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speed improvement eucast_rules(), support more old MO codes

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-05-20 12:00:18 +02:00
parent b0033dae1b
commit 4ca00e1868
35 changed files with 590 additions and 683 deletions
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21
R/eucast_rules.R
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@ -226,7 +226,7 @@ eucast_rules <- function(x,
}
}
cols_ab <- get_column_abx(tbl = x,
cols_ab <- get_column_abx(x = x,
soft_dependencies = c("AMC",
"AMK",
"AMX",
@ -291,8 +291,7 @@ eucast_rules <- function(x,
"SXT",
"VAN"),
hard_dependencies = NULL,
verbose = verbose,
...)
verbose = verbose)
AMC <- cols_ab['AMC']
AMK <- cols_ab['AMK']
@ -674,8 +673,11 @@ eucast_rules <- function(x,
'out of', formatnr(nrow(tbl_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()
# print added values ----
if (verbose_info %>% filter(is.na(old)) %>% nrow() == 0) {
if (n_added == 0) {
colour <- cat # is function
} else {
colour <- blue # is function
@ -685,7 +687,7 @@ eucast_rules <- function(x,
filter(is.na(old)) %>%
nrow()), "test results"),
"\n")))
if (verbose_info %>% filter(is.na(old)) %>% nrow() > 0) {
if (n_added > 0) {
verbose_info %>%
filter(is.na(old)) %>%
# sort it well: S < I < R
@ -700,17 +702,20 @@ eucast_rules <- function(x,
}
# print changed values ----
if (verbose_info %>% filter(!is.na(old)) %>% nrow() == 0) {
if (n_changed == 0) {
colour <- cat # is function
} else {
colour <- blue # is function
}
cat(colour(paste0("\n=> ", wouldve, "changed ",
if (n_added + n_changed > 0) {
cat("\n")
}
cat(colour(paste0("=> ", wouldve, "changed ",
bold(formatnr(verbose_info %>%
filter(!is.na(old)) %>%
nrow()), "test results"),
"\n")))
if (verbose_info %>% filter(!is.na(old)) %>% nrow() > 0) {
if (n_changed > 0) {
verbose_info %>%
filter(!is.na(old)) %>%
# sort it well: S < I < R