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(v1.3.0.9026) eucast expert rules 3.2

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dr. M.S. (Matthijs) Berends
2020-09-24 00:30:11 +02:00
parent a1411ddafc
commit c19095a3d5
107 changed files with 48638 additions and 3953 deletions
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12
data-raw/reproduction_of_intrinsic_resistant.R
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@ -27,15 +27,17 @@ for (i in seq_len(nrow(antibiotics))) {
}
int_resis <- eucast_rules(int_resis,
eucast_rules_df = subset(AMR:::eucast_rules_file, is.na(have_these_values)))
eucast_rules_df = subset(AMR:::eucast_rules_file,
is.na(have_these_values) & reference.version == 3.2),
info = FALSE)
int_resis <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R"))] %>%
int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R"))] %>%
tidyr::pivot_longer(-microorganism) %>%
filter(value == "R") %>%
select(microorganism, antibiotic = name)
int_resis$microorganism <- mo_name(int_resis$microorganism, language = NULL)
int_resis2$microorganism <- mo_name(int_resis2$microorganism, language = NULL)
intrinsic_resistant <- as.data.frame(int_resis, stringsAsFactors = FALSE)
usethis::use_data(intrinsic_resistant, internal = FALSE, overwrite = TRUE, version = 2)
intrinsic_resistant <- as.data.frame(int_resis2, stringsAsFactors = FALSE)
usethis::use_data(intrinsic_resistant, internal = FALSE, overwrite = TRUE, version = 2, compress = "xz")
rm(intrinsic_resistant)