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(v2.1.1.9285) mdro fix
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11
R/mo.R
11
R/mo.R
@ -276,12 +276,17 @@ as.mo <- function(x,
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AMR_env$mo_failures <- NULL
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# Laboratory systems: remove (translated) entries like "no growth", "not E. coli", etc.
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x[trimws2(x) %like% translate_into_language("no .*growth", language = language)] <- NA_character_
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x[trimws2(x) %like% paste0("^(", translate_into_language("no|not", language = language), ") ")] <- NA_character_
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x[trimws2(x) %like% translate_AMR("no .*growth", language = language)] <- NA_character_
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x[trimws2(x) %like% paste0("^(", translate_AMR("no|not", language = language), ") ")] <- NA_character_
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# groups are in our taxonomic table with a capital G
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x <- gsub(" group( |$)", " Group\\1", x, perl = TRUE)
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# convert translations
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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)?$"], perl = TRUE)
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x[x %like_case% "strept[o\u00F6]?[ck]o[ck](ken)?$"] <- gsub("(.* )?strept[o\u00F6]?[ck]o[ck](ken)?$", "streptococcus", x[x %like_case% "strept[o\u00F6]?[ck]o[ck](ken)?$"], perl = TRUE)
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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)?$"], perl = TRUE)
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# run over all unique leftovers
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x_unique <- unique(x[is.na(out) & !is.na(x)])
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@ -1065,6 +1070,8 @@ convert_colloquial_input <- function(x) {
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out[x %like_case% "mil+er+i gr"] <- "B_STRPT_MILL"
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out[x %like_case% "((strepto|^s).* viridans|^vgs[^a-z]*$)"] <- "B_STRPT_VIRI"
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out[x %like_case% "(viridans.* (strepto|^s).*|^vgs[^a-z]*$)"] <- "B_STRPT_VIRI"
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out[x %like_case% "meningo[ck]o[ck](ken)?$"] <- "B_NESSR_MNNG"
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out[x %like_case% "pneumo[ck]o[ck](ken)?$"] <- "B_STRPT_PNMN"
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# Salmonella in different languages, like "Salmonella grupo B"
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out[x %like_case% "salmonella.* [abcdefgh]$"] <- gsub(".*salmonella.* ([abcdefgh])$",
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