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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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10
data-raw/salmonellae.R
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@ -1410,6 +1410,7 @@ serovars <- c(
"Tudu",
"Tumodi",
"Typhi",
"Typhimurium",
"Typhisuis",
"Tyresoe",
"Uccle",
@ -1567,14 +1568,11 @@ salmonellae <- tibble(
gbif_parent = 9701185
)
salmonellae <- salmonellae %>%
# remove e.g. Salmonella Enteritidis if Salmonella enteritidis already existed
filter(!tolower(fullname) %in% tolower(AMR::microorganisms$fullname))
groups <- c(
"Paratyphi A",
"Paratyphi B",
"Paratyphi C",
"Group A",
"Group B",
"Group C",
"Group D"
@ -1591,3 +1589,7 @@ salmonellae <- salmonellae %>%
))
saveRDS(salmonellae, "data-raw/salmonellae.rds", version = 2)
# This was later needed to get the right parents for groups
microorganisms$lpsn_parent[which(microorganisms$genus == "Salmonella" & microorganisms$rank == "species")] <- "516547"
microorganisms$gbif_parent[which(microorganisms$genus == "Salmonella" & microorganisms$rank == "species")] <- "3221815"