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(v1.5.0.9041) SNOMED update

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dr. M.S. (Matthijs) Berends
2021-03-11 21:42:30 +01:00
parent 8d6ceb6a15
commit 4e0a9533ad
65 changed files with 86943 additions and 67626 deletions
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14
data-raw/reproduction_of_antibiotics.R
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@ -166,7 +166,7 @@ abx2$abbr <- lapply(as.list(abx2$abbr), function(x) unlist(strsplit(x, "|", fixe
# vector with official names, returns vector with CIDs
get_CID <- function(ab) {
CID <- rep(NA_integer_, length(ab))
p <- progress_estimated(n = length(ab), min_time = 0)
p <- progress_ticker(n = length(ab), min_time = 0)
for (i in 1:length(ab)) {
p$tick()$print()
@ -208,10 +208,10 @@ abx2[is.na(CIDs),] %>% View()
# returns list with synonyms (brand names), with CIDs as names
get_synonyms <- function(CID, clean = TRUE) {
synonyms <- rep(NA_character_, length(CID))
p <- progress_estimated(n = length(CID), min_time = 0)
#p <- progress_ticker(n = length(CID), min_time = 0)
for (i in 1:length(CID)) {
p$tick()$print()
#p$tick()$print()
synonyms_txt <- ""
@ -564,6 +564,14 @@ antibiotics[which(antibiotics$ab == "CPT"), "atc"] <- "J01DI02"
antibiotics[which(antibiotics$ab == "FAR"), "atc"] <- "J01DI03"
# ceftobiprole
antibiotics[which(antibiotics$ab == "BPR"), "atc"] <- "J01DI01"
# ceftazidime / avibactam
antibiotics[which(antibiotics$ab == "CZA"), "atc"] <- "J01DD52"
antibiotics[which(antibiotics$ab == "CZA"), "cid"] <- 90643431
antibiotics[which(antibiotics$ab == "CZA"), "atc_group1"] <- "Other beta-lactam antibacterials"
antibiotics[which(antibiotics$ab == "CZA"), "atc_group2"] <- "Third-generation cephalosporins"
antibiotics[which(antibiotics$ab == "CZA"), "iv_ddd"] <- 6
antibiotics[which(antibiotics$ab == "CZA"), "iv_units"] <- "g"
antibiotics[which(antibiotics$ab == "CZA"), "synonyms"] <- list(c("Avycaz", "Zavicefta"))
# typo
antibiotics[which(antibiotics$ab == "RXT"), "name"] <- "Roxithromycin"