From fda7929c0aaf3249df62e6bebb2aeee8c128e495 Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Mon, 28 Apr 2025 10:10:42 +0200 Subject: [PATCH] docs and citation --- .Rbuildignore | 2 +- CITATION.cff | 1245 +++++++++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 18 +- NEWS.md | 4 + R/sysdata.rda | Bin 1208 -> 1354 bytes SESSION.md | 132 +++--- 6 files changed, 1333 insertions(+), 68 deletions(-) create mode 100644 CITATION.cff diff --git a/.Rbuildignore b/.Rbuildignore index 3a9512e..7db599e 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -11,5 +11,5 @@ ^_pkgdown\.yml$ ^docs$ ^pkgdown$ -^dev$ ^data-raw$ +^CITATION\.cff$ diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..6e787a4 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,1245 @@ +# -------------------------------------------- +# CITATION file created with {cffr} R package +# See also: https://docs.ropensci.org/cffr/ +# -------------------------------------------- + +cff-version: 1.2.0 +message: 'To cite package "FreesearchR" in publications use:' +type: software +license: AGPL-3.0-or-later +title: 'FreesearchR: A free and open-source browser based data analysis tool for researchers + with publication ready output' +version: 25.4.3 +doi: 10.5281/zenodo.14527429 +abstract: Easily evaluate and analysis clinical health data in your browser on a server + or on your own device. Import data from multiple sources, summarise, modify and + visualise data and export key metrics and regression analysis results in a publication + ready format. +authors: +- family-names: Damsbo + given-names: Andreas Gammelgaard + email: agdamsbo@clin.au.dk + orcid: https://orcid.org/0000-0002-7559-1154 +repository-code: https://github.com/agdamsbo/FreesearchR +url: https://agdamsbo.github.io/FreesearchR/ +contact: +- family-names: Damsbo + given-names: Andreas Gammelgaard + email: agdamsbo@clin.au.dk + orcid: https://orcid.org/0000-0002-7559-1154 +references: +- 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: '2025' + doi: 10.32614/CRAN.package.assertthat +- type: software + title: bslib + abstract: 'bslib: Custom ''Bootstrap'' ''Sass'' Themes for ''shiny'' and ''rmarkdown''' + notes: Imports + url: https://rstudio.github.io/bslib/ + repository: https://CRAN.R-project.org/package=bslib + authors: + - family-names: Sievert + given-names: Carson + email: carson@posit.co + orcid: https://orcid.org/0000-0002-4958-2844 + - family-names: Cheng + given-names: Joe + email: joe@posit.co + - family-names: Aden-Buie + given-names: Garrick + email: garrick@posit.co + orcid: https://orcid.org/0000-0002-7111-0077 + year: '2025' + doi: 10.32614/CRAN.package.bslib +- 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: '2025' + doi: 10.32614/CRAN.package.dplyr +- 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: '2025' + doi: 10.32614/CRAN.package.glue +- type: software + title: gtsummary + abstract: 'gtsummary: Presentation-Ready Data Summary and Analytic Result Tables' + notes: Imports + url: https://www.danieldsjoberg.com/gtsummary/ + repository: https://CRAN.R-project.org/package=gtsummary + authors: + - family-names: Sjoberg + given-names: Daniel D. + email: danield.sjoberg@gmail.com + orcid: https://orcid.org/0000-0003-0862-2018 + - family-names: Larmarange + given-names: Joseph + orcid: https://orcid.org/0000-0001-7097-700X + - family-names: Curry + given-names: Michael + orcid: https://orcid.org/0000-0002-0261-4044 + - family-names: Rua + given-names: Emily + name-particle: de la + orcid: https://orcid.org/0009-0000-8738-5561 + - family-names: Lavery + given-names: Jessica + orcid: https://orcid.org/0000-0002-2746-5647 + - family-names: Whiting + given-names: Karissa + orcid: https://orcid.org/0000-0002-4683-1868 + - family-names: Zabor + given-names: Emily C. + orcid: https://orcid.org/0000-0002-1402-4498 + year: '2025' + doi: 10.32614/CRAN.package.gtsummary +- type: software + title: here + abstract: 'here: A Simpler Way to Find Your Files' + notes: Imports + 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: '2025' + doi: 10.32614/CRAN.package.here +- type: software + title: quarto + abstract: 'quarto: R Interface to ''Quarto'' Markdown Publishing System' + notes: Imports + url: https://quarto-dev.github.io/quarto-r/ + repository: https://CRAN.R-project.org/package=quarto + authors: + - family-names: Allaire + given-names: JJ + email: jj@posit.co + orcid: https://orcid.org/0000-0003-0174-9868 + - family-names: Dervieux + given-names: Christophe + email: cderv@posit.co + orcid: https://orcid.org/0000-0003-4474-2498 + year: '2025' + doi: 10.32614/CRAN.package.quarto +- type: software + title: haven + abstract: 'haven: Import and Export ''SPSS'', ''Stata'' and ''SAS'' Files' + notes: Imports + url: https://haven.tidyverse.org + repository: https://CRAN.R-project.org/package=haven + authors: + - family-names: Wickham + given-names: Hadley + email: hadley@posit.co + - family-names: Miller + given-names: Evan + - family-names: Smith + given-names: Danny + year: '2025' + doi: 10.32614/CRAN.package.haven +- type: software + title: readODS + abstract: 'readODS: Read and Write ODS Files' + notes: Imports + url: https://docs.ropensci.org/readODS/ + repository: https://CRAN.R-project.org/package=readODS + authors: + - family-names: Schutten + given-names: Gerrit-Jan + email: phonixor@gmail.com + - family-names: Chan + given-names: Chung-hong + email: chainsawtiney@gmail.com + orcid: https://orcid.org/0000-0002-6232-7530 + - family-names: Brohan + given-names: Peter + email: peter.brohan@gmail.com + - family-names: Steuer + given-names: Detlef + email: steuer@hsu-hh.de + orcid: https://orcid.org/0000-0003-2676-5290 + - family-names: Leeper + given-names: Thomas J. + email: thosjleeper@gmail.com + orcid: https://orcid.org/0000-0003-4097-6326 + year: '2025' + doi: 10.32614/CRAN.package.readODS +- 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: '2025' + doi: 10.32614/CRAN.package.readr +- type: software + title: shiny + abstract: 'shiny: Web Application Framework for R' + notes: Imports + url: https://shiny.posit.co/ + repository: https://CRAN.R-project.org/package=shiny + authors: + - family-names: Chang + given-names: Winston + email: winston@posit.co + orcid: https://orcid.org/0000-0002-1576-2126 + - family-names: Cheng + given-names: Joe + email: joe@posit.co + - family-names: Allaire + given-names: JJ + email: jj@posit.co + - family-names: Sievert + given-names: Carson + email: carson@posit.co + orcid: https://orcid.org/0000-0002-4958-2844 + - family-names: Schloerke + given-names: Barret + email: barret@posit.co + orcid: https://orcid.org/0000-0001-9986-114X + - family-names: Xie + given-names: Yihui + email: yihui@posit.co + - 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family-names: Wickham + given-names: Hadley + email: hadley@posit.co + year: '2025' + doi: 10.32614/CRAN.package.testthat + version: '>= 3.0.0' +- type: software + title: shinytest + abstract: 'shinytest: Test Shiny Apps' + notes: Suggests + url: https://github.com/rstudio/shinytest + repository: https://CRAN.R-project.org/package=shinytest + authors: + - family-names: Chang + given-names: Winston + email: winston@posit.co + - family-names: Csárdi + given-names: Gábor + email: gabor@posit.co + - family-names: Wickham + given-names: Hadley + email: hadley@posit.co + year: '2025' + doi: 10.32614/CRAN.package.shinytest +- 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: '2025' + doi: 10.32614/CRAN.package.covr +- type: software + title: cffr + abstract: 'cffr: Generate Citation File Format (''cff'') Metadata for R Packages' + notes: Suggests + url: https://docs.ropensci.org/cffr/ + repository: https://CRAN.R-project.org/package=cffr + authors: + - family-names: Hernangómez + given-names: Diego + email: diego.hernangomezherrero@gmail.com + orcid: https://orcid.org/0000-0001-8457-4658 + year: '2025' + doi: 10.32614/CRAN.package.cffr +- 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: '2025' + version: '>= 3.5' + diff --git a/DESCRIPTION b/DESCRIPTION index 24d87ee..ecafe43 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,10 +1,13 @@ Package: FreesearchR -Title: Clinical Health Data Analysis -Version: 25.4.3 -Authors@R: - person("Andreas Gammelgaard", "Damsbo", , "agdamsbo@clin.au.dk", role = c("aut", "cre"), - comment = c(ORCID = "0000-0002-7559-1154")) -Description: Free and open source browser based clinical health data exploration and analysis with publication ready output. +Title: A free and open-source browser based data analysis tool for researchers with publication ready output +Version: 25.4.4 +Authors@R: c( + person("Andreas Gammelgaard", "Damsbo",email="agdamsbo@clin.au.dk", role = c("aut", "cre"), + comment = c(ORCID = "0000-0002-7559-1154")), + person("Jutta Mari Adelin", "Jørgensen", role="ctb"), + person("Anne Brink", "Behrndtz", role="ctb") + ) +Description: Easily evaluate and analysis clinical health data in your browser on a server or on your own device. Import data from multiple sources, summarise, modify and visualise data and export key metrics and regression analysis results in a publication ready format. License: AGPL (>= 3) Encoding: UTF-8 Roxygen: list(markdown = TRUE) @@ -73,7 +76,8 @@ Suggests: rmarkdown, testthat (>= 3.0.0), shinytest, - covr + covr, + cffr URL: https://github.com/agdamsbo/FreesearchR, https://agdamsbo.github.io/FreesearchR/ BugReports: https://github.com/agdamsbo/FreesearchR/issues VignetteBuilder: knitr diff --git a/NEWS.md b/NEWS.md index 3dd549c..4336c49 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# FreesearchR 25.4.4 + +Minor updates in docs and easier citation. + # FreesearchR 25.4.3 - *NEW*: Added a variables type filter to easily exclude unwanted types. This also includes having data type rather than data class in the summary table. Will evaluate. 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