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AMR/data-raw/internals.R

84 lines
4.6 KiB
R

# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.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.gitlab.io/AMR. #
# ==================================================================== #
# Run this file to update the package using: -------------------------------
# source("data-raw/internals.R")
# --------------------------------------------------------------------------
# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
skip = 10,
sep = "\t",
stringsAsFactors = FALSE,
header = TRUE,
strip.white = TRUE,
na = c(NA, "", NULL))
# take the order of the reference.rule_group column in the original data file
eucast_rules_file$reference.rule_group <- factor(eucast_rules_file$reference.rule_group,
levels = unique(eucast_rules_file$reference.rule_group),
ordered = TRUE)
eucast_rules_file <- dplyr::arrange(eucast_rules_file,
reference.rule_group,
reference.rule)
eucast_rules_file$reference.rule_group <- as.character(eucast_rules_file$reference.rule_group)
# Translations ----
translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
sep = "\t",
stringsAsFactors = FALSE,
header = TRUE,
blank.lines.skip = TRUE,
fill = TRUE,
strip.white = TRUE,
encoding = "UTF-8",
fileEncoding = "UTF-8",
na.strings = c(NA, "", NULL),
allowEscapes = TRUE, # else "\\1" will be imported as "\\\\1"
quote = "")
# Old microorganism codes -------------------------------------------------
microorganisms.translation <- readRDS("data-raw/microorganisms.translation.rds")
# Export to package as internal data ----
usethis::use_data(eucast_rules_file, translations_file, microorganisms.translation,
internal = TRUE,
overwrite = TRUE,
version = 2)
# Remove from global environment ----
rm(eucast_rules_file)
rm(translations_file)
rm(microorganisms.translation)
# Save to raw data to repository ----
usethis::ui_done(paste0("Saving raw data to {usethis::ui_value('/data-raw/')}"))
devtools::load_all(quiet = TRUE)
# give official names to ABs and MOs
write.table(dplyr::mutate(rsi_translation, ab = ab_name(ab), mo = mo_name(mo)),
"data-raw/rsi_translation.txt", sep = "\t", na = "", row.names = FALSE)
write.table(dplyr::mutate_if(microorganisms, ~!is.numeric(.), as.character),
"data-raw/microorganisms.txt", sep = "\t", na = "", row.names = FALSE)
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)