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(v2.1.1.9061) animal host fix

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dr. M.S. (Matthijs) Berends 2024-06-19 15:41:45 +02:00
parent c67d003e9e
commit 82585901a7
4 changed files with 13 additions and 6 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 2.1.1.9060 Version: 2.1.1.9061
Date: 2024-06-19 Date: 2024-06-19
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)

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 2.1.1.9060 # AMR 2.1.1.9061
*(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).)* *(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).)*

13
R/sir.R
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@ -832,7 +832,7 @@ get_guideline <- function(guideline, reference_data) {
} }
convert_host <- function(x, lang = get_AMR_locale()) { convert_host <- function(x, lang = get_AMR_locale()) {
x <- trimws2(tolower(as.character(x))) x <- gsub("[^a-zA-Z ]", "", trimws2(tolower(as.character(x))), perl = TRUE)
x_out <- rep(NA_character_, length(x)) x_out <- rep(NA_character_, length(x))
x_out[trimws2(tolower(x)) == "human"] <- "human" x_out[trimws2(tolower(x)) == "human"] <- "human"
x_out[trimws2(tolower(x)) == "ecoff"] <- "ecoff" x_out[trimws2(tolower(x)) == "ecoff"] <- "ecoff"
@ -860,8 +860,15 @@ convert_host <- function(x, lang = get_AMR_locale()) {
x_out[is.na(x_out) & (x %like% "sheep|ovine" | x %like% translate_AMR("sheep|sheeps|ovine", lang))] <- "sheep" x_out[is.na(x_out) & (x %like% "sheep|ovine" | x %like% translate_AMR("sheep|sheeps|ovine", lang))] <- "sheep"
x_out[is.na(x_out) & (x %like% "snake|serpentine" | x %like% translate_AMR("snake|snakes|serpentine", lang))] <- "snakes" x_out[is.na(x_out) & (x %like% "snake|serpentine" | x %like% translate_AMR("snake|snakes|serpentine", lang))] <- "snakes"
x_out[is.na(x_out) & (x %like% "turkey|meleagrine" | x %like% translate_AMR("turkey|turkeys|meleagrine", lang))] <- "turkey" x_out[is.na(x_out) & (x %like% "turkey|meleagrine" | x %like% translate_AMR("turkey|turkeys|meleagrine", lang))] <- "turkey"
if (message_not_thrown_before("convert_host", x) && any(is.na(x_out) & !is.na(x))) { if (any(x_out %in% c(NA_character_, "animal"))) {
warning_("The following host(s) are invalid: ", vector_and(x[is.na(x_out) & !is.na(x)]), call = FALSE, immediate = TRUE) x_out[is.na(x_out) & x == "animal"] <- AMR_env$host_preferred_order[1]
if (message_not_thrown_before("as.sir", "convert_host_missing")) {
message_(ifelse(any(is.na(x_out) & !is.na(x), na.rm = TRUE),
paste0("The following host(s) are invalid: ", vector_and(x[is.na(x_out) & !is.na(x)]), ". "),
""),
"For missing animal hosts, assuming \"", AMR_env$host_preferred_order[1], "\", since these have the highest breakpoint availability.")
x_out[is.na(x_out)] <- AMR_env$host_preferred_order[1]
}
} }
x_out[x_out == "ecoff"] <- "ECOFF" x_out[x_out == "ecoff"] <- "ECOFF"
x_out x_out

2
inst/tinytest/test-sir.R
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@ -36,7 +36,7 @@ expect_identical(
c("EUCAST", "CLSI") c("EUCAST", "CLSI")
) )
# no missing SDDs # no missing SDDs
expect_identical(sum(is.na(AMR::clinical_breakpoints$is_SDD)), 0) expect_identical(sum(is.na(AMR::clinical_breakpoints$is_SDD)), 0L)
expect_true(as.sir("S") < as.sir("I")) expect_true(as.sir("S") < as.sir("I"))
expect_true(as.sir("I") < as.sir("R")) expect_true(as.sir("I") < as.sir("R"))