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DESCRIPTION
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DESCRIPTION
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Package: AMR
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Version: 1.8.2.9030
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Version: 1.8.2.9031
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Date: 2022-10-21
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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using evidence-based methods, as described in <doi:10.18637/jss.v104.i03>.
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data analysis and to work with microbial and antimicrobial properties by
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using evidence-based methods, as described in <doi:10.18637/jss.v104.i03>.
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Authors@R: c(
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person(family = "Berends", c("Matthijs", "S."), role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7620-1800"), email = "m.berends@certe.nl"),
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person(family = "Luz", c("Christian", "F."), role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-5809-5995")),
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person(family = "Souverein", c("Dennis"), role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-0455-0336")),
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person(family = "Hassing", c("Erwin", "E.", "A."), role = c("aut", "ctb")),
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person(family = "Albers", c("Casper", "J."), role = "ths", comment = c(ORCID = "0000-0002-9213-6743")),
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person(family = "Dutey-Magni", c("Peter"), role = "ctb", comment = c(ORCID = "0000-0002-8942-9836")),
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person(family = "Fonville", c("Judith", "M."), role = "ctb"),
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person(family = "Friedrich", c("Alex", "W."), role = "ths", comment = c(ORCID = "0000-0003-4881-038X")),
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person(family = "Glasner", c("Corinna"), role = "ths", comment = c(ORCID = "0000-0003-1241-1328")),
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person(family = "Hazenberg", c("Eric", "H.", "L.", "C.", "M."), role = "ctb"),
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person(family = "Knight", c("Gwen"), role = "ctb", comment = c(ORCID = "0000-0002-7263-9896")),
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person(family = "Lenglet", c("Annick"), role = "ctb", comment = c(ORCID = "0000-0003-2013-8405")),
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person(family = "Meijer", c("Bart", "C."), role = "ctb"),
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person(family = "Mykhailenko", c("Dmytro"), role = "ctb"),
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person(family = "Mymrikov", c("Anton"), role = "ctb"),
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person(family = "Ny", c("Sofia"), role = "ctb", comment = c(ORCID = "0000-0002-2017-1363")),
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person(family = "Schade", c("Rogier", "P."), role = "ctb"),
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person(family = "Sinha", c("Bhanu", "N.", "M."), role = "ths", comment = c(ORCID = "0000-0003-1634-0010")),
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person(family = "Underwood", c("Anthony"), role = "ctb", comment = c(ORCID = "0000-0002-8547-4277")))
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person(family = "Berends", c("Matthijs", "S."), role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7620-1800"), email = "m.berends@certe.nl"),
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person(family = "Luz", c("Christian", "F."), role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-5809-5995")),
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person(family = "Souverein", c("Dennis"), role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-0455-0336")),
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person(family = "Hassing", c("Erwin", "E.", "A."), role = c("aut", "ctb")),
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person(family = "Albers", c("Casper", "J."), role = "ths", comment = c(ORCID = "0000-0002-9213-6743")),
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person(family = "Dutey-Magni", c("Peter"), role = "ctb", comment = c(ORCID = "0000-0002-8942-9836")),
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person(family = "Fonville", c("Judith", "M."), role = "ctb"),
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person(family = "Friedrich", c("Alex", "W."), role = "ths", comment = c(ORCID = "0000-0003-4881-038X")),
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person(family = "Glasner", c("Corinna"), role = "ths", comment = c(ORCID = "0000-0003-1241-1328")),
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person(family = "Hazenberg", c("Eric", "H.", "L.", "C.", "M."), role = "ctb"),
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person(family = "Knight", c("Gwen"), role = "ctb", comment = c(ORCID = "0000-0002-7263-9896")),
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person(family = "Lenglet", c("Annick"), role = "ctb", comment = c(ORCID = "0000-0003-2013-8405")),
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person(family = "Meijer", c("Bart", "C."), role = "ctb"),
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person(family = "Mykhailenko", c("Dmytro"), role = "ctb"),
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person(family = "Mymrikov", c("Anton"), role = "ctb"),
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person(family = "Ny", c("Sofia"), role = "ctb", comment = c(ORCID = "0000-0002-2017-1363")),
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person(family = "Salm", c("Jonas"), role = "ctb"),
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person(family = "Schade", c("Rogier", "P."), role = "ctb"),
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person(family = "Sinha", c("Bhanu", "N.", "M."), role = "ths", comment = c(ORCID = "0000-0003-1634-0010")),
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person(family = "Underwood", c("Anthony"), role = "ctb", comment = c(ORCID = "0000-0002-8547-4277")))
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Depends: R (>= 3.0.0)
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Enhances:
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cleaner,
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janitor,
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skimr,
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tibble,
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tidyselect
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tidyselect,
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tsibble
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Suggests:
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curl,
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data.table,
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4
NEWS.md
4
NEWS.md
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# AMR 1.8.2.9030
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# AMR 1.8.2.9031
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This version will eventually become v2.0! We're happy to reach a new major milestone soon!
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@ -49,7 +49,7 @@ This version will eventually become v2.0! We're happy to reach a new major miles
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### Other
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* 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
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* Added Peter Dutey-Magni, Dmytro Mykhailenko and Anton Mymrikov as contributors, to thank them for their valuable input
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* Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, and Jonas Salm as contributors, to thank them for their valuable input
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* All R and Rmd files in this project are now styled using the `styler` package
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* Set scalar conditional expressions (`&&` and `||`) where possible to comply with the upcoming R 4.3
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* An enormous lot of code cleaning, fixing some small bugs on the way
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3
R/rsi.R
3
R/rsi.R
@ -719,8 +719,9 @@ as_rsi_method <- function(method_short,
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mo.bak <- list(...)$mo.bak
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} else {
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mo.bak <- mo
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mo <- suppressWarnings(as.mo(mo))
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}
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# be sure to take current taxonomy, as the rsi_translation data set only contains current taxonomy
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mo <- suppressWarnings(suppressMessages(as.mo(mo, keep_synonyms = FALSE)))
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guideline_coerced <- get_guideline(guideline, reference_data)
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if (is.na(ab)) {
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message_("Returning NAs for unknown drug: '", font_bold(ab.bak),
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@ -94,6 +94,7 @@ Other contributors:
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\item Dmytro Mykhailenko [contributor]
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\item Anton Mymrikov [contributor]
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\item Sofia Ny (\href{https://orcid.org/0000-0002-2017-1363}{ORCID}) [contributor]
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\item Jonas Salm [contributor]
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\item Rogier P. Schade [contributor]
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\item Bhanu N. M. Sinha (\href{https://orcid.org/0000-0003-1634-0010}{ORCID}) [thesis advisor]
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\item Anthony Underwood (\href{https://orcid.org/0000-0002-8547-4277}{ORCID}) [contributor]
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@ -31,8 +31,9 @@
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$(document).ready(function() {
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// Replace 'Developers' with 'Maintainers' on the main page
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// Replace 'Developers' with 'Maintainers' on the main page, and "Contributors" on the Authors page
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$(".developers h2").text("Maintainers");
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$(".citation h2").text("Contributors");
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// replace \donttest and \dontrun texts in Examples
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if ($("#ref-examples ~ div pre").length > 0) {
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if (typeof(x) != "undefined") {
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x = x.replace(/Author, maintainer/g, "Principle developer");
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x = x.replace(/Author, contributor/g, "Contributing maintainer");
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x = x.replace(/Author, thesis advisor/g, "Doctoral advisor");
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x = x.replace(/Thesis advisor/g, "Doctoral advisor");
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// authors
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x = x.replace("Alex", "Prof. Dr. Alex");
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x = x.replace(/Thesis advisor/g, "(former) Doctoral advisor");
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// contributors
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x = x.replace("Alex", "Prof. Alex");
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x = x.replace("Anthony", "Dr. Anthony");
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x = x.replace("Bart", "Dr. Bart");
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x = x.replace("Bhanu", "Prof. Dr. Bhanu");
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x = x.replace("Casper", "Prof. Dr. Casper");
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x = x.replace("Bhanu", "Prof. Bhanu");
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x = x.replace("Casper", "Prof. Casper");
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x = x.replace("Christian", "Dr. Christian");
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x = x.replace("Corinna", "Dr. Corinna");
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x = x.replace("Dennis", "Dr. Dennis");
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x = x.replace("Gwen", "Dr. Gwen");
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x = x.replace("Jonas", "Dr. Jonas");
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x = x.replace("Judith", "Dr. Judith");
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x = x.replace("Matthijs", "Dr. Matthijs");
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x = x.replace("Peter", "Dr. Peter");
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