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(v2.1.1.9061) animal host fix
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Package: AMR
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Version: 2.1.1.9060
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Version: 2.1.1.9061
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Date: 2024-06-19
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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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2
NEWS.md
2
NEWS.md
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# AMR 2.1.1.9060
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# AMR 2.1.1.9061
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*(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://msberends.github.io/AMR/#latest-development-version).)*
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13
R/sir.R
13
R/sir.R
@ -832,7 +832,7 @@ get_guideline <- function(guideline, reference_data) {
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}
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convert_host <- function(x, lang = get_AMR_locale()) {
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x <- trimws2(tolower(as.character(x)))
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x <- gsub("[^a-zA-Z ]", "", trimws2(tolower(as.character(x))), perl = TRUE)
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x_out <- rep(NA_character_, length(x))
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x_out[trimws2(tolower(x)) == "human"] <- "human"
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x_out[trimws2(tolower(x)) == "ecoff"] <- "ecoff"
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@ -860,8 +860,15 @@ convert_host <- function(x, lang = get_AMR_locale()) {
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x_out[is.na(x_out) & (x %like% "sheep|ovine" | x %like% translate_AMR("sheep|sheeps|ovine", lang))] <- "sheep"
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x_out[is.na(x_out) & (x %like% "snake|serpentine" | x %like% translate_AMR("snake|snakes|serpentine", lang))] <- "snakes"
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x_out[is.na(x_out) & (x %like% "turkey|meleagrine" | x %like% translate_AMR("turkey|turkeys|meleagrine", lang))] <- "turkey"
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if (message_not_thrown_before("convert_host", x) && any(is.na(x_out) & !is.na(x))) {
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warning_("The following host(s) are invalid: ", vector_and(x[is.na(x_out) & !is.na(x)]), call = FALSE, immediate = TRUE)
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if (any(x_out %in% c(NA_character_, "animal"))) {
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x_out[is.na(x_out) & x == "animal"] <- AMR_env$host_preferred_order[1]
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if (message_not_thrown_before("as.sir", "convert_host_missing")) {
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message_(ifelse(any(is.na(x_out) & !is.na(x), na.rm = TRUE),
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paste0("The following host(s) are invalid: ", vector_and(x[is.na(x_out) & !is.na(x)]), ". "),
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""),
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"For missing animal hosts, assuming \"", AMR_env$host_preferred_order[1], "\", since these have the highest breakpoint availability.")
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x_out[is.na(x_out)] <- AMR_env$host_preferred_order[1]
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}
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}
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x_out[x_out == "ecoff"] <- "ECOFF"
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x_out
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@ -36,7 +36,7 @@ expect_identical(
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c("EUCAST", "CLSI")
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)
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# no missing SDDs
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expect_identical(sum(is.na(AMR::clinical_breakpoints$is_SDD)), 0)
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expect_identical(sum(is.na(AMR::clinical_breakpoints$is_SDD)), 0L)
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expect_true(as.sir("S") < as.sir("I"))
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expect_true(as.sir("I") < as.sir("R"))
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