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(v2.1.1.9281) speed improvement is_sir_eligible

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dr. M.S. (Matthijs) Berends 2025-05-20 11:31:42 +02:00
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commit a94452b9be
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3 changed files with 5 additions and 5 deletions
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DESCRIPTION
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Package: AMR Package: AMR
Version: 2.1.1.9279 Version: 2.1.1.9281
Date: 2025-05-16 Date: 2025-05-20
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) 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

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NEWS.md
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# AMR 2.1.1.9279 # AMR 2.1.1.9281
*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://amr-for-r.org/#get-this-package).)* *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://amr-for-r.org/#get-this-package).)*

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R/sir.R
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@ -445,9 +445,9 @@ is_sir_eligible <- function(x, threshold = 0.05) {
%in% class(x))) { %in% class(x))) {
# no transformation needed # no transformation needed
return(FALSE) return(FALSE)
} else if (!all(is.na(x)) && all(toupper(x) %in% c("S", "SDD", "I", "R", "NI", NA))) { } else if (!all(is.na(x)) && all(x %in% c("S", "SDD", "I", "R", "NI", NA, "s", "sdd", "i", "r", "ni"))) {
return(TRUE) return(TRUE)
} else if (!all(is.na(x)) && !any(c("S", "SDD", "I", "R", "NI") %in% gsub("([SIR])\\1+", "\\1", gsub("[^A-Z]", "", toupper(x), perl = TRUE), perl = TRUE), na.rm = TRUE)) { } else if (!all(is.na(x)) && !any(c("S", "SDD", "I", "R", "NI") %in% gsub("([SIR])\\1+", "\\1", gsub("[^A-Z]", "", toupper(unique(x[1:10000])), perl = TRUE), perl = TRUE), na.rm = TRUE)) {
return(FALSE) return(FALSE)
} else { } else {
x <- x[!is.na(x) & !is.null(x) & !x %in% c("", "-", "NULL")] x <- x[!is.na(x) & !is.null(x) & !x %in% c("", "-", "NULL")]