diff --git a/.Rbuildignore b/.Rbuildignore index cbc29aa..9c38ef6 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -9,3 +9,4 @@ ^\.Rproj\.user$ ^\.lintr$ ^cran-comments\.md$ +^CITATION\.cff$ diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..e6a0300 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,430 @@ +# -------------------------------------------- +# CITATION file created with {cffr} R package +# See also: https://docs.ropensci.org/cffr/ +# -------------------------------------------- + +cff-version: 1.2.0 +message: 'To cite package "epiCo" in publications use:' +type: software +license: MIT +title: 'epiCo: Statistical and Visualization Tools for the Analysis of Outbreaks of + Vector-Borne Diseases (VBDs) in Colombia' +version: 1.0.0 +abstract: Provides statistical and visualization tools for the analysis of demographic + indicators, and spatio-temporal behavior and characterization of outbreaks of vector-borne + diseases (VBDs) in Colombia. It implements travel times estimated from [Bravo-Vega + C., Santos-Vega M., & Cordovez J.M. (2022)], + and the endemic chanel method [Bortman, M. (1999)]. +authors: +- family-names: Umaña + given-names: Juan D. + email: jd.umana10@uniandes.edu.co + orcid: https://orcid.org/0000-0003-0316-6164 +- family-names: Montenegro-Torres + given-names: Juan + email: jf.montenegro@uniandes.edu.co + orcid: https://orcid.org/0000-0003-2755-4743 +- family-names: Otero + given-names: Julian + email: jd.otero10@uniandes.edu.co + orcid: https://orcid.org/0009-0006-0429-7747 +repository-code: https://github.com/epiverse-trace/epiCo +url: https://epiverse-trace.github.io/epiCo/ +contact: +- family-names: Umaña + given-names: Juan D. + email: jd.umana10@uniandes.edu.co + orcid: https://orcid.org/0000-0003-0316-6164 +keywords: +- colombia +- decision-support +- demographics +- epiverse +- outbreak-analysis +- r +- r-package +- spatio-temporal-analysis +- vector-borne-diseases +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: '>= 3.2.0' +- 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 +- 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: ggraph + abstract: 'ggraph: An Implementation of Grammar of Graphics for Graphs and Networks' + notes: Imports + url: https://ggraph.data-imaginist.com + repository: https://CRAN.R-project.org/package=ggraph + authors: + - family-names: Pedersen + given-names: Thomas Lin + email: thomasp85@gmail.com + orcid: https://orcid.org/0000-0002-5147-4711 + year: '2024' + doi: 10.32614/CRAN.package.ggraph +- type: software + title: igraph + abstract: 'igraph: Network Analysis and Visualization' + notes: Imports + url: https://r.igraph.org/ + repository: https://CRAN.R-project.org/package=igraph + authors: + - family-names: Csárdi + given-names: Gábor + email: csardi.gabor@gmail.com + orcid: https://orcid.org/0000-0001-7098-9676 + - family-names: Nepusz + given-names: Tamás + email: ntamas@gmail.com + orcid: https://orcid.org/0000-0002-1451-338X + - family-names: Traag + given-names: Vincent + orcid: https://orcid.org/0000-0003-3170-3879 + - family-names: Horvát + given-names: Szabolcs + email: szhorvat@gmail.com + orcid: https://orcid.org/0000-0002-3100-523X + - family-names: Zanini + given-names: Fabio + email: fabio.zanini@unsw.edu.au + orcid: https://orcid.org/0000-0001-7097-8539 + - family-names: Noom + given-names: Daniel + - family-names: Müller + given-names: Kirill + email: kirill@cynkra.com + orcid: https://orcid.org/0000-0002-1416-3412 + year: '2024' + doi: 10.32614/CRAN.package.igraph +- type: software + title: incidence + abstract: 'incidence: Compute, Handle, Plot and Model Incidence of Dated Events' + notes: Imports + url: https://www.repidemicsconsortium.org/incidence/ + repository: https://CRAN.R-project.org/package=incidence + authors: + - family-names: Jombart + given-names: Thibaut + email: thibautjombart@gmail.com + - family-names: Kamvar + given-names: Zhian N. + email: zkamvar@gmail.com + orcid: https://orcid.org/0000-0003-1458-7108 + - family-names: FitzJohn + given-names: Rich + email: rich.fitzjohn@gmail.com + year: '2024' + doi: 10.32614/CRAN.package.incidence +- type: software + title: leaflet + abstract: 'leaflet: Create Interactive Web Maps with the JavaScript ''Leaflet'' + Library' + notes: Imports + url: https://rstudio.github.io/leaflet/ + repository: https://CRAN.R-project.org/package=leaflet + authors: + - family-names: Cheng + given-names: Joe + email: joe@posit.co + - family-names: Schloerke + given-names: Barret + email: barret@posit.co + orcid: https://orcid.org/0000-0001-9986-114X + - family-names: Karambelkar + given-names: Bhaskar + - family-names: Xie + given-names: Yihui + year: '2024' + doi: 10.32614/CRAN.package.leaflet +- 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: magrittr + abstract: 'magrittr: A Forward-Pipe Operator for R' + notes: Imports + 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: '2024' + doi: 10.32614/CRAN.package.magrittr +- type: software + title: RColorBrewer + abstract: 'RColorBrewer: ColorBrewer Palettes' + notes: Imports + repository: https://CRAN.R-project.org/package=RColorBrewer + authors: + - family-names: Neuwirth + given-names: Erich + email: erich.neuwirth@univie.ac.at + year: '2024' + doi: 10.32614/CRAN.package.RColorBrewer +- 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: 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@posit.co + - family-names: Pedersen + given-names: Thomas Lin + email: thomas.pedersen@posit.co + orcid: https://orcid.org/0000-0002-5147-4711 + - family-names: Seidel + given-names: Dana + year: '2024' + doi: 10.32614/CRAN.package.scales +- type: software + title: spdep + abstract: 'spdep: Spatial Dependence: Weighting Schemes, Statistics' + notes: Imports + url: https://github.com/r-spatial/spdep/ + repository: https://CRAN.R-project.org/package=spdep + authors: + - family-names: Bivand + given-names: Roger + email: Roger.Bivand@nhh.no + orcid: https://orcid.org/0000-0003-2392-6140 + year: '2024' + doi: 10.32614/CRAN.package.spdep +- 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' + doi: 10.32614/CRAN.package.stats +- type: software + title: treemapify + abstract: 'treemapify: Draw Treemaps in ''ggplot2''' + notes: Imports + url: https://wilkox.org/treemapify/ + repository: https://CRAN.R-project.org/package=treemapify + authors: + - family-names: Wilkins + given-names: David + email: david@wilkox.org + orcid: https://orcid.org/0000-0002-3385-8981 + year: '2024' + doi: 10.32614/CRAN.package.treemapify +- 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' + doi: 10.32614/CRAN.package.utils +- type: software + title: checkmate + abstract: 'checkmate: Fast and Versatile Argument Checks' + notes: Suggests + url: https://mllg.github.io/checkmate/ + repository: https://CRAN.R-project.org/package=checkmate + authors: + - family-names: Lang + given-names: Michel + email: michellang@gmail.com + orcid: https://orcid.org/0000-0001-9754-0393 + year: '2024' + doi: 10.32614/CRAN.package.checkmate +- 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: '2024' + doi: 10.32614/CRAN.package.covr +- 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: 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: 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' +