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(v2.1.1.9049) new 2024 breakpoints, add AMO, set NI instead of N

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dr. M.S. (Matthijs) Berends
2024-06-14 22:39:01 +02:00
parent de17de1be9
commit 9bf7584d58
57 changed files with 4375 additions and 135 deletions
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12
R/aa_helper_functions.R
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@ -743,9 +743,9 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_ca
# class 'sir' should be sorted like this
v <- c("S", "I", "R")
}
if (identical(v, c("I", "N", "R", "S", "SDD"))) {
if (identical(v, c("I", "NI", "R", "S", "SDD"))) {
# class 'sir' should be sorted like this
v <- c("S", "SDD", "I", "R", "N")
v <- c("S", "SDD", "I", "R", "NI")
}
# oxford comma
if (last_sep %in% c(" or ", " and ") && length(v) > 2) {
@ -1342,6 +1342,10 @@ progress_ticker <- function(n = 1, n_min = 0, print = TRUE, clear = TRUE, title
if (!is.null(progress_bar)) {
# so we use progress::progress_bar
# a close()-method was also added, see below for that
title <- trimws2(title)
if (title != "") {
title <- paste0(title, " ")
}
pb <- progress_bar$new(
format = paste0(title,
ifelse(only_bar_percent == TRUE, "[:bar] :percent", "[:bar] :percent (:current/:total,:eta)")),
@ -1538,14 +1542,14 @@ add_MO_lookup_to_AMR_env <- function() {
MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 3
# the fullname lowercase, important for the internal algorithms in as.mo()
MO_lookup$fullname_lower <- tolower(trimws(paste(
MO_lookup$fullname_lower <- tolower(trimws2(paste(
MO_lookup$genus,
MO_lookup$species,
MO_lookup$subspecies
)))
ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname, perl = TRUE)
MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname", drop = TRUE])
MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
MO_lookup$fullname_lower <- trimws2(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
# special for Salmonella - they have cities as subspecies but not the species (enterica) in the fullname:
MO_lookup$fullname_lower[which(MO_lookup$subspecies %like_case% "^[A-Z]")] <- gsub(" enterica ", " ", MO_lookup$fullname_lower[which(MO_lookup$subspecies %like_case% "^[A-Z]")], fixed = TRUE)