From 60477eddb4c57ca1c2e50340fa5ced6d814f6dfd Mon Sep 17 00:00:00 2001 From: James Azam Date: Tue, 31 Oct 2023 17:30:50 +0000 Subject: [PATCH] Keep CITATION and `citation.cff` in sync with DESCRIPTION (#467) * Add citation.cff file and associated GHA workflow * Add NEWS item * Update contents of CITATION to sync with DESCRIPTION * Revised NEWS item * Fix a path * Pull before push --- .Rbuildignore | 3 +- .github/workflows/update-citation-cff.yaml | 59 ++ CITATION.cff | 775 +++++++++++++++++++++ NEWS.md | 1 + inst/CITATION | 21 +- 5 files changed, 851 insertions(+), 8 deletions(-) create mode 100644 .github/workflows/update-citation-cff.yaml create mode 100644 CITATION.cff diff --git a/.Rbuildignore b/.Rbuildignore index 2824401fe..8fa3e90ca 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -24,4 +24,5 @@ ^\.devcontainer$ ^CRAN-SUBMISSION$ ^touchstone$ -^\.benchmark$ \ No newline at end of file +^\.benchmark$ +^CITATION\.cff$ diff --git a/.github/workflows/update-citation-cff.yaml b/.github/workflows/update-citation-cff.yaml new file mode 100644 index 000000000..93662175a --- /dev/null +++ b/.github/workflows/update-citation-cff.yaml @@ -0,0 +1,59 @@ +# 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: + push: + tags-ignore: + - '*' + paths: + - DESCRIPTION + - inst/CITATION + - .github/workflows/update-citation-cff.yaml + 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 pull --rebase origin ${{ github.ref.name }} + git push origin || echo "No changes to commit" + + + diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 000000000..09982d76b --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,775 @@ +# ----------------------------------------------------------- +# CITATION file created with {cffr} R package, v0.5.0 +# See also: https://docs.ropensci.org/cffr/ +# ----------------------------------------------------------- + +cff-version: 1.2.0 +message: 'To cite package "EpiNow2" in publications use:' +type: software +license: MIT +title: 'EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters' +version: 1.4.9000 +doi: 10.5281/zenodo.3957489 +abstract: Estimates the time-varying reproduction number, rate of spread, and doubling + time using a range of open-source tools (Abbott et al. (2020) ), + and current best practices (Gostic et al. (2020) ). + It aims to help users avoid some of the limitations of naive implementations in + a framework that is informed by community feedback and is actively supported. +authors: +- family-names: Abbott + given-names: Sam + email: sam.abbott@lshtm.ac.uk + orcid: https://orcid.org/0000-0001-8057-8037 +- family-names: Hellewell + given-names: Joel + email: joel.hellewell@lshtm.ac.uk + orcid: https://orcid.org/0000-0003-2683-0849 +- family-names: Sherratt + given-names: Katharine + email: katharine.sherratt@lshtm.ac.uk +- family-names: Gostic + given-names: Katelyn + email: kgostic@uchicago.edu +- family-names: Hickson + given-names: Joe + email: joseph.hickson@metoffice.gov.uk +- family-names: Badr + given-names: Hamada S. + email: badr@jhu.edu + orcid: https://orcid.org/0000-0002-9808-2344 +- family-names: DeWitt + given-names: Michael + email: me.dewitt.jr@gmail.com + orcid: https://orcid.org/0000-0001-8940-1967 +- family-names: Azam + given-names: James M. + email: james.azam@lshtm.ac.uk + orcid: https://orcid.org/0000-0001-5782-7330 +- name: EpiForecasts +- family-names: Funk + given-names: Sebastian + email: sebastian.funk@lshtm.ac.uk + orcid: https://orcid.org/0000-0002-2842-3406 +preferred-citation: + type: manual + title: 'EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological + Parameters' + authors: + - name: Sam Abbott + - name: Joel Hellewell + - name: Katharine Sherratt + - name: Katelyn Gostic + - name: Joe Hickson + - name: Hamada S. Badr + - name: Michael DeWitt + - name: Robin Thompson + - name: EpiForecasts + - name: Sebastian Funk + year: '2020' + doi: 10.5281/zenodo.3957489 +repository: https://CRAN.R-project.org/package=EpiNow2 +repository-code: https://github.com/epiforecasts/EpiNow2 +url: https://epiforecasts.io/EpiNow2/ +contact: +- family-names: Abbott + given-names: Sam + email: sam.abbott@lshtm.ac.uk + orcid: https://orcid.org/0000-0001-8057-8037 +keywords: +- backcalculation +- covid-19 +- gaussian-processes +- open-source +- reproduction-number +- rstats +- stan +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 + location: + name: Vienna, Austria + year: '2023' + institution: + name: R Foundation for Statistical Computing + version: '>= 3.5.0' +- type: software + title: data.table + abstract: 'data.table: Extension of `data.frame`' + notes: Imports + url: https://r-datatable.com + repository: https://CRAN.R-project.org/package=data.table + authors: + - family-names: Dowle + given-names: Matt + email: mattjdowle@gmail.com + - family-names: Srinivasan + given-names: Arun + email: asrini@pm.me + year: '2023' +- type: software + title: futile.logger + abstract: 'futile.logger: A Logging Utility for R' + notes: Imports + repository: https://CRAN.R-project.org/package=futile.logger + authors: + - family-names: Rowe + given-names: Brian Lee Yung + year: '2023' + version: '>= 1.4' +- type: software + title: future + abstract: 'future: Unified Parallel and Distributed Processing in R for Everyone' + notes: Imports + url: https://future.futureverse.org + repository: https://CRAN.R-project.org/package=future + authors: + - family-names: Bengtsson + given-names: Henrik + email: henrikb@braju.com + year: '2023' +- type: software + title: future.apply + abstract: 'future.apply: Apply Function to Elements in Parallel using Futures' + notes: Imports + url: https://future.apply.futureverse.org + repository: https://CRAN.R-project.org/package=future.apply + authors: + - family-names: Bengtsson + given-names: Henrik + email: henrikb@braju.com + year: '2023' +- 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 + year: '2023' +- type: software + title: lifecycle + abstract: 'lifecycle: Manage the Life Cycle of your Package Functions' + notes: Imports + url: https://lifecycle.r-lib.org/ + repository: https://CRAN.R-project.org/package=lifecycle + authors: + - family-names: Henry + given-names: Lionel + email: lionel@rstudio.com + - family-names: Wickham + given-names: Hadley + email: hadley@rstudio.com + orcid: https://orcid.org/0000-0003-4757-117X + year: '2023' +- 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: '2023' +- type: software + title: methods + abstract: 'R: A Language and Environment for Statistical Computing' + notes: Imports + authors: + - name: R Core Team + location: + name: Vienna, Austria + year: '2023' + institution: + name: R Foundation for Statistical Computing +- type: software + title: patchwork + abstract: 'patchwork: The Composer of Plots' + notes: Imports + url: https://patchwork.data-imaginist.com + repository: https://CRAN.R-project.org/package=patchwork + authors: + - family-names: Pedersen + given-names: Thomas Lin + email: thomasp85@gmail.com + orcid: https://orcid.org/0000-0002-5147-4711 + year: '2023' +- type: software + title: progressr + abstract: 'progressr: An Inclusive, Unifying API for Progress Updates' + notes: Imports + url: https://progressr.futureverse.org + repository: https://CRAN.R-project.org/package=progressr + authors: + - family-names: Bengtsson + given-names: Henrik + email: henrikb@braju.com + year: '2023' +- type: software + title: purrr + abstract: 'purrr: Functional Programming Tools' + notes: Imports + url: https://purrr.tidyverse.org/ + repository: https://CRAN.R-project.org/package=purrr + authors: + - family-names: Wickham + given-names: Hadley + email: hadley@rstudio.com + orcid: https://orcid.org/0000-0003-4757-117X + - family-names: Henry + given-names: Lionel + email: lionel@rstudio.com + year: '2023' +- type: software + title: R.utils + abstract: 'R.utils: Various Programming Utilities' + notes: Imports + url: https://henrikbengtsson.github.io/R.utils/ + repository: https://CRAN.R-project.org/package=R.utils + authors: + - family-names: Bengtsson + given-names: Henrik + email: henrikb@braju.com + year: '2023' + version: '>= 2.0.0' +- type: software + title: Rcpp + abstract: 'Rcpp: Seamless R and C++ Integration' + notes: Imports + url: https://www.rcpp.org + repository: https://CRAN.R-project.org/package=Rcpp + authors: + - family-names: Eddelbuettel + given-names: Dirk + - family-names: Francois + given-names: Romain + - family-names: Allaire + given-names: JJ + - family-names: Ushey + given-names: Kevin + - family-names: Kou + given-names: Qiang + - family-names: Russell + given-names: Nathan + - family-names: Ucar + given-names: Inaki + - family-names: Bates + given-names: Douglas + - family-names: Chambers + given-names: John + year: '2023' + version: '>= 0.12.0' +- 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: '2023' + version: '>= 0.4.7' +- type: software + title: rstan + abstract: 'rstan: R Interface to Stan' + notes: Imports + url: https://mc-stan.org/rstan/ + repository: https://CRAN.R-project.org/package=rstan + authors: + - family-names: Guo + given-names: Jiqiang + email: guojq28@gmail.com + - family-names: Gabry + given-names: Jonah + email: jsg2201@columbia.edu + - family-names: Goodrich + given-names: Ben + email: benjamin.goodrich@columbia.edu + - family-names: Johnson + given-names: Andrew + email: andrew.johnson@arjohnsonau.com + - family-names: Weber + given-names: Sebastian + email: sdw.post@waebers.de + year: '2023' + version: '>= 2.26.0' +- type: software + title: rstantools + abstract: 'rstantools: Tools for Developing R Packages Interfacing with ''Stan''' + notes: Imports + url: https://mc-stan.org/rstantools/ + repository: https://CRAN.R-project.org/package=rstantools + authors: + - family-names: Gabry + given-names: Jonah + email: jsg2201@columbia.edu + - family-names: Goodrich + given-names: Ben + email: benjamin.goodrich@columbia.edu + - family-names: Lysy + given-names: Martin + email: mlysy@uwaterloo.ca + - family-names: Johnson + given-names: Andrew + year: '2023' + version: '>= 2.2.0' +- type: software + title: runner + abstract: 'runner: Running Operations for Vectors' + notes: Imports + url: https://github.com/gogonzo/runner + repository: https://CRAN.R-project.org/package=runner + authors: + - family-names: Kałędkowski + given-names: Dawid + email: dawid.kaledkowski@gmail.com + orcid: https://orcid.org/0000-0001-9533-457X + year: '2023' +- type: software + title: scales + abstract: 'scales: Scale Functions for Visualization' + notes: Imports + url: https://scales.r-lib.org + repository: https://CRAN.R-project.org/package=scales + authors: + - family-names: Wickham + given-names: Hadley + email: hadley@rstudio.com + - family-names: Seidel + given-names: Dana + year: '2023' +- type: software + title: stats + abstract: 'R: A Language and Environment for Statistical Computing' + notes: Imports + authors: + - name: R Core Team + location: + name: Vienna, Austria + year: '2023' + institution: + name: R Foundation for Statistical Computing +- type: software + title: truncnorm + abstract: 'truncnorm: Truncated Normal Distribution' + notes: Imports + url: https://github.com/olafmersmann/truncnorm + repository: https://CRAN.R-project.org/package=truncnorm + authors: + - family-names: Mersmann + given-names: Olaf + email: olafm@p-value.net + - family-names: Trautmann + given-names: Heike + - family-names: Steuer + given-names: Detlef + - family-names: Bornkamp + given-names: Björn + year: '2023' +- type: software + title: utils + abstract: 'R: A Language and Environment for Statistical Computing' + notes: Imports + authors: + - name: R Core Team + location: + name: Vienna, Austria + year: '2023' + institution: + name: R Foundation for Statistical Computing +- type: software + title: covr + abstract: 'covr: Test Coverage for Packages' + notes: Suggests + url: https://covr.r-lib.org + repository: https://CRAN.R-project.org/package=covr + authors: + - family-names: Hester + given-names: Jim + email: james.f.hester@gmail.com + year: '2023' +- type: software + title: dplyr + abstract: 'dplyr: A Grammar of Data Manipulation' + notes: Suggests + 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: '2023' +- type: software + title: here + abstract: 'here: A Simpler Way to Find Your Files' + notes: Suggests + url: https://here.r-lib.org/ + repository: https://CRAN.R-project.org/package=here + authors: + - family-names: Müller + given-names: Kirill + email: krlmlr+r@mailbox.org + orcid: https://orcid.org/0000-0002-1416-3412 + year: '2023' +- type: software + title: kableExtra + abstract: 'kableExtra: Construct Complex Table with ''kable'' and Pipe Syntax' + notes: Suggests + url: http://haozhu233.github.io/kableExtra/ + repository: https://CRAN.R-project.org/package=kableExtra + authors: + - family-names: Zhu + given-names: Hao + email: haozhu233@gmail.com + orcid: https://orcid.org/0000-0002-3386-6076 + year: '2023' +- 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: '2023' +- type: software + title: magrittr + abstract: 'magrittr: A Forward-Pipe Operator for R' + notes: Suggests + url: https://magrittr.tidyverse.org + repository: https://CRAN.R-project.org/package=magrittr + authors: + - family-names: Bache + given-names: Stefan Milton + email: stefan@stefanbache.dk + - family-names: Wickham + given-names: Hadley + email: hadley@rstudio.com + year: '2023' +- type: software + title: precommit + abstract: 'precommit: Pre-Commit Hooks' + notes: Suggests + url: https://lorenzwalthert.github.io/precommit/ + repository: https://CRAN.R-project.org/package=precommit + authors: + - family-names: Walthert + given-names: Lorenz + year: '2023' +- 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: '2023' +- type: software + title: spelling + abstract: 'spelling: Tools for Spell Checking in R' + notes: Suggests + url: https://docs.ropensci.org/spelling/ + repository: https://CRAN.R-project.org/package=spelling + authors: + - family-names: Ooms + given-names: Jeroen + email: jeroen@berkeley.edu + orcid: https://orcid.org/0000-0002-4035-0289 + - family-names: Hester + given-names: Jim + email: james.hester@rstudio.com + year: '2023' +- type: software + title: styler + abstract: 'styler: Non-Invasive Pretty Printing of R Code' + notes: Suggests + url: https://styler.r-lib.org + repository: https://CRAN.R-project.org/package=styler + authors: + - family-names: Müller + given-names: Kirill + email: kirill@cynkra.com + orcid: https://orcid.org/0000-0002-1416-3412 + - family-names: Walthert + given-names: Lorenz + email: lorenz.walthert@icloud.com + year: '2023' +- 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: '2023' +- type: software + title: tidyr + abstract: 'tidyr: Tidy Messy Data' + notes: Suggests + 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: '2023' +- type: software + title: usethis + abstract: 'usethis: Automate Package and Project Setup' + notes: Suggests + url: https://usethis.r-lib.org + repository: https://CRAN.R-project.org/package=usethis + authors: + - family-names: Wickham + given-names: Hadley + email: hadley@posit.co + orcid: https://orcid.org/0000-0003-4757-117X + - family-names: Bryan + given-names: Jennifer + email: jenny@posit.co + orcid: https://orcid.org/0000-0002-6983-2759 + - family-names: Barrett + given-names: Malcolm + email: malcolmbarrett@gmail.com + orcid: https://orcid.org/0000-0003-0299-5825 + - family-names: Teucher + given-names: Andy + email: andy.teucher@posit.co + orcid: https://orcid.org/0000-0002-7840-692X + year: '2023' +- type: software + title: withr + abstract: 'withr: Run Code ''With'' Temporarily Modified Global State' + notes: Suggests + url: https://withr.r-lib.org + repository: https://CRAN.R-project.org/package=withr + authors: + - family-names: Hester + given-names: Jim + - family-names: Henry + given-names: Lionel + email: lionel@rstudio.com + - family-names: Müller + given-names: Kirill + email: krlmlr+r@mailbox.org + - family-names: Ushey + given-names: Kevin + email: kevinushey@gmail.com + - family-names: Wickham + given-names: Hadley + email: hadley@rstudio.com + - family-names: Chang + given-names: Winston + year: '2023' +- type: software + title: BH + abstract: 'BH: Boost C++ Header Files' + notes: LinkingTo + url: https://dirk.eddelbuettel.com/code/bh.html + repository: https://CRAN.R-project.org/package=BH + authors: + - family-names: Eddelbuettel + given-names: Dirk + - family-names: Emerson + given-names: John W. + - family-names: Kane + given-names: Michael J. + year: '2023' + version: '>= 1.66.0' +- type: software + title: RcppEigen + abstract: 'RcppEigen: ''Rcpp'' Integration for the ''Eigen'' Templated Linear Algebra + Library' + notes: LinkingTo + url: https://dirk.eddelbuettel.com/code/rcpp.eigen.html + repository: https://CRAN.R-project.org/package=RcppEigen + authors: + - family-names: Bates + given-names: Douglas + - family-names: Eddelbuettel + given-names: Dirk + - family-names: Francois + given-names: Romain + - family-names: Eigen + given-names: Yixuan Qiu; the authors of Eigen for the included version of + year: '2023' + version: '>= 0.3.3.3.0' +- type: software + title: RcppParallel + abstract: 'RcppParallel: Parallel Programming Tools for ''Rcpp''' + notes: LinkingTo + url: https://rcppcore.github.io/RcppParallel/ + repository: https://CRAN.R-project.org/package=RcppParallel + authors: + - family-names: Allaire + given-names: JJ + email: jj@rstudio.com + - family-names: Francois + given-names: Romain + - family-names: Ushey + given-names: Kevin + email: kevin@rstudio.com + - family-names: Vandenbrouck + given-names: Gregory + - family-names: Geelnard + given-names: Marcus + - name: Intel + year: '2023' + version: '>= 5.0.1' +- type: software + title: StanHeaders + abstract: 'StanHeaders: C++ Header Files for Stan' + notes: LinkingTo + url: https://mc-stan.org/ + repository: https://CRAN.R-project.org/package=StanHeaders + authors: + - family-names: Goodrich + given-names: Ben + email: benjamin.goodrich@columbia.edu + - family-names: Gelman + given-names: Andrew + - family-names: Carpenter + given-names: Bob + - family-names: Hoffman + given-names: Matt + - family-names: Lee + given-names: Daniel + - family-names: Betancourt + given-names: Michael + - family-names: Brubaker + given-names: Marcus + - family-names: Guo + given-names: Jiqiang + - family-names: Li + given-names: Peter + - family-names: Riddell + given-names: Allen + - family-names: Inacio + given-names: Marco + - family-names: Morris + given-names: Mitzi + - family-names: Arnold + given-names: Jeffrey + - family-names: Goedman + given-names: Rob + - family-names: Lau + given-names: Brian + - family-names: Trangucci + given-names: Rob + - family-names: Gabry + given-names: Jonah + - family-names: Kucukelbir + given-names: Alp + - family-names: Grant + given-names: Robert + - family-names: Tran + given-names: Dustin + - family-names: Malecki + given-names: Michael + - family-names: Gao + given-names: Yuanjun + year: '2023' + version: '>= 2.26.0' +identifiers: +- type: url + value: https://epiforecasts.io/EpiNow2/dev/ diff --git a/NEWS.md b/NEWS.md index fabb049d2..9489c6cdc 100644 --- a/NEWS.md +++ b/NEWS.md @@ -9,6 +9,7 @@ * Two new vignettes have been added to cover the workflow and example uses. By @sbfnk in #458 and reviewed by @jamesmbaazam. * Removed references to the no longer existing `forecast_infections` function. By @sbfnk in #460 and reviewed by @seabbs. * The contribution guide has been improved to include more detail on ways to contribute new features/enhancements, report bugs, and improve or suggest vignettes. By @jamesmbaazam in #464 and reviewed by @seabbs. +* Updated the code in `inst/CITATION` and added a GitHub Actions workflow to auto-generate `citation.cff` so that the two citation files are always in sync with `DESCRIPTION`. By @jamesmbazam in #467, with contributions from @Bisaloo, and reviewed by @seabbs and @sbfnk. ## Package diff --git a/inst/CITATION b/inst/CITATION index 36fb96915..1a9a3c6d2 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -1,10 +1,17 @@ +# Code copied from citation() +author <- meta$`Authors@R` +if (length(author)) { + aar <- .read_authors_at_R_field(author) + author <- Filter(function(e) { + !(is.null(e$given) && is.null(e$family)) && !is.na(match("aut", + e$role)) + }, aar) +} + bibentry( bibtype = "Manual", - title = "EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters", - author = c(person("Sam Abbott"), person("Joel Hellewell"), - person("Katharine Sherratt"), person("Katelyn Gostic"), - person("Joe Hickson"), person("Hamada S. Badr"), person("Michael DeWitt"), - person("Robin Thompson"), person("EpiForecasts"), person("Sebastian Funk")), - year = "2020", - doi = "10.5281/zenodo.3957489" + title = paste0(meta$Package, ": ", gsub("[[:space:]]+", " ", meta$Title)), + author = author, + year = format(meta$Date, "%Y"), + doi = "10.5281/zenodo.3957489" )