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(v0.7.1.90012) mo_shortname fix

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dr. M.S. (Matthijs) Berends
2019-07-10 21:36:51 +02:00
parent a56a87c7db
commit 68230d0712
68 changed files with 1154 additions and 1794 deletions
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9
R/mo_property.R
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@ -151,9 +151,14 @@ mo_shortname <- function(x, language = get_locale(), ...) {
x.mo <- AMR::as.mo(x, ...)
metadata <- get_mo_failures_uncertainties_renamed()
replace_empty <- function(x) {
x[x == ""] <- "spp."
x
}
# get first char of genus and complete species in English
shortnames <- paste0(substr(mo_genus(x.mo, language = NULL), 1, 1), ". ", mo_species(x.mo, language = NULL))
shortnames <- paste0(substr(mo_genus(x.mo, language = NULL), 1, 1), ". ", replace_empty(mo_species(x.mo, language = NULL)))
# exceptions for Staphylococci
shortnames[shortnames == "S. coagulase-negative" ] <- "CoNS"
shortnames[shortnames == "S. coagulase-positive" ] <- "CoPS"