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(v1.5.0.9026) vignette update, support for GISA

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dr. M.S. (Matthijs) Berends
2021-02-25 12:31:12 +01:00
parent a673407904
commit 1737d56ae4
36 changed files with 604 additions and 480 deletions
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R/mo.R
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@ -711,8 +711,8 @@ exec_as.mo <- function(x,
}
# translate known trivial abbreviations to genus + species ----
if (toupper(x_backup_without_spp[i]) %in% c("MRSA", "MSSA", "VISA", "VRSA", "BORSA")
| x_backup_without_spp[i] %like_case% "(^| )(mrsa|mssa|visa|vrsa|borsa|la-?mrsa|ca-?mrsa)( |$)") {
if (toupper(x_backup_without_spp[i]) %in% c("MRSA", "MSSA", "VISA", "VRSA", "BORSA", "GISA")
| x_backup_without_spp[i] %like_case% "(^| )(mrsa|mssa|visa|vrsa|borsa|gisa|la-?mrsa|ca-?mrsa)( |$)") {
x[i] <- lookup(fullname == "Staphylococcus aureus", uncertainty = -1)
next
}