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use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi

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dr. M.S. (Matthijs) Berends
2023-02-06 11:57:22 +01:00
parent 4b133d4c96
commit 9e99e66f01
69 changed files with 1670 additions and 650 deletions
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data-raw/salonella_fix.R Normal file
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snomed2 <- microorganisms %>% filter(mo %in% c("B_SLMNL_TYPH", "B_SLMNL_HMRM", "B_SLMNL_PRTY")) %>%
pull(snomed)
new_typhi <- microorganisms %>%
filter(mo == "B_SLMNL_THSS") %>%
slice(c(1,1, 1)) %>%
mutate(mo = c("B_SLMNL_TYPH", "B_SLMNL_HMRM", "B_SLMNL_PRTY"),
fullname = c("Salmonella Typhi", "Salmonella Typhimurium", "Salmonella Paratyphi"),
subspecies = c("Typhi", "Typhimurium", "Paratyphi"),
snomed = snomed2)
new_groupa <- microorganisms %>%
filter(mo == "B_SLMNL_GRPB") %>%
mutate(mo = "B_SLMNL_GRPA",
fullname = gsub("roup B", "roup A", fullname),
species = gsub("roup B", "roup A", species))
microorganisms$mo <- as.character(microorganisms$mo)
microorganisms <- microorganisms %>%
filter(!mo %in% c("B_SLMNL_TYPH", "B_SLMNL_HMRM", "B_SLMNL_PRTY")) %>%
bind_rows(new_typhi, new_groupa) %>%
arrange(fullname)
microorganisms$lpsn_parent[which(microorganisms$genus == "Salmonella" & microorganisms$rank == "species")] <- "516547"
microorganisms$gbif_parent[which(microorganisms$genus == "Salmonella" & microorganisms$rank == "species")] <- "3221815"
class(microorganisms$mo) <- c("mo", "character")