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added Becker 2019

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dr. M.S. (Matthijs) Berends
2019-03-26 14:24:03 +01:00
parent c6a12266e7
commit 29f444543d
45 changed files with 674 additions and 476 deletions
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11
R/mo_property.R
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@ -446,6 +446,8 @@ mo_translate <- function(x, language) {
# Spanish
language == "es" ~ x[x_tobetranslated] %>%
# not 'negativa'
# https://www.sciencedirect.com/science/article/pii/S0123939215000739
gsub("Coagulase-negative Staphylococcus","Staphylococcus coagulasa negativo", ., fixed = TRUE) %>%
gsub("Coagulase-positive Staphylococcus","Staphylococcus coagulasa positivo", ., fixed = TRUE) %>%
gsub("Beta-haemolytic Streptococcus", "Streptococcus Beta-hemol\u00edtico", ., fixed = TRUE) %>%
@ -461,6 +463,8 @@ mo_translate <- function(x, language) {
gsub("unknown species", "especie desconocida", ., fixed = TRUE) %>%
gsub("unknown subspecies", "subespecie desconocida", ., fixed = TRUE) %>%
gsub("unknown rank", "rango desconocido", ., fixed = TRUE) %>%
gsub("(CoNS)", "(SCN)", ., fixed = TRUE) %>%
gsub("(CoPS)", "(SCP)", ., fixed = TRUE) %>%
gsub("Gram negative", "Gram negativo", ., fixed = TRUE) %>%
gsub("Gram positive", "Gram positivo", ., fixed = TRUE) %>%
gsub("Bacteria", "Bacterias", ., fixed = TRUE) %>%
@ -579,7 +583,12 @@ mo_validate <- function(x, property, ...) {
# check onLoad() in R/zzz.R: data tables are created there.
}
if (!all(x %in% microorganisms[, property])
# try to catch an error when inputting an invalid parameter
# so the call can be set to FALSE
tryCatch(x[1L] %in% AMR::microorganisms[1, property],
error = function(e) stop(e$message, call. = FALSE))
if (!all(x %in% AMR::microorganisms[, property])
| Becker %in% c(TRUE, "all")
| Lancefield %in% c(TRUE, "all")) {
exec_as.mo(x, property = property, ...)