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(v0.7.1.9077) mo codes fix

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dr. M.S. (Matthijs) Berends
2019-09-20 14:18:29 +02:00
parent 3596adb295
commit 40e6b3e8f6
26 changed files with 256 additions and 256 deletions
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11
R/zzz.R
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@ -28,7 +28,7 @@
microorganisms.oldDT <- as.data.table(AMR::microorganisms.old)
# for fullname_lower: keep only dots, letters, numbers, slashes, spaces and dashes
microorganisms.oldDT$fullname_lower <- gsub("[^.a-z0-9/ \\-]+", "", tolower(microorganisms.oldDT$fullname))
setkey(microorganisms.oldDT, col_id, fullname)
setkey(microorganisms.oldDT, prevalence, fullname)
assign(x = "microorganismsDT",
value = make_DT(),
@ -81,12 +81,17 @@
#' @importFrom data.table as.data.table setkey
make_DT <- function() {
microorganismsDT <- as.data.table(AMR::microorganisms)
microorganismsDT <- as.data.table(AMR::microorganisms %>%
mutate(kingdom_index = case_when(kingdom == "Bacteria" ~ 1,
kingdom == "Fungi" ~ 2,
kingdom == "Protozoa" ~ 3,
kingdom == "Archaea" ~ 4,
TRUE ~ 6)))
# for fullname_lower: keep only dots, letters, numbers, slashes, spaces and dashes
microorganismsDT$fullname_lower <- gsub("[^.a-z0-9/ \\-]+", "", tolower(microorganismsDT$fullname))
setkey(microorganismsDT,
prevalence,
kingdom,
kingdom_index,
fullname)
microorganismsDT
}