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(v1.3.0.9002) intrinsic_resistant data set

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dr. M.S. (Matthijs) Berends
2020-08-14 13:36:10 +02:00
parent 7d16bec21f
commit 08d62bb5d5
111 changed files with 50487 additions and 525 deletions
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8
R/eucast_rules.R
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@ -668,7 +668,13 @@ eucast_rules <- function(x,
# Official EUCAST rules ---------------------------------------------------
eucast_notification_shown <- FALSE
eucast_rules_df <- eucast_rules_file # internal data file
if (!is.null(list(...)$eucast_rules_df)) {
# this allows: eucast_rules(x, eucast_rules_df = AMR:::eucast_rules_file %>% filter(is.na(have_these_values)))
eucast_rules_df <- list(...)$eucast_rules_df
} else {
# otherwise internal data file, created in data-raw/internals.R
eucast_rules_df <- eucast_rules_file
}
for (i in seq_len(nrow(eucast_rules_df))) {
rule_previous <- eucast_rules_df[max(1, i - 1), "reference.rule"]