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mirror of https://github.com/msberends/AMR.git synced 2025-07-08 11:11:54 +02:00

(v1.2.0.9034) code cleaning

This commit is contained in:
2020-07-13 09:17:24 +02:00
parent c0cf7ab02b
commit 6ab468362d
36 changed files with 266 additions and 265 deletions

View File

@ -519,7 +519,7 @@ eucast_rules <- function(x,
left_join_microorganisms(by = col_mo, suffix = c("_oldcols", ""))
x$gramstain <- mo_gramstain(x[, col_mo, drop = TRUE], language = NULL)
x$genus_species <- paste(x$genus, x$species)
if (ab_missing(AMP) & !ab_missing(AMX)) {
# ampicillin column is missing, but amoxicillin is available
message(font_blue(paste0("NOTE: Using column `", font_bold(AMX), "` as input for ampicillin (J01CA01) since many EUCAST rules depend on it.")))
@ -702,8 +702,8 @@ eucast_rules <- function(x,
if (info == TRUE & !rule_group_current %like% "other" & eucast_notification_shown == FALSE) {
cat(paste0("\n", font_grey(strrep("-", options()$width - 1)),
"\nRules by the ", font_bold("European Committee on Antimicrobial Susceptibility Testing (EUCAST)"),
"\n", font_blue("http://eucast.org/"), "\n"))
"\nRules by the ", font_bold("European Committee on Antimicrobial Susceptibility Testing (EUCAST)"),
"\n", font_blue("http://eucast.org/"), "\n"))
eucast_notification_shown <- TRUE
}
@ -843,9 +843,9 @@ eucast_rules <- function(x,
cat(paste0("\n", font_grey(strrep("-", options()$width - 1)), "\n"))
cat(font_bold(paste("The rules", paste0(wouldve, "affected"),
formatnr(n_distinct(verbose_info$row)),
"out of", formatnr(nrow(x_original)),
"rows, making a total of", formatnr(nrow(verbose_info)), "edits\n")))
formatnr(n_distinct(verbose_info$row)),
"out of", formatnr(nrow(x_original)),
"rows, making a total of", formatnr(nrow(verbose_info)), "edits\n")))
n_added <- verbose_info %>% filter(is.na(old)) %>% nrow()
n_changed <- verbose_info %>% filter(!is.na(old)) %>% nrow()
@ -858,8 +858,8 @@ eucast_rules <- function(x,
}
cat(colour(paste0("=> ", wouldve, "added ",
font_bold(formatnr(verbose_info %>%
filter(is.na(old)) %>%
nrow()), "test results"),
filter(is.na(old)) %>%
nrow()), "test results"),
"\n")))
if (n_added > 0) {
added_summary <- verbose_info %>%
@ -882,8 +882,8 @@ eucast_rules <- function(x,
}
cat(colour(paste0("=> ", wouldve, "changed ",
font_bold(formatnr(verbose_info %>%
filter(!is.na(old)) %>%
nrow()), "test results"),
filter(!is.na(old)) %>%
nrow()), "test results"),
"\n")))
if (n_changed > 0) {
changed_summary <- verbose_info %>%