mirror of https://github.com/msberends/AMR.git
83 lines
3.5 KiB
R
83 lines
3.5 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# SOURCE #
|
|
# https://gitlab.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# 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. #
|
|
# #
|
|
# This R package was created for academic research and 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.gitab.io/AMR. #
|
|
# ==================================================================== #
|
|
|
|
# print successful as.mo coercions to file, not uncertain ones
|
|
#' @importFrom dplyr distinct
|
|
set_mo_history <- function(x, mo, force = FALSE) {
|
|
file_location <- base::path.expand('~/.Rhistory_mo')
|
|
if (base::interactive() | force == TRUE) {
|
|
mo_hist <- read_mo_history(force = force)
|
|
df <- distinct(data.frame(x, mo, stringsAsFactors = FALSE), x, .keep_all = TRUE)
|
|
x <- df$x
|
|
mo <- df$mo
|
|
for (i in 1:length(x)) {
|
|
if (NROW(mo_hist[base::which(mo_hist$x == x[i] & mo_hist$package_version == utils::packageVersion("AMR")),]) == 0) {
|
|
base::write(x = c(x[i], mo[i], base::as.character(utils::packageVersion("AMR"))),
|
|
file = file_location,
|
|
ncolumns = 3,
|
|
append = TRUE,
|
|
sep = "\t")
|
|
}
|
|
}
|
|
}
|
|
return(base::invisible())
|
|
}
|
|
|
|
get_mo_history <- function(x, force = FALSE) {
|
|
file_read <- read_mo_history(force = force)
|
|
if (base::is.null(file_read)) {
|
|
NA
|
|
} else {
|
|
data.frame(x, stringsAsFactors = FALSE) %>%
|
|
left_join(file_read, by = "x") %>%
|
|
pull(mo)
|
|
}
|
|
}
|
|
|
|
#' @importFrom dplyr %>% filter distinct
|
|
read_mo_history <- function(force = FALSE) {
|
|
file_location <- base::path.expand('~/.Rhistory_mo')
|
|
if (!base::file.exists(file_location) | (!base::interactive() & force == FALSE)) {
|
|
return(NULL)
|
|
}
|
|
file_read <- utils::read.table(file = file_location,
|
|
header = FALSE,
|
|
sep = "\t",
|
|
col.names = c("x", "mo", "package_version"),
|
|
stringsAsFactors = FALSE)
|
|
# Below: filter on current package version.
|
|
# Even current fullnames may be replaced by new taxonomic names, so new versions of
|
|
# the Catalogue of Life must not lead to data corruption.
|
|
file_read %>%
|
|
filter(package_version == utils::packageVersion("AMR")) %>%
|
|
distinct(x, mo, .keep_all = TRUE)
|
|
}
|
|
|
|
#' @rdname as.mo
|
|
#' @export
|
|
clean_mo_history <- function() {
|
|
file_location <- base::path.expand('~/.Rhistory_mo')
|
|
if (base::file.exists(file_location)) {
|
|
base::unlink(file_location)
|
|
}
|
|
}
|
|
|