P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-10 00:23:03 +02:00
Code Releases Activity

(v1.4.0.9040) LA-MRSA / CA-MRSA

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-12-16 16:18:53 +01:00
parent 203bc20eb0
commit 1faa816090
19 changed files with 366 additions and 364 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
R/mo.R
View File

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