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(v1.4.0.9040) LA-MRSA / CA-MRSA
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10
R/mo.R
10
R/mo.R
@ -677,17 +677,17 @@ exec_as.mo <- function(x,
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# translate known trivial abbreviations to genus + species ----
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if (toupper(x_backup_without_spp[i]) %in% c("MRSA", "MSSA", "VISA", "VRSA", "BORSA")
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| x_backup_without_spp[i] %like_case% " (mrsa|mssa|visa|vrsa) ") {
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| x_backup_without_spp[i] %like_case% "(^| )(mrsa|mssa|visa|vrsa|borsa|la-?mrsa|ca-?mrsa)( |$)") {
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x[i] <- lookup(fullname == "Staphylococcus aureus", uncertainty = -1)
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next
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}
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if (toupper(x_backup_without_spp[i]) %in% c("MRSE", "MSSE")
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| x_backup_without_spp[i] %like_case% " (mrse|msse) ") {
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| x_backup_without_spp[i] %like_case% "(^| )(mrse|msse)( |$)") {
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x[i] <- lookup(fullname == "Staphylococcus epidermidis", uncertainty = -1)
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next
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}
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if (toupper(x_backup_without_spp[i]) == "VRE"
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| x_backup_without_spp[i] %like_case% " vre "
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| x_backup_without_spp[i] %like_case% "(^| )vre "
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| x_backup_without_spp[i] %like_case% "(enterococci|enterokok|enterococo)[a-z]*?$") {
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x[i] <- lookup(genus == "Enterococcus", uncertainty = -1)
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next
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@ -711,7 +711,7 @@ exec_as.mo <- function(x,
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next
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}
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if (toupper(x_backup_without_spp[i]) == "MRPA"
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| x_backup_without_spp[i] %like_case% " mrpa ") {
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| x_backup_without_spp[i] %like_case% "(^| )mrpa( |$)") {
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# multi resistant P. aeruginosa
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x[i] <- lookup(fullname == "Pseudomonas aeruginosa", uncertainty = -1)
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next
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@ -722,7 +722,7 @@ exec_as.mo <- function(x,
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next
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}
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if (toupper(x_backup_without_spp[i]) %in% c("PISP", "PRSP", "VISP", "VRSP")
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| x_backup_without_spp[i] %like_case% " (pisp|prsp|visp|vrsp) ") {
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| x_backup_without_spp[i] %like_case% "(^| )(pisp|prsp|visp|vrsp)( |$)") {
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# peni I, peni R, vanco I, vanco R: S. pneumoniae
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x[i] <- lookup(fullname == "Streptococcus pneumoniae", uncertainty = -1)
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next
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