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(v2.1.1.9285) mdro fix

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dr. M.S. (Matthijs) Berends
2025-05-21 16:51:40 +02:00
parent 8d2c5afab6
commit 80f08f91da
4 changed files with 19 additions and 11 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 2.1.1.9281 Version: 2.1.1.9285
Date: 2025-05-20 Date: 2025-05-21
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

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 2.1.1.9281 # AMR 2.1.1.9285
*(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).)*

13
R/mdro.R
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@ -499,10 +499,11 @@ mdro <- function(x = NULL,
if (!"AMP" %in% names(cols_ab) && "AMX" %in% names(cols_ab)) { if (!"AMP" %in% names(cols_ab) && "AMX" %in% names(cols_ab)) {
# ampicillin column is missing, but amoxicillin is available # ampicillin column is missing, but amoxicillin is available
if (isTRUE(info)) { if (isTRUE(info)) {
message_("Using column '", cols_ab[names(cols_ab) == "AMX"], "' as input for ampicillin since many MDRO rules depend on it.") message_("Using column '", cols_ab[names(cols_ab) == "AMX"], "' as input for ampicillin since many MDRO rules depend on it.", add_fn = font_red)
} }
cols_ab <- c(cols_ab, c(AMP = unname(cols_ab[names(cols_ab) == "AMX"]))) cols_ab <- c(cols_ab, c(AMP = unname(cols_ab[names(cols_ab) == "AMX"])))
} }
cols_ab <- cols_ab[!duplicated(cols_ab)]
# nolint start # nolint start
AMC <- cols_ab["AMC"] AMC <- cols_ab["AMC"]
@ -1607,20 +1608,20 @@ mdro <- function(x = NULL,
reason = "E. faecium: vanA/vanB gene + penicillin group" reason = "E. faecium: vanA/vanB gene + penicillin group"
) )
# Staphylococcus aureus # Staphylococcus aureus complex (= aureus, argenteus or schweitzeri)
trans_tbl( trans_tbl(
2, 2,
rows = which(x$genus == "Staphylococcus" & x$species == "aureus" & (is.na(mecA) | is.na(mecC))), rows = which(x$genus == "Staphylococcus" & x$species %in% c("aureus", "argenteus", "schweitzeri") & (is.na(mecA) | is.na(mecC))),
cols = c(AMC, TZP, FLC, OXA, FOX, FOX1), cols = c(AMC, TZP, FLC, OXA, FOX, FOX1),
any_all = "any", any_all = "any",
reason = "S. aureus: potential MRSA" reason = "S. aureus complex: potential MRSA"
) )
trans_tbl( trans_tbl(
3, 3,
rows = which(x$genus == "Staphylococcus" & x$species == "aureus" & (mecA == TRUE | mecC == TRUE)), rows = which(x$genus == "Staphylococcus" & x$species %in% c("aureus", "argenteus", "schweitzeri") & (mecA == TRUE | mecC == TRUE)),
cols = "any", cols = "any",
any_all = "any", any_all = "any",
reason = "S. aureus: mecA/mecC gene" reason = "S. aureus complex: mecA/mecC gene"
) )
# Candida auris # Candida auris

11
R/mo.R
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@ -276,12 +276,17 @@ as.mo <- function(x,
AMR_env$mo_failures <- NULL AMR_env$mo_failures <- NULL
# Laboratory systems: remove (translated) entries like "no growth", "not E. coli", etc. # Laboratory systems: remove (translated) entries like "no growth", "not E. coli", etc.
x[trimws2(x) %like% translate_into_language("no .*growth", language = language)] <- NA_character_ x[trimws2(x) %like% translate_AMR("no .*growth", language = language)] <- NA_character_
x[trimws2(x) %like% paste0("^(", translate_into_language("no|not", language = language), ") ")] <- NA_character_ x[trimws2(x) %like% paste0("^(", translate_AMR("no|not", language = language), ") ")] <- NA_character_
# groups are in our taxonomic table with a capital G # groups are in our taxonomic table with a capital G
x <- gsub(" group( |$)", " Group\\1", x, perl = TRUE) x <- gsub(" group( |$)", " Group\\1", x, perl = TRUE)
# convert translations
x[x %like_case% "enter[o\u00F6]?[ck]o[ck](ken)?$"] <- gsub("(.* )?enter[o\u00F6]?[ck]o[ck](ken)?$", "enterococcus", x[x %like_case% "enter[o\u00F6]?[ck]o[ck](ken)?$"], perl = TRUE)
x[x %like_case% "strept[o\u00F6]?[ck]o[ck](ken)?$"] <- gsub("(.* )?strept[o\u00F6]?[ck]o[ck](ken)?$", "streptococcus", x[x %like_case% "strept[o\u00F6]?[ck]o[ck](ken)?$"], perl = TRUE)
x[x %like_case% "staph[yij]?[lo]*[ck]o[ck](ken)?$"] <- gsub("(.* )?staph[yij]?[lo]*[ck]o[ck](ken)?$", "staphylococcus", x[x %like_case% "staph[yij]?[lo]*[ck]o[ck](ken)?$"], perl = TRUE)
# run over all unique leftovers # run over all unique leftovers
x_unique <- unique(x[is.na(out) & !is.na(x)]) x_unique <- unique(x[is.na(out) & !is.na(x)])
@ -1065,6 +1070,8 @@ convert_colloquial_input <- function(x) {
out[x %like_case% "mil+er+i gr"] <- "B_STRPT_MILL" out[x %like_case% "mil+er+i gr"] <- "B_STRPT_MILL"
out[x %like_case% "((strepto|^s).* viridans|^vgs[^a-z]*$)"] <- "B_STRPT_VIRI" out[x %like_case% "((strepto|^s).* viridans|^vgs[^a-z]*$)"] <- "B_STRPT_VIRI"
out[x %like_case% "(viridans.* (strepto|^s).*|^vgs[^a-z]*$)"] <- "B_STRPT_VIRI" out[x %like_case% "(viridans.* (strepto|^s).*|^vgs[^a-z]*$)"] <- "B_STRPT_VIRI"
out[x %like_case% "meningo[ck]o[ck](ken)?$"] <- "B_NESSR_MNNG"
out[x %like_case% "pneumo[ck]o[ck](ken)?$"] <- "B_STRPT_PNMN"
# Salmonella in different languages, like "Salmonella grupo B" # Salmonella in different languages, like "Salmonella grupo B"
out[x %like_case% "salmonella.* [abcdefgh]$"] <- gsub(".*salmonella.* ([abcdefgh])$", out[x %like_case% "salmonella.* [abcdefgh]$"] <- gsub(".*salmonella.* ([abcdefgh])$",