P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 20:21:58 +02:00
Code Releases Activity

(v1.7.1.9070) Better WHONET support

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-12-13 10:18:28 +01:00
parent f90e27c1b0
commit 578e7dfee9
74 changed files with 20758 additions and 47402 deletions
Download Patch File Download Diff File Expand all files Collapse all files

23
data-raw/reproduction_of_antibiotics.R
View File

@ -461,7 +461,7 @@ antibiotics[which(antibiotics$ab == "MEZ"), "abbreviations"][[1]] <- list(c(anti
antibiotics[which(antibiotics$ab == "MIF"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MIF"), "abbreviations"][[1]], "mica"))
antibiotics[which(antibiotics$ab == "MCZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MCZ"), "abbreviations"][[1]], "mico"))
antibiotics[which(antibiotics$ab == "MNO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MNO"), "abbreviations"][[1]], "mino"))
antibiotics[which(antibiotics$ab == "LTM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "LTM"), "abbreviations"][[1]], "moxa"))
antibiotics[which(antibiotics$ab == "LTM"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "LTM"), "abbreviations"][[1]], "moxa", "moxalactam"))
antibiotics[which(antibiotics$ab == "MFX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "MFX"), "abbreviations"][[1]], "moxi"))
antibiotics[which(antibiotics$ab == "NAL"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "NAL"), "abbreviations"][[1]], "nali"))
antibiotics[which(antibiotics$ab == "NEO"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "NEO"), "abbreviations"][[1]], "neom"))
@ -516,6 +516,10 @@ antibiotics[which(antibiotics$ab == "FOS"), "synonyms"][[1]] <- list(sort(c(anti
antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "TZP"), "abbreviations"][[1]], "piptazo")))
antibiotics[which(antibiotics$ab == "RFP"), "abbreviations"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "RFP"), "abbreviations"][[1]], "RPT")))
antibiotics[which(antibiotics$ab == "RTP"), "abbreviations"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "RTP"), "abbreviations"][[1]], "RET")))
antibiotics[which(antibiotics$ab == "TYL1"), "abbreviations"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "TYL1"), "abbreviations"][[1]], "TVN")))
antibiotics <- antibiotics %>%
mutate(ab = as.character(ab)) %>%
rbind(antibiotics %>%
@ -595,6 +599,23 @@ antibiotics[which(antibiotics$ab == "CZA"), "synonyms"] <- list(c("Avycaz", "Zav
antibiotics[which(antibiotics$ab == "RXT"), "name"] <- "Roxithromycin"
antibiotics[which(antibiotics$ab == "PEN"), "atc"] <- "J01CE01"
# WHONET cleanup
antibiotics[which(antibiotics$ab == "BCZ"), "name"] <- "Bicyclomycin"
antibiotics[which(antibiotics$ab == "CCL"), "name"] <- "Cefetecol"
antibiotics[which(antibiotics$ab == "ENV"), "name"] <- "Enviomycin"
antibiotics[which(antibiotics$ab == "KIT"), "name"] <- "Kitasamycin"
antibiotics[which(antibiotics$ab == "LSP"), "name"] <- "Linco-spectin"
antibiotics[which(antibiotics$ab == "MEC"), "name"] <- "Mecillinam"
antibiotics[which(antibiotics$ab == "PMR"), "name"] <- "Pimaricin"
antibiotics[which(antibiotics$ab == "BCZ"), "abbreviations"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "BCZ"), "abbreviations"][[1]], "Bicozamycin"))))
antibiotics[which(antibiotics$ab == "CCL"), "abbreviations"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "CCL"), "abbreviations"][[1]], "Cefcatacol"))))
antibiotics[which(antibiotics$ab == "ENV"), "abbreviations"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "ENV"), "abbreviations"][[1]], "Tuberactinomycin"))))
antibiotics[which(antibiotics$ab == "KIT"), "abbreviations"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "KIT"), "abbreviations"][[1]], "Leucomycin"))))
antibiotics[which(antibiotics$ab == "LSP"), "abbreviations"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "LSP"), "abbreviations"][[1]], "lincomycin/spectinomycin"))))
antibiotics[which(antibiotics$ab == "MEC"), "abbreviations"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "MEC"), "abbreviations"][[1]], "Amdinocillin"))))
antibiotics[which(antibiotics$ab == "PMR"), "abbreviations"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "PMR"), "abbreviations"][[1]], "Natamycin"))))
# set cephalosporins groups for the ones that could not be determined automatically:
antibiotics <- antibiotics %>%
mutate(group = case_when(