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(v1.7.1.9073) as.rsi() fix for UTIs

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dr. M.S. (Matthijs) Berends
2021-12-14 21:47:14 +01:00
parent 5eef01165e
commit bd4bb1d72f
25 changed files with 27787 additions and 27785 deletions
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18
data-raw/reproduction_of_intrinsic_resistant.R
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@@ -25,29 +25,27 @@
library(AMR)
library(dplyr)
int_resis <- data.frame(microorganism = microorganisms$mo, stringsAsFactors = FALSE)
int_resis <- data.frame(mo = microorganisms$mo, stringsAsFactors = FALSE)
for (i in seq_len(nrow(antibiotics))) {
int_resis$new <- as.rsi("S")
colnames(int_resis)[ncol(int_resis)] <- antibiotics$name[i]
colnames(int_resis)[ncol(int_resis)] <- antibiotics$ab[i]
}
int_resis <- eucast_rules(int_resis,
int_resis <- eucast_rules(int_resis,
eucast_rules_df = subset(AMR:::EUCAST_RULES_DF,
is.na(have_these_values) & reference.version == 3.3),
info = FALSE)
int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R"))] %>%
tidyr::pivot_longer(-microorganism) %>%
tidyr::pivot_longer(-mo) %>%
filter(value == "R") %>%
select(microorganism, antibiotic = name)
select(mo, ab = name)
# remove lab drugs
untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate|macromethod|screening|/nacubactam"), "name", drop = TRUE]
untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate|macromethod|screening|/nacubactam"), "ab", drop = TRUE]
int_resis2 <- int_resis2 %>%
filter(!antibiotic %in% untreatable) %>%
arrange(microorganism, antibiotic)
int_resis2$microorganism <- mo_name(int_resis2$microorganism, language = NULL)
filter(!ab %in% untreatable) %>%
arrange(mo, ab)
intrinsic_resistant <- as.data.frame(int_resis2, stringsAsFactors = FALSE)
usethis::use_data(intrinsic_resistant, internal = FALSE, overwrite = TRUE, version = 2, compress = "xz")