From d0b54f640cfbdbc633cf309cc3ff04b18d4b94e2 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Fri, 21 Oct 2022 21:56:54 +0200 Subject: [PATCH] Update contributors list --- DESCRIPTION | 48 +++++++++++++++++++++++++----------------------- NEWS.md | 4 ++-- R/rsi.R | 3 ++- man/AMR.Rd | 1 + pkgdown/extra.js | 15 ++++++++------- 5 files changed, 38 insertions(+), 33 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 2eaa4bfb..d8f4795c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,30 +1,31 @@ Package: AMR -Version: 1.8.2.9030 +Version: 1.8.2.9031 Date: 2022-10-21 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) - data analysis and to work with microbial and antimicrobial properties by - using evidence-based methods, as described in . + data analysis and to work with microbial and antimicrobial properties by + using evidence-based methods, as described in . Authors@R: c( - person(family = "Berends", c("Matthijs", "S."), role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7620-1800"), email = "m.berends@certe.nl"), - person(family = "Luz", c("Christian", "F."), role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-5809-5995")), - person(family = "Souverein", c("Dennis"), role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-0455-0336")), - person(family = "Hassing", c("Erwin", "E.", "A."), role = c("aut", "ctb")), - person(family = "Albers", c("Casper", "J."), role = "ths", comment = c(ORCID = "0000-0002-9213-6743")), - person(family = "Dutey-Magni", c("Peter"), role = "ctb", comment = c(ORCID = "0000-0002-8942-9836")), - person(family = "Fonville", c("Judith", "M."), role = "ctb"), - person(family = "Friedrich", c("Alex", "W."), role = "ths", comment = c(ORCID = "0000-0003-4881-038X")), - person(family = "Glasner", c("Corinna"), role = "ths", comment = c(ORCID = "0000-0003-1241-1328")), - person(family = "Hazenberg", c("Eric", "H.", "L.", "C.", "M."), role = "ctb"), - person(family = "Knight", c("Gwen"), role = "ctb", comment = c(ORCID = "0000-0002-7263-9896")), - person(family = "Lenglet", c("Annick"), role = "ctb", comment = c(ORCID = "0000-0003-2013-8405")), - person(family = "Meijer", c("Bart", "C."), role = "ctb"), - person(family = "Mykhailenko", c("Dmytro"), role = "ctb"), - person(family = "Mymrikov", c("Anton"), role = "ctb"), - person(family = "Ny", c("Sofia"), role = "ctb", comment = c(ORCID = "0000-0002-2017-1363")), - person(family = "Schade", c("Rogier", "P."), role = "ctb"), - person(family = "Sinha", c("Bhanu", "N.", "M."), role = "ths", comment = c(ORCID = "0000-0003-1634-0010")), - person(family = "Underwood", c("Anthony"), role = "ctb", comment = c(ORCID = "0000-0002-8547-4277"))) + person(family = "Berends", c("Matthijs", "S."), role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7620-1800"), email = "m.berends@certe.nl"), + person(family = "Luz", c("Christian", "F."), role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-5809-5995")), + person(family = "Souverein", c("Dennis"), role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-0455-0336")), + person(family = "Hassing", c("Erwin", "E.", "A."), role = c("aut", "ctb")), + person(family = "Albers", c("Casper", "J."), role = "ths", comment = c(ORCID = "0000-0002-9213-6743")), + person(family = "Dutey-Magni", c("Peter"), role = "ctb", comment = c(ORCID = "0000-0002-8942-9836")), + person(family = "Fonville", c("Judith", "M."), role = "ctb"), + person(family = "Friedrich", c("Alex", "W."), role = "ths", comment = c(ORCID = "0000-0003-4881-038X")), + person(family = "Glasner", c("Corinna"), role = "ths", comment = c(ORCID = "0000-0003-1241-1328")), + person(family = "Hazenberg", c("Eric", "H.", "L.", "C.", "M."), role = "ctb"), + person(family = "Knight", c("Gwen"), role = "ctb", comment = c(ORCID = "0000-0002-7263-9896")), + person(family = "Lenglet", c("Annick"), role = "ctb", comment = c(ORCID = "0000-0003-2013-8405")), + person(family = "Meijer", c("Bart", "C."), role = "ctb"), + person(family = "Mykhailenko", c("Dmytro"), role = "ctb"), + person(family = "Mymrikov", c("Anton"), role = "ctb"), + person(family = "Ny", c("Sofia"), role = "ctb", comment = c(ORCID = "0000-0002-2017-1363")), + person(family = "Salm", c("Jonas"), role = "ctb"), + person(family = "Schade", c("Rogier", "P."), role = "ctb"), + person(family = "Sinha", c("Bhanu", "N.", "M."), role = "ths", comment = c(ORCID = "0000-0003-1634-0010")), + person(family = "Underwood", c("Anthony"), role = "ctb", comment = c(ORCID = "0000-0002-8547-4277"))) Depends: R (>= 3.0.0) Enhances: cleaner, @@ -32,7 +33,8 @@ Enhances: janitor, skimr, tibble, - tidyselect + tidyselect, + tsibble Suggests: curl, data.table, diff --git a/NEWS.md b/NEWS.md index 764dd0d4..c466a9fa 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.8.2.9030 +# AMR 1.8.2.9031 This version will eventually become v2.0! We're happy to reach a new major milestone soon! @@ -49,7 +49,7 @@ This version will eventually become v2.0! We're happy to reach a new major miles ### Other * New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions -* Added Peter Dutey-Magni, Dmytro Mykhailenko and Anton Mymrikov as contributors, to thank them for their valuable input +* Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, and Jonas Salm as contributors, to thank them for their valuable input * All R and Rmd files in this project are now styled using the `styler` package * Set scalar conditional expressions (`&&` and `||`) where possible to comply with the upcoming R 4.3 * An enormous lot of code cleaning, fixing some small bugs on the way diff --git a/R/rsi.R b/R/rsi.R index 9b218b48..5a49ca18 100755 --- a/R/rsi.R +++ b/R/rsi.R @@ -719,8 +719,9 @@ as_rsi_method <- function(method_short, mo.bak <- list(...)$mo.bak } else { mo.bak <- mo - mo <- suppressWarnings(as.mo(mo)) } + # be sure to take current taxonomy, as the rsi_translation data set only contains current taxonomy + mo <- suppressWarnings(suppressMessages(as.mo(mo, keep_synonyms = FALSE))) guideline_coerced <- get_guideline(guideline, reference_data) if (is.na(ab)) { message_("Returning NAs for unknown drug: '", font_bold(ab.bak), diff --git a/man/AMR.Rd b/man/AMR.Rd index aa94bf7c..d4d85ba4 100644 --- a/man/AMR.Rd +++ b/man/AMR.Rd @@ -94,6 +94,7 @@ Other contributors: \item Dmytro Mykhailenko [contributor] \item Anton Mymrikov [contributor] \item Sofia Ny (\href{https://orcid.org/0000-0002-2017-1363}{ORCID}) [contributor] + \item Jonas Salm [contributor] \item Rogier P. Schade [contributor] \item Bhanu N. M. Sinha (\href{https://orcid.org/0000-0003-1634-0010}{ORCID}) [thesis advisor] \item Anthony Underwood (\href{https://orcid.org/0000-0002-8547-4277}{ORCID}) [contributor] diff --git a/pkgdown/extra.js b/pkgdown/extra.js index d6f3b46a..2df4735c 100644 --- a/pkgdown/extra.js +++ b/pkgdown/extra.js @@ -31,8 +31,9 @@ $(document).ready(function() { - // Replace 'Developers' with 'Maintainers' on the main page + // Replace 'Developers' with 'Maintainers' on the main page, and "Contributors" on the Authors page $(".developers h2").text("Maintainers"); + $(".citation h2").text("Contributors"); // replace \donttest and \dontrun texts in Examples if ($("#ref-examples ~ div pre").length > 0) { @@ -52,18 +53,18 @@ $(document).ready(function() { if (typeof(x) != "undefined") { x = x.replace(/Author, maintainer/g, "Principle developer"); x = x.replace(/Author, contributor/g, "Contributing maintainer"); - x = x.replace(/Author, thesis advisor/g, "Doctoral advisor"); - x = x.replace(/Thesis advisor/g, "Doctoral advisor"); - // authors - x = x.replace("Alex", "Prof. Dr. Alex"); + x = x.replace(/Thesis advisor/g, "(former) Doctoral advisor"); + // contributors + x = x.replace("Alex", "Prof. Alex"); x = x.replace("Anthony", "Dr. Anthony"); x = x.replace("Bart", "Dr. Bart"); - x = x.replace("Bhanu", "Prof. Dr. Bhanu"); - x = x.replace("Casper", "Prof. Dr. Casper"); + x = x.replace("Bhanu", "Prof. Bhanu"); + x = x.replace("Casper", "Prof. Casper"); x = x.replace("Christian", "Dr. Christian"); x = x.replace("Corinna", "Dr. Corinna"); x = x.replace("Dennis", "Dr. Dennis"); x = x.replace("Gwen", "Dr. Gwen"); + x = x.replace("Jonas", "Dr. Jonas"); x = x.replace("Judith", "Dr. Judith"); x = x.replace("Matthijs", "Dr. Matthijs"); x = x.replace("Peter", "Dr. Peter");