.github.io/bioRad
• Size: 353 MB
• Stars: 29
• Watchers: 8
• Forks: 17
• Open Issues: 70
• Releases: 17
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: .github/CODE_OF_CONDUCT.md
  • Citation: CITATION.cff
  • Codemeta: codemeta.json

README.Rmd

          ---
output: github_document
---



```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# bioRad 


[![CRAN status](https://www.r-pkg.org/badges/version/bioRad)](https://cran.r-project.org/package=bioRad)
[![R-CMD-check](https://github.com/adokter/bioRad/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/adokter/bioRad/actions/workflows/R-CMD-check.yaml)
[![repo status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![codecov](https://codecov.io/gh/adokter/bioRad/branch/master/graph/badge.svg?token=pDmyO4JVJu)](https://app.codecov.io/gh/adokter/bioRad)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3370004.svg)](https://doi.org/10.5281/zenodo.3370004)
[![vol2birdR DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7992026.svg)](https://doi.org/10.5281/zenodo.7992026)



bioRad provides standardized methods for extracting and reporting biological signals from weather radars. It includes functionality to inspect low-level radar data, process these data into meaningful biological information on animal speeds and directions at different altitudes in the atmosphere, visualize these biological extractions, and calculate further summary statistics.

To get started, see:

* [Dokter et al. (2019)](https://doi.org/10.1111/ecog.04028): a paper describing the package.
* [bioRad vignette](https://adriaandokter.com/bioRad/articles/bioRad.html): an introduction to bioRad's main functionalities.
* [Function reference](https://adriaandokter.com/bioRad/reference/index.html): an overview of all bioRad functions.
* [Introductory exercises](https://adriaandokter.com/bioRad/articles/rad_aero_19.html): a tutorial with code examples and exercises.

More vignettes:

* [Range correction](https://adriaandokter.com/bioRad/articles/range_correction.html): estimate spatial images of vertically integrated density corrected for range effects.

Documentation for the latest development version can be found [here](https://adriaandokter.com/bioRad/dev/).

## Installation

### Install system libraries
For OS X and Linux the GNU Scientific Library (GSL), PROJ and HDF5 libraries need to be installed as system libraries prior to installation, which are required by dependency package **[vol2birdR](https://adriaandokter.com/vol2birdR/)**:

| System                                    | Command
|:------------------------------------------|:---------------------------------------------|
|**OS X (using Homebrew)**                  | `brew install hdf5 proj gsl`
|**Debian-based systems (including Ubuntu)**| `sudo apt-get install libhdf5-dev libproj-dev gsl-bin libgsl-dev`
|**Systems supporting yum and RPMs**        | `sudo yum install hdf5-devel proj-devel gsl gsl-devel`


Additional required system libraries on Linux (Ubuntu)

The following system libraries are required before installing bioRad on Linux systems. In terminal, install these with:

```
sudo apt install libcurl4-openssl-dev
sudo apt install libssl-dev
sudo apt install libgdal-dev
```




### Install bioRad
You can install the released version of bioRad from [CRAN](https://CRAN.R-project.org) with:

```{r eval = FALSE}
install.packages("bioRad")
```

Alternatively, you can install the latest development version from [GitHub](https://github.com/adokter/bioRad) with:

```{r eval = FALSE}
# install.packages("devtools")
devtools::install_github("adokter/bioRad")
```

Then load the package with:

```{r load_bioRad}
library(bioRad)
```

### (optional) Enable MistNet
To enable MistNet, the following vol2birdR commands should be executed:
```{r, eval=FALSE}
vol2birdR::install_mistnet()
vol2birdR::install_mistnet_model()
```
Read the [vol2birdR documentation](https://adriaandokter.com/vol2birdR/articles/vol2birdR.html) for more details.

## Usage

### Radar data example

bioRad can read weather radar data (= polar volumes) in the [`ODIM`](http://eumetnet.eu/wp-content/uploads/2017/01/OPERA_hdf_description_2014.pdf) format and formats supported by the [RSL library](https://trmm-fc.gsfc.nasa.gov/trmm_gv/software/rsl/), such as NEXRAD data. NEXRAD data (US) are [available as open data](https://www.ncdc.noaa.gov/nexradinv/) and on [AWS](https://registry.opendata.aws/noaa-nexrad/).

Here we read an example polar volume data file with `read_pvolfile()`, extract the scan/sweep at elevation angle 3 with `get_scan()`, project the data to a plan position indicator with `project_as_ppi()` and plot the _radial velocity_ of detected targets with `plot()`:

```{r plot_ppi, warning = FALSE, message = FALSE}
library(tidyverse) # To pipe %>% the steps below
system.file("extdata", "volume.h5", package = "bioRad") %>%
  read_pvolfile() %>%
  get_scan(3) %>%
  project_as_ppi() %>%
  plot(param = "VRADH") # VRADH = radial velocity in m/s
```

_Radial velocities towards the radar are negative, while radial velocities away from the radar are positive, so in this plot there is movement from the top right to the bottom left._

### Vertical profile data example

Weather radar data can be processed into vertical profiles of biological targets using `calculate_vp()`. This type of data is [available as open data](https://aloftdata.eu) for over 100 European weather radars.

Once vertical profile data are loaded into bioRad, these can be bound into time series using `bind_into_vpts()`. Here we read an example time series, project it on a regular time grid with `regularize_vpts()` and plot it with `plot()`:

```{r plot_vpts, warning = FALSE, message = FALSE}
example_vpts %>%
  regularize_vpts() %>%
  plot()
```

_The gray bars in the plot indicate gaps in the data._

The altitudes in the profile can be integrated with `integrate_profile()` resulting in a dataframe with rows for datetimes and columns for quantities. Here we plot the quantity _migration traffic rate_ (column `mtr`) with `plot()`:

```{r plot_vpi, warning = FALSE, message = FALSE}
my_vpi <- integrate_profile(example_vpts)

plot(my_vpi, quantity = "mtr") # mtr = migration traffic rate
```

To know the total number of birds passing over the radar during the full time series, we use the last value of the _cumulative migration traffic_ (column `mt`):

```{r mt_value, warning = FALSE, message = FALSE}
my_vpi %>%
  pull(mt) %>% # Extract column mt as a vector
  last()
```

For more exercises, see [this tutorial](https://adriaandokter.com/bioRad/articles/rad_aero_19.html).

## Meta

* We welcome [contributions](https://adriaandokter.com/bioRad/CONTRIBUTING.html) including bug reports.
* License: MIT
* Get citation information for `bioRad` in R doing `citation("bioRad")`.
* Please note that this project is released with a [Contributor Code of Conduct](https://adriaandokter.com/bioRad/CODE_OF_CONDUCT.html). By participating in this project you agree to abide by its terms.

        

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "bioRad" in publications use:'
type: software
license: MIT
title: 'bioRad: Biological Analysis and Visualization of Weather Radar Data'
version: 0.8.1.9000
doi: 10.1111/ecog.04028
identifiers:
- type: doi
  value: 10.32614/CRAN.package.bioRad
- type: url
  value: https://adriaandokter.com/bioRad/
abstract: '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" <https://doi.org/10.1111/ecog.04028> for
  a software paper describing package and methodologies.'
authors:
- family-names: Dokter
  given-names: Adriaan M.
  email: [email protected]
  orcid: https://orcid.org/0000-0001-6573-066X
- family-names: Desmet
  given-names: Peter
  email: [email protected]
  orcid: https://orcid.org/0000-0002-8442-8025
- family-names: Kranstauber
  given-names: Bart
  email: [email protected]
  orcid: https://orcid.org/0000-0001-8303-780X
- family-names: Nilsson
  given-names: Cecilia
  email: [email protected]
  orcid: https://orcid.org/0000-0001-8957-4411
- family-names: Van Hoey
  given-names: Stijn
  email: [email protected]
  orcid: https://orcid.org/0000-0001-6413-3185
preferred-citation:
  type: article
  title: 'bioRad: biological analysis and visualization of weather radar data'
  authors:
  - family-names: Dokter
    given-names: Adriaan M.
    email: [email protected]
    orcid: https://orcid.org/0000-0001-6573-066X
  - family-names: Desmet
    given-names: Peter
    email: [email protected]
    orcid: https://orcid.org/0000-0002-8442-8025
  - family-names: Spaaks
    given-names: Jurriaan H.
  - family-names: Van Hoey
    given-names: Stijn
    email: [email protected]
    orcid: https://orcid.org/0000-0001-6413-3185
  - family-names: Veen
    given-names: Lourens
  - family-names: Verlinden
    given-names: Liesbeth
  - family-names: Nilsson
    given-names: Cecilia
    email: [email protected]
    orcid: https://orcid.org/0000-0001-8957-4411
  - family-names: Haase
    given-names: Günther
  - family-names: Leijnse
    given-names: Hidde
  - family-names: Farnsworth
    given-names: Andrew
  - family-names: Bouten
    given-names: Willem
  - family-names: Shamoun-Baranes
    given-names: Judy
  journal: Ecography
  year: '2019'
  volume: '42'
  doi: 10.1111/ecog.04028
  start: 852-860
repository: https://CRAN.R-project.org/package=bioRad
repository-code: https://github.com/adokter/bioRad
url: https://github.com/adokter/bioRad/
contact:
- family-names: Dokter
  given-names: Adriaan M.
  email: [email protected]
  orcid: https://orcid.org/0000-0001-6573-066X
keywords:
- aeroecology
- enram
- eumetnet-opera
- lifewatch
- movement-ecology
- nexrad
- oscibio
- package
- r
- radar
- weather-radar
- wsr-88d
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- type: software
  title: viridisLite
  abstract: 'viridisLite: Colorblind-Friendly Color Maps (Lite Version)'
  notes: Imports
  url: https://sjmgarnier.github.io/viridisLite/
  repository: https://CRAN.R-project.org/package=viridisLite
  authors:
  - family-names: Garnier
    given-names: Simon
    email: [email protected]
  year: '2024'
  doi: 10.32614/CRAN.package.viridisLite
- type: software
  title: aws.s3
  abstract: 'aws.s3: ''AWS S3'' Client Package'
  notes: Suggests
  url: https://github.com/cloudyr/aws.s3
  repository: https://CRAN.R-project.org/package=aws.s3
  authors:
  - family-names: Leeper
    given-names: Thomas J.
    email: [email protected]
    orcid: https://orcid.org/0000-0003-4097-6326
  year: '2024'
  doi: 10.32614/CRAN.package.aws.s3
- type: software
  title: ggspatial
  abstract: 'ggspatial: Spatial Data Framework for ggplot2'
  notes: Suggests
  url: https://paleolimbot.github.io/ggspatial/
  repository: https://CRAN.R-project.org/package=ggspatial
  authors:
  - family-names: Dunnington
    given-names: Dewey
    email: [email protected]
    orcid: https://orcid.org/0000-0002-9415-4582
  year: '2024'
  doi: 10.32614/CRAN.package.ggspatial
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
  authors:
  - family-names: Xie
    given-names: Yihui
    email: [email protected]
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2024'
  doi: 10.32614/CRAN.package.knitr
- type: software
  title: prettymapr
  abstract: 'prettymapr: Scale Bar, North Arrow, and Pretty Margins in R'
  notes: Suggests
  url: https://github.com/paleolimbot/prettymapr
  repository: https://CRAN.R-project.org/package=prettymapr
  authors:
  - family-names: Dunnington
    given-names: Dewey
    email: [email protected]
  year: '2024'
  doi: 10.32614/CRAN.package.prettymapr
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  url: https://pkgs.rstudio.com/rmarkdown/
  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
  - family-names: Allaire
    given-names: JJ
    email: [email protected]
  - family-names: Xie
    given-names: Yihui
    email: [email protected]
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Dervieux
    given-names: Christophe
    email: [email protected]
    orcid: https://orcid.org/0000-0003-4474-2498
  - family-names: McPherson
    given-names: Jonathan
    email: [email protected]
  - family-names: Luraschi
    given-names: Javier
  - family-names: Ushey
    given-names: Kevin
    email: [email protected]
  - family-names: Atkins
    given-names: Aron
    email: [email protected]
  - family-names: Wickham
    given-names: Hadley
    email: [email protected]
  - family-names: Cheng
    given-names: Joe
    email: [email protected]
  - family-names: Chang
    given-names: Winston
    email: [email protected]
  - family-names: Iannone
    given-names: Richard
    email: [email protected]
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2024'
  doi: 10.32614/CRAN.package.rmarkdown
- type: software
  title: rosm
  abstract: 'rosm: Plot Raster Map Tiles from Open Street Map and Other Sources'
  notes: Suggests
  url: https://github.com/paleolimbot/rosm
  repository: https://CRAN.R-project.org/package=rosm
  authors:
  - family-names: Dunnington
    given-names: Dewey
    email: [email protected]
    orcid: https://orcid.org/0000-0002-9415-4582
  year: '2024'
  doi: 10.32614/CRAN.package.rosm
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: [email protected]
  year: '2024'
  doi: 10.32614/CRAN.package.testthat
  version: '>= 3.0.0'
- type: software
  title: vdiffr
  abstract: 'vdiffr: Visual Regression Testing and Graphical Diffing'
  notes: Suggests
  url: https://vdiffr.r-lib.org/
  repository: https://CRAN.R-project.org/package=vdiffr
  authors:
  - family-names: Henry
    given-names: Lionel
    email: [email protected]
  - family-names: Pedersen
    given-names: Thomas Lin
    email: [email protected]
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Luciani
    given-names: T Jake
    email: [email protected]
  - family-names: Decorde
    given-names: Matthieu
    email: [email protected]
  - family-names: Lise
    given-names: Vaudor
    email: [email protected]
  year: '2024'
  doi: 10.32614/CRAN.package.vdiffr
- type: software
  title: vol2birdR
  abstract: 'vol2birdR: Vertical Profiles of Biological Signals in Weather Radar Data'
  notes: Suggests
  url: https://github.com/adokter/vol2birdR/
  repository: https://CRAN.R-project.org/package=vol2birdR
  authors:
  - family-names: Henja
    given-names: Anders
    email: [email protected]
  - family-names: Dokter
    given-names: Adriaan M.
    email: [email protected]
    orcid: https://orcid.org/0000-0001-6573-066X
  year: '2024'
  doi: 10.32614/CRAN.package.vol2birdR

---

Owner metadata

• Name: Adriaan Dokter
• Login: adokter
• Email:
• Kind: user
• Description:
• Website: http://adriaandokter.com
• Location:
• Twitter:
• Company: Lab of ornithology, Cornell University
• Icon url: https://avatars.githubusercontent.com/u/8268415?u=9a31996e5983bb33a62836b08ab12c7b87c8f748&v=4
• Repositories: 25
• Last ynced at: 2024-06-11T15:36:14.141Z
• Profile URL: https://github.com/adokter

---

GitHub Events

Total

• Create event: 13
• Release event: 2
• Issues event: 33
• Delete event: 30
• Member event: 1
• Issue comment event: 39
• Push event: 82
• Pull request review comment event: 5
• Pull request review event: 6
• Pull request event: 31

Last Year

• Create event: 13
• Release event: 2
• Issues event: 33
• Delete event: 30
• Member event: 1
• Issue comment event: 39
• Push event: 82
• Pull request review comment event: 5
• Pull request review event: 6
• Pull request event: 31

---

Committers metadata

Last synced: 4 days ago

Name	Email	Commits
adokter	a****r@g****m	1123
peterdesmet	p****t@i****e	491
stijnvanhoey	s****y@g****m	361
iskandari	s****i@g****m	278
Pieter Huybrechts	4****H	236
bart	b****t@e****m	86
Cecilia Nilsson	c****n@b****e	62
Raphaël Nussbaumer	r****s@g****m	23
Bart Hoekstra	b****a@g****m	9
Bart	b****t@m****s	6
GitHub Actions	a****s@g****m	5
Nicolas Noé	n****e@i****e	5
bart	y****u@e****m	4
Berend-Christiaan Wijers	b****s@m****m	3
Plieper	l****k@g****m	2
fyiguo	6****o	2
Baptiste Schmid	b****d@v****h	1
iskandari	s****i@g****O	1
Alexander Tedeschi	a****4@a****u	1
Adriaan Michiel Dokter	a****7@c****u	1
Dan Sheldon	s****n@c****u	1

Committer domains:

• inbo.be: 2
• cs.umass.edu: 1
• cornell.edu: 1
• ag-clo-at744.ad.cornell.edu: 1
• gmail.como: 1
• vogelwarte.ch: 1
• msn.com: 1
• github.com: 1
• biol.lu.se: 1

---

Issue and Pull Request metadata

Last synced: 1 day ago

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/adokter/bioRad

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Package metadata

• Total packages: 1
• Total downloads:
  • cran: 769 last-month
• Total dependent packages: 0
• Total dependent repositories: 0
• Total versions: 14
• Total maintainers: 1

---

Dependencies

Score: 14.286032802705742