diff --git a/.Rbuildignore b/.Rbuildignore index dd3bc837..e522dedc 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -18,3 +18,4 @@ inst/extdata/vpts.txt.zip ^doc$ ^Meta$ ^rosm\.cache$ +^CITATION\.cff$ diff --git a/.github/workflows/update-citation-cff.yaml b/.github/workflows/update-citation-cff.yaml new file mode 100644 index 00000000..4d2e1a11 --- /dev/null +++ b/.github/workflows/update-citation-cff.yaml @@ -0,0 +1,58 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/master/examples +# The action runs when: +# - A new release is published +# - The DESCRIPTION or inst/CITATION are modified +# - Can be run manually +# For customizing the triggers, visit https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows +on: + release: + types: [published] + push: + branches: [master, main] + paths: + - DESCRIPTION + - inst/CITATION + workflow_dispatch: + +name: Update CITATION.cff + +jobs: + update-citation-cff: + runs-on: macos-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: + - uses: actions/checkout@v3 + - uses: r-lib/actions/setup-r@v2 + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: | + any::cffr + any::V8 + + - name: Update CITATION.cff + run: | + + library(cffr) + + # Customize with your own code + # See https://docs.ropensci.org/cffr/articles/cffr.html + + # Write your own keys + mykeys <- list() + + # Create your CITATION.cff file + cff_write(keys = mykeys) + + shell: Rscript {0} + + - name: Commit results + run: | + git config --local user.name "github-actions[bot]" + git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" + git add CITATION.cff + git commit -m 'Update CITATION.cff' || echo "No changes to commit" + git push origin || echo "No changes to commit" + + + diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 00000000..7a171f94 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,670 @@ +# -------------------------------------------- +# 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" for + a software paper describing package and methodologies.' +authors: +- family-names: Dokter + given-names: Adriaan M. + email: biorad@cornell.edu + orcid: https://orcid.org/0000-0001-6573-066X +- family-names: Desmet + given-names: Peter + email: peter.desmet@inbo.be + orcid: https://orcid.org/0000-0002-8442-8025 +- family-names: Kranstauber + given-names: Bart + email: b.kranstauber@uva.nl + orcid: https://orcid.org/0000-0001-8303-780X +- family-names: Nilsson + given-names: Cecilia + email: cecilia.nilsson709@gmail.com + orcid: https://orcid.org/0000-0001-8957-4411 +- family-names: Van Hoey + given-names: Stijn + email: stijnvanhoey@gmail.com + 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: biorad@cornell.edu + orcid: https://orcid.org/0000-0001-6573-066X + - family-names: Desmet + given-names: Peter + email: peter.desmet@inbo.be + orcid: https://orcid.org/0000-0002-8442-8025 + - family-names: Spaaks + given-names: Jurriaan H. + - family-names: Van Hoey + given-names: Stijn + email: stijnvanhoey@gmail.com + 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: cecilia.nilsson709@gmail.com + 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: biorad@cornell.edu + 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 +references: +- type: software + title: 'R: A Language and Environment for Statistical Computing' + notes: Depends + url: https://www.R-project.org/ + authors: + - name: R Core Team + institution: + name: R Foundation for Statistical Computing + address: Vienna, Austria + year: '2024' + version: '>= 3.5.0' +- type: software + title: assertthat + abstract: 'assertthat: Easy Pre and Post Assertions' + notes: Imports + repository: https://CRAN.R-project.org/package=assertthat + authors: + - family-names: Wickham + given-names: Hadley + email: hadley@rstudio.com + year: '2024' + doi: 10.32614/CRAN.package.assertthat +- type: software + title: curl + abstract: 'curl: A Modern and Flexible Web Client for R' + notes: Imports + url: https://jeroen.r-universe.dev/curl + repository: https://CRAN.R-project.org/package=curl + authors: + - family-names: Ooms + given-names: Jeroen + email: jeroen@berkeley.edu + orcid: https://orcid.org/0000-0002-4035-0289 + year: '2024' + doi: 10.32614/CRAN.package.curl +- type: software + title: dplyr + abstract: 'dplyr: A Grammar of Data Manipulation' + notes: Imports + url: https://dplyr.tidyverse.org + repository: https://CRAN.R-project.org/package=dplyr + authors: + - family-names: Wickham + given-names: Hadley + email: hadley@posit.co + orcid: https://orcid.org/0000-0003-4757-117X + - family-names: François + given-names: Romain + orcid: https://orcid.org/0000-0002-2444-4226 + - family-names: Henry + given-names: Lionel + - family-names: Müller + given-names: Kirill + orcid: https://orcid.org/0000-0002-1416-3412 + - family-names: Vaughan + given-names: Davis + email: davis@posit.co + orcid: https://orcid.org/0000-0003-4777-038X + year: '2024' + doi: 10.32614/CRAN.package.dplyr + version: '>= 1.1.0' +- type: software + title: fields + abstract: 'fields: Tools for Spatial Data' + notes: Imports + url: https://github.com/dnychka/fieldsRPackage + repository: https://CRAN.R-project.org/package=fields + authors: + - family-names: Nychka + given-names: Douglas + email: douglasnychka@gmail.com + - family-names: Furrer + given-names: Reinhard + email: reinhard.furrer@math.uzh.ch + - family-names: Paige + given-names: John + email: paigejo@uw.edu + - family-names: Sain + given-names: Stephan + email: sainsr2@gmail.com + - family-names: Gerber + given-names: Florian + email: flora.fauna.gerber@gmail.com + - family-names: Iverson + given-names: Matthew + email: miverson@mines.edu + - family-names: Johnson + given-names: Rider + year: '2024' + doi: 10.32614/CRAN.package.fields +- type: software + title: ggplot2 + abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics' + notes: Imports + url: https://ggplot2.tidyverse.org + repository: https://CRAN.R-project.org/package=ggplot2 + authors: + - family-names: Wickham + given-names: Hadley + email: hadley@posit.co + orcid: https://orcid.org/0000-0003-4757-117X + - family-names: Chang + given-names: Winston + orcid: https://orcid.org/0000-0002-1576-2126 + - family-names: Henry + given-names: Lionel + - family-names: Pedersen + given-names: Thomas Lin + email: thomas.pedersen@posit.co + orcid: https://orcid.org/0000-0002-5147-4711 + - family-names: Takahashi + given-names: Kohske + - family-names: Wilke + given-names: Claus + orcid: https://orcid.org/0000-0002-7470-9261 + - family-names: Woo + given-names: Kara + orcid: https://orcid.org/0000-0002-5125-4188 + - family-names: Yutani + given-names: Hiroaki + orcid: https://orcid.org/0000-0002-3385-7233 + - family-names: Dunnington + given-names: Dewey + orcid: https://orcid.org/0000-0002-9415-4582 + - family-names: Brand + given-names: Teun + name-particle: van den + orcid: https://orcid.org/0000-0002-9335-7468 + year: '2024' + doi: 10.32614/CRAN.package.ggplot2 +- type: software + title: glue + abstract: 'glue: Interpreted String Literals' + notes: Imports + url: https://glue.tidyverse.org/ + repository: https://CRAN.R-project.org/package=glue + authors: + - family-names: Hester + given-names: Jim + orcid: https://orcid.org/0000-0002-2739-7082 + - family-names: Bryan + given-names: Jennifer + email: jenny@posit.co + orcid: https://orcid.org/0000-0002-6983-2759 + year: '2024' + doi: 10.32614/CRAN.package.glue +- type: software + title: graphics + abstract: 'R: A Language and Environment for Statistical Computing' + notes: Imports + authors: + - name: R Core Team + institution: + name: R Foundation for Statistical Computing + address: Vienna, Austria + year: '2024' +- type: software + title: jsonlite + abstract: 'jsonlite: A Simple and Robust JSON Parser and Generator for R' + notes: Imports + url: https://jeroen.r-universe.dev/jsonlite + repository: https://CRAN.R-project.org/package=jsonlite + authors: + - family-names: Ooms + given-names: Jeroen + email: jeroen@berkeley.edu + orcid: https://orcid.org/0000-0002-4035-0289 + year: '2024' + doi: 10.32614/CRAN.package.jsonlite +- type: software + title: lubridate + abstract: 'lubridate: Make Dealing with Dates a Little Easier' + notes: Imports + url: https://lubridate.tidyverse.org + repository: https://CRAN.R-project.org/package=lubridate + authors: + - family-names: Spinu + given-names: Vitalie + email: spinuvit@gmail.com + - family-names: Grolemund + given-names: Garrett + - family-names: Wickham + given-names: Hadley + year: '2024' + doi: 10.32614/CRAN.package.lubridate +- type: software + title: lutz + abstract: 'lutz: Look Up Time Zones of Point Coordinates' + notes: Imports + url: https://andyteucher.ca/lutz/ + repository: https://CRAN.R-project.org/package=lutz + authors: + - family-names: Teucher + given-names: Andy + email: andy.teucher@gmail.com + orcid: https://orcid.org/0000-0002-7840-692X + year: '2024' + doi: 10.32614/CRAN.package.lutz +- type: software + title: methods + abstract: 'R: A Language and Environment for Statistical Computing' + notes: Imports + authors: + - name: R Core Team + institution: + name: R Foundation for Statistical Computing + address: Vienna, Austria + year: '2024' +- type: software + title: raster + abstract: 'raster: Geographic Data Analysis and Modeling' + notes: Imports + url: https://rspatial.org/raster + repository: https://CRAN.R-project.org/package=raster + authors: + - family-names: Hijmans + given-names: Robert J. + email: r.hijmans@gmail.com + orcid: https://orcid.org/0000-0001-5872-2872 + year: '2024' + doi: 10.32614/CRAN.package.raster +- type: software + title: readr + abstract: 'readr: Read Rectangular Text Data' + notes: Imports + url: https://readr.tidyverse.org + repository: https://CRAN.R-project.org/package=readr + authors: + - family-names: Wickham + given-names: Hadley + email: hadley@posit.co + - family-names: Hester + given-names: Jim + - family-names: Bryan + given-names: Jennifer + email: jenny@posit.co + orcid: https://orcid.org/0000-0002-6983-2759 + year: '2024' + doi: 10.32614/CRAN.package.readr +- type: software + title: rhdf5 + abstract: 'rhdf5: R Interface to HDF5' + notes: Imports + url: https://github.com/grimbough/rhdf5 + repository: https://bioconductor.org/ + authors: + - family-names: Fischer + given-names: Bernd + - family-names: Smith + given-names: Mike + email: mike.smith@embl.de + orcid: https://orcid.org/0000-0002-7800-3848 + - family-names: Pau + given-names: Gregoire + year: '2024' + doi: 10.18129/B9.bioc.rhdf5 +- type: software + title: rlang + abstract: 'rlang: Functions for Base Types and Core R and ''Tidyverse'' Features' + notes: Imports + url: https://rlang.r-lib.org + repository: https://CRAN.R-project.org/package=rlang + authors: + - family-names: Henry + given-names: Lionel + email: lionel@posit.co + - family-names: Wickham + given-names: Hadley + email: hadley@posit.co + year: '2024' + doi: 10.32614/CRAN.package.rlang +- type: software + title: sf + abstract: 'sf: Simple Features for R' + notes: Imports + url: https://r-spatial.github.io/sf/ + repository: https://CRAN.R-project.org/package=sf + authors: + - family-names: Pebesma + given-names: Edzer + email: edzer.pebesma@uni-muenster.de + orcid: https://orcid.org/0000-0001-8049-7069 + year: '2024' + doi: 10.32614/CRAN.package.sf +- type: software + title: sp + abstract: 'sp: Classes and Methods for Spatial Data' + notes: Imports + url: https://github.com/edzer/sp/ + repository: https://CRAN.R-project.org/package=sp + authors: + - family-names: Pebesma + given-names: Edzer + email: edzer.pebesma@uni-muenster.de + - family-names: Bivand + given-names: Roger + email: Roger.Bivand@nhh.no + year: '2024' + doi: 10.32614/CRAN.package.sp +- type: software + title: stats + abstract: 'R: A Language and Environment for Statistical Computing' + notes: Imports + authors: + - name: R Core Team + institution: + name: R Foundation for Statistical Computing + address: Vienna, Austria + year: '2024' +- type: software + title: stringr + abstract: 'stringr: Simple, Consistent Wrappers for Common String Operations' + notes: Imports + url: https://stringr.tidyverse.org + repository: https://CRAN.R-project.org/package=stringr + authors: + - family-names: Wickham + given-names: Hadley + email: hadley@posit.co + year: '2024' + doi: 10.32614/CRAN.package.stringr +- type: software + title: suntools + abstract: 'suntools: Calculate Sun Position, Sunrise, Sunset, Solar Noon and Twilight' + notes: Imports + url: https://github.com/adokter/suntools/ + repository: https://CRAN.R-project.org/package=suntools + authors: + - family-names: Bivand + given-names: Roger + email: Roger.Bivand@nhh.no + orcid: https://orcid.org/0000-0003-2392-6140 + - family-names: Luque + given-names: Sebastian + year: '2024' + doi: 10.32614/CRAN.package.suntools +- type: software + title: tidyr + abstract: 'tidyr: Tidy Messy Data' + notes: Imports + url: https://tidyr.tidyverse.org + repository: https://CRAN.R-project.org/package=tidyr + authors: + - family-names: Wickham + given-names: Hadley + email: hadley@posit.co + - family-names: Vaughan + given-names: Davis + email: davis@posit.co + - family-names: Girlich + given-names: Maximilian + year: '2024' + doi: 10.32614/CRAN.package.tidyr +- type: software + title: tidyselect + abstract: 'tidyselect: Select from a Set of Strings' + notes: Imports + url: https://tidyselect.r-lib.org + repository: https://CRAN.R-project.org/package=tidyselect + authors: + - family-names: Henry + given-names: Lionel + email: lionel@posit.co + - family-names: Wickham + given-names: Hadley + email: hadley@posit.co + year: '2024' + doi: 10.32614/CRAN.package.tidyselect +- type: software + title: utils + abstract: 'R: A Language and Environment for Statistical Computing' + notes: Imports + authors: + - name: R Core Team + institution: + name: R Foundation for Statistical Computing + address: Vienna, Austria + year: '2024' +- type: software + title: viridis + abstract: 'viridis: Colorblind-Friendly Color Maps for R' + notes: Imports + url: https://sjmgarnier.github.io/viridis/ + repository: https://CRAN.R-project.org/package=viridis + authors: + - family-names: Garnier + given-names: Simon + email: garnier@njit.edu + year: '2024' + doi: 10.32614/CRAN.package.viridis +- 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: garnier@njit.edu + 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: thosjleeper@gmail.com + 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: dewey@fishandwhistle.net + 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: xie@yihui.name + 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: dewey@fishandwhistle.net + 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: jj@posit.co + - family-names: Xie + given-names: Yihui + email: xie@yihui.name + orcid: https://orcid.org/0000-0003-0645-5666 + - family-names: Dervieux + given-names: Christophe + email: cderv@posit.co + orcid: https://orcid.org/0000-0003-4474-2498 + - family-names: McPherson + given-names: Jonathan + email: jonathan@posit.co + - family-names: Luraschi + given-names: Javier + - family-names: Ushey + given-names: Kevin + email: kevin@posit.co + - family-names: Atkins + given-names: Aron + email: aron@posit.co + - family-names: Wickham + given-names: Hadley + email: hadley@posit.co + - family-names: Cheng + given-names: Joe + email: joe@posit.co + - family-names: Chang + given-names: Winston + email: winston@posit.co + - family-names: Iannone + given-names: Richard + email: rich@posit.co + 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: dewey@fishandwhistle.net + 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: hadley@posit.co + 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: lionel@posit.co + - family-names: Pedersen + given-names: Thomas Lin + email: thomas.pedersen@posit.co + orcid: https://orcid.org/0000-0002-5147-4711 + - family-names: Luciani + given-names: T Jake + email: jake@apache.org + - family-names: Decorde + given-names: Matthieu + email: matthieu.decorde@ens-lyon.fr + - family-names: Lise + given-names: Vaudor + email: lise.vaudor@ens-lyon.fr + 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: anders.henja@gmail.com + - family-names: Dokter + given-names: Adriaan M. + email: vol2birdr@cornell.edu + orcid: https://orcid.org/0000-0001-6573-066X + year: '2024' + doi: 10.32614/CRAN.package.vol2birdR + diff --git a/README.Rmd b/README.Rmd index 0dae5087..b5f4fa90 100644 --- a/README.Rmd +++ b/README.Rmd @@ -21,6 +21,10 @@ knitr::opts_chunk$set( [![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.13362111.svg)](https://doi.org/10.5281/zenodo.13362111) +[![vol2birdR CRAN status](https://www.r-pkg.org/badges/version/vol2birdR)](https://cran.r-project.org/package=vol2birdR) + + 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.