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(v0.8.0.9032) fix regex error

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dr. M.S. (Matthijs) Berends
2019-11-15 16:50:46 +01:00
parent 09e2730b53
commit 67f3f4387b
11 changed files with 49 additions and 43 deletions
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30
R/zzz.R
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@ -49,23 +49,27 @@
#' @importFrom data.table as.data.table setkey
#' @importFrom dplyr %>% mutate case_when
make_DT <- function() {
microorganismsDT <- as.data.table(AMR::microorganisms %>%
mutate(kingdom_index = case_when(kingdom == "Bacteria" ~ 1,
kingdom == "Fungi" ~ 2,
kingdom == "Protozoa" ~ 3,
kingdom == "Archaea" ~ 4,
TRUE ~ 99),
# for fullname_lower: keep only dots, letters,
# numbers, slashes, spaces and dashes
fullname_lower = gsub("[^.a-z0-9/ \\-]+", "",
# use this paste instead of `fullname` to
# work with Viridans Group Streptococci, etc.
tolower(trimws(paste(genus, species, subspecies))))))
microorganismsDT <- AMR::microorganisms %>%
mutate(kingdom_index = case_when(kingdom == "Bacteria" ~ 1,
kingdom == "Fungi" ~ 2,
kingdom == "Protozoa" ~ 3,
kingdom == "Archaea" ~ 4,
TRUE ~ 99),
# for fullname_lower: keep only dots, letters,
# numbers, slashes, spaces and dashes
fullname_lower = gsub("[^.a-z0-9/ \\-]+", "",
# use this paste instead of `fullname` to
# work with Viridans Group Streptococci, etc.
tolower(trimws(ifelse(genus == "",
fullname,
paste(genus, species, subspecies)))))) %>%
as.data.table()
# so arrange data on prevalence first, then kingdom, then full name
setkey(microorganismsDT,
prevalence,
kingdom_index,
fullname)
fullname_lower)
microorganismsDT
}