P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 03:22:00 +02:00
Code Releases Activity

(v1.0.1.9005) as.mo() improvements

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-04-13 21:09:56 +02:00
parent 219cff403f
commit d1cb7d3b6f
97 changed files with 2849 additions and 2098 deletions
Download Patch File Download Diff File Expand all files Collapse all files

992
data-raw/antibiotics.txt
View File

File diff suppressed because it is too large Load Diff

27
data-raw/reproduction_of_antibiotics.R
View File

@ -301,7 +301,7 @@ antibiotics[which(antibiotics$ab == "FLC"), "abbreviations"][[1]] <- list(c("clo
antibiotics[which(antibiotics$ab == "CEC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CEC"), "abbreviations"][[1]], "CFC")) # cefaclor old WHONET4 code
antibiotics[which(antibiotics$ab == "AMX"), "synonyms"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "AMX"), "synonyms"][[1]], "Amoxy")))
# 'Polymixin B' (POL) and 'Polymyxin B' (PLB) both exist, so:
antibiotics[which(antibiotics$ab == "PLB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PLB"), "abbreviations"][[1]], "POL", "Polymixin", "Polymixin B"))
antibiotics[which(antibiotics$ab == "PLB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PLB"), "abbreviations"][[1]], "POL", "Polymixin", "Polymixin B", "Poly B"))
antibiotics <- filter(antibiotics, ab != "POL")
# 'Latamoxef' (LTM) and 'Moxalactam (Latamoxef)' (MOX) both exist, so:
antibiotics[which(antibiotics$ab == "LTM"), "abbreviations"][[1]] <- list(c("MOX", "moxa"))
@ -323,7 +323,19 @@ antibiotics[which(antibiotics$ab == as.ab("cefotaxim")), "abbreviations"][[1]] <
antibiotics[which(antibiotics$ab == as.ab("ceftazidime")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("ceftazidime")), "abbreviations"][[1]], "cftz"))
antibiotics[which(antibiotics$ab == as.ab("cefepime")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefepime")), "abbreviations"][[1]], "cfpi"))
antibiotics[which(antibiotics$ab == as.ab("cefoxitin")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cefoxitin")), "abbreviations"][[1]], "cfxt"))
antibiotics[which(antibiotics$ab == as.ab("cotrimoxazol")), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == as.ab("cotrimoxazol")), "abbreviations"][[1]], "trsx"))
# More GLIMS codes
antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "cftz"))
antibiotics[which(antibiotics$ab == "CRO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CRO"), "abbreviations"][[1]], "cftr"))
antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]], "cftx"))
antibiotics[which(antibiotics$ab == "CXM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CXM"), "abbreviations"][[1]], "cfrx"))
antibiotics[which(antibiotics$ab == "CZO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CZO"), "abbreviations"][[1]], "cfzl"))
antibiotics[which(antibiotics$ab == "FOX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FOX"), "abbreviations"][[1]], "cfxt"))
antibiotics[which(antibiotics$ab == "PIP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PIP"), "abbreviations"][[1]], "pipc"))
antibiotics[which(antibiotics$ab == "PIP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PIP"), "abbreviations"][[1]], "PIPC"))
antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]], "COTRIM"))
antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "SXT"), "abbreviations"][[1]], "trsx"))
antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]], "PIPTAZ"))
antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]], "pita"))
# ESBL E-test codes:
antibiotics[which(antibiotics$ab == "CCV"), "abbreviations"][[1]] <- list(c("xtzl"))
antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "xtz", "cefta"))
@ -351,7 +363,6 @@ old_sym <- old_sym[!old_sym %in% c("Cotrimoxazole", "Bactrimel")]
antibiotics[which(antibiotics$ab == "SMX"), "synonyms"][[1]] <- list(old_sym)
antibiotics[which(antibiotics$ab == "SXT"), "synonyms"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "COL"), "synonyms"][[1]], "Cotrimoxazole", "Bactrimel", "Septra", "Bactrim", "Cotrimazole"))))
## new ATC codes
# ceftaroline
antibiotics[which(antibiotics$ab == "CPT"), "atc"] <- "J01DI02"
@ -362,7 +373,6 @@ antibiotics[which(antibiotics$ab == "BPR"), "atc"] <- "J01DI01"
# typo
antibiotics[which(antibiotics$ab == "RXT"), "name"] <- "Roxithromycin"
antibiotics[which(antibiotics$ab == "PEN"), "atc"] <- "J01CE01"
@ -408,8 +418,15 @@ antibiotics <- antibiotics %>%
antibiotics <- as.data.frame(antibiotics, stringsAsFactors = FALSE)
class(antibiotics$ab) <- "ab"
# make all abbreviations and synonyms lower case, unique and alphabetically sorted
for (i in 1:nrow(antibiotics)) {
abb <- sort(unique(tolower(antibiotics[i, "abbreviations"][[1]])))
syn <- sort(unique(tolower(antibiotics[i, "synonyms"][[1]])))
antibiotics[i, "abbreviations"][[1]] <- ifelse(length(abb[!abb == ""]) == 0, list(""), list(abb))
antibiotics[i, "synonyms"][[1]] <- ifelse(length(syn[!syn == ""]) == 0, list(""), list(syn))
}
# REFER TO data-raw/loinc.R FOR ADDING LOINC CODES
dim(antibiotics) # for R/data.R
usethis::use_data(antibiotics, overwrite = TRUE)
rm(antibiotics)

1
data-raw/reproduction_of_microorganisms.R
View File

@ -890,6 +890,5 @@ rm(microorganisms.translation)
devtools::load_all(".")
# TO DO AFTER THIS
# * Update the year and dim()s in R/data.R
# * Rerun data-raw/reproduction_of_rsi_translation.R
# * Run unit tests