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new species groups, updated clinical breakpoints

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dr. M.S. (Matthijs) Berends
2023-07-08 17:30:05 +02:00
parent 2d97cca6d9
commit acb534102b
172 changed files with 44445 additions and 52835 deletions
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30
R/aa_helper_functions.R
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@ -1,11 +1,11 @@
# ==================================================================== #
# TITLE #
# TITLE: #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# SOURCE CODE: #
# https://github.com/msberends/AMR #
# #
# CITE AS #
# PLEASE CITE THIS SOFTWARE AS: #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
@ -1182,20 +1182,20 @@ is_dark <- function() {
}
isTRUE(AMR_env$is_dark_theme)
}
font_black <- function(..., collapse = " ") {
font_black <- function(..., collapse = " ", adapt = TRUE) {
before <- "\033[38;5;232m"
after <- "\033[39m"
if (is_dark()) {
if (isTRUE(adapt) && is_dark()) {
# white
before <- "\033[37m"
after <- "\033[39m"
}
try_colour(..., before = before, after = after, collapse = collapse)
}
font_white <- function(..., collapse = " ") {
font_white <- function(..., collapse = " ", adapt = TRUE) {
before <- "\033[37m"
after <- "\033[39m"
if (is_dark()) {
if (isTRUE(adapt) && is_dark()) {
# black
before <- "\033[38;5;232m"
after <- "\033[39m"
@ -1283,7 +1283,7 @@ font_stripstyle <- function(x) {
x
}
progress_ticker <- function(n = 1, n_min = 0, print = TRUE, ...) {
progress_ticker <- function(n = 1, n_min = 0, print = TRUE, clear = TRUE, title = "", only_bar_percent = FALSE, ...) {
if (print == FALSE || n < n_min) {
# create fake/empty object
pb <- list()
@ -1299,9 +1299,11 @@ progress_ticker <- function(n = 1, n_min = 0, print = TRUE, ...) {
progress_bar <- import_fn("progress_bar", "progress", error_on_fail = FALSE)
if (!is.null(progress_bar)) {
# so we use progress::progress_bar
# a close() method was also added, see below this function
# a close()-method was also added, see below for that
pb <- progress_bar$new(
format = "[:bar] :percent (:current/:total,:eta)",
format = paste0(title,
ifelse(only_bar_percent == TRUE, "[:bar] :percent", "[:bar] :percent (:current/:total,:eta)")),
clear = clear,
total = n
)
} else {
@ -1487,11 +1489,11 @@ add_MO_lookup_to_AMR_env <- function() {
MO_lookup$kingdom_index <- NA_real_
MO_lookup[which(MO_lookup$kingdom == "Bacteria" | MO_lookup$mo == "UNKNOWN"), "kingdom_index"] <- 1
MO_lookup[which(MO_lookup$kingdom == "Fungi"), "kingdom_index"] <- 2
MO_lookup[which(MO_lookup$kingdom == "Protozoa"), "kingdom_index"] <- 3
MO_lookup[which(MO_lookup$kingdom == "Archaea"), "kingdom_index"] <- 4
MO_lookup[which(MO_lookup$kingdom == "Fungi"), "kingdom_index"] <- 1.25
MO_lookup[which(MO_lookup$kingdom == "Protozoa"), "kingdom_index"] <- 1.5
MO_lookup[which(MO_lookup$kingdom == "Archaea"), "kingdom_index"] <- 2
# all the rest
MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
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(