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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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2
data-raw/internals.R
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@ -81,3 +81,5 @@ write.table(dplyr::mutate_if(antibiotics, ~!is.numeric(.), as.character),
"data-raw/antibiotics.txt", sep = "\t", na = "", row.names = FALSE)
write.table(dplyr::mutate_all(antivirals, as.character),
"data-raw/antivirals.txt", sep = "\t", na = "", row.names = FALSE)
write.table(intrinsic_resistant,
"data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE)

49463
data-raw/intrinsic_resistant.txt Normal file
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41
data-raw/reproduction_of_intrinsic_resistant.R Normal file
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@ -0,0 +1,41 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
library(AMR)
int_resis <- data.frame(microorganism = microorganisms$mo, stringsAsFactors = FALSE)
for (i in seq_len(nrow(antibiotics))) {
int_resis$new <- as.rsi("S")
colnames(int_resis)[ncol(int_resis)] <- antibiotics$name[i]
}
int_resis <- eucast_rules(int_resis,
eucast_rules_df = subset(AMR:::eucast_rules_file, is.na(have_these_values)))
int_resis <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R"))] %>%
tidyr::pivot_longer(-microorganism) %>%
filter(value == "R") %>%
select(microorganism, antibiotic = name)
int_resis$microorganism <- mo_name(int_resis$microorganism, language = NULL)
intrinsic_resistant <- as.data.frame(int_resis, stringsAsFactors = FALSE)
usethis::use_data(intrinsic_resistant, internal = FALSE, overwrite = TRUE, version = 2)
rm(intrinsic_resistant)