Update contributors list

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
+  data analysis and to work with microbial and antimicrobial properties by
-    using evidence-based methods, as described in <doi:10.18637/jss.v104.i03>.
+  using evidence-based methods, as described in <doi:10.18637/jss.v104.i03>.
 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 = "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 = "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 = "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 = "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 = "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 = "Dutey-Magni", c("Peter"), role = "ctb", comment = c(ORCID = "0000-0002-8942-9836")),
- person(family = "Fonville",    c("Judith", "M."), role = "ctb"),
+  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 = "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 = "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 = "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 = "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 = "Lenglet",     c("Annick"), role = "ctb", comment = c(ORCID = "0000-0003-2013-8405")),
- person(family = "Meijer",      c("Bart", "C."), role = "ctb"),
+  person(family = "Meijer",      c("Bart", "C."), role = "ctb"),
- person(family = "Mykhailenko", c("Dmytro"), role = "ctb"),
+  person(family = "Mykhailenko", c("Dmytro"), role = "ctb"),
- person(family = "Mymrikov",    c("Anton"), 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 = "Ny",          c("Sofia"), role = "ctb", comment = c(ORCID = "0000-0002-2017-1363")),
- person(family = "Schade",      c("Rogier", "P."), role = "ctb"),
+  person(family = "Salm",        c("Jonas"), role = "ctb"),
- person(family = "Sinha",       c("Bhanu", "N.", "M."), role = "ths", comment = c(ORCID = "0000-0003-1634-0010")),
+  person(family = "Schade",      c("Rogier", "P."), role = "ctb"),
- person(family = "Underwood",   c("Anthony"), role = "ctb", comment = c(ORCID = "0000-0002-8547-4277")))
+  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,

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

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),

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]

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, "(former) Doctoral advisor");
-      x = x.replace(/Thesis advisor/g, "Doctoral advisor");
+      // contributors
-      // authors
+      x = x.replace("Alex", "Prof. Alex");
-      x = x.replace("Alex", "Prof. Dr. Alex");
       x = x.replace("Anthony", "Dr. Anthony");
       x = x.replace("Bart", "Dr. Bart");
-      x = x.replace("Bhanu", "Prof. Dr. Bhanu");
+      x = x.replace("Bhanu", "Prof. Bhanu");
-      x = x.replace("Casper", "Prof. Dr. Casper");
+      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");