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styled, unit test fix

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dr. M.S. (Matthijs) Berends
2022-08-28 10:31:50 +02:00
parent 4cb1db4554
commit 4d050aef7c
147 changed files with 10897 additions and 8169 deletions
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19
data-raw/reproduction_of_intrinsic_resistant.R
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@@ -9,7 +9,7 @@
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# Diagnostics & Advice, and University Medical Center Groningen. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
@@ -32,19 +32,22 @@ for (i in seq_len(nrow(antibiotics))) {
}
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)
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")), drop = FALSE] %>%
int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R")), drop = FALSE] %>%
tidyr::pivot_longer(-mo) %>%
filter(value == "R") %>%
filter(value == "R") %>%
select(mo, ab = name)
# remove lab drugs
untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate|macromethod|screening|/nacubactam"), "ab", drop = TRUE]
int_resis2 <- int_resis2 %>%
filter(!ab %in% untreatable) %>%
int_resis2 <- int_resis2 %>%
filter(!ab %in% untreatable) %>%
arrange(mo, ab)
intrinsic_resistant <- as.data.frame(int_resis2, stringsAsFactors = FALSE)