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(v1.2.0.9026) move to github

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dr. M.S. (Matthijs) Berends
2020-07-08 14:48:06 +02:00
parent 2134fc76e2
commit 76fc8e1b14
211 changed files with 1090 additions and 1748 deletions
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22
R/aa_helper_functions.R
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,7 +16,7 @@
# 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. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
# functions from dplyr, will perhaps become poorman
@ -77,18 +77,22 @@ check_dataset_integrity <- function() {
"class", "order", "family", "genus",
"species", "subspecies", "rank",
"species_id", "source", "ref", "prevalence") %in% colnames(microorganisms),
na.rm = TRUE) & NROW(microorganisms) == NROW(MO_lookup)
na.rm = TRUE)
check_antibiotics <- all(c("ab", "atc", "cid", "name", "group",
"atc_group1", "atc_group2", "abbreviations",
"synonyms", "oral_ddd", "oral_units",
"iv_ddd", "iv_units", "loinc") %in% colnames(antibiotics),
na.rm = TRUE)
}, error = function(e)
stop('Please use the command \'library("AMR")\' before using this function, to load the required reference data.', call. = FALSE)
stop_('please use the command \'library("AMR")\' before using this function, to load the required reference data.', call = FALSE)
)
if (!check_microorganisms | !check_antibiotics) {
stop("Data set `microorganisms` or data set `antibiotics` is overwritten by your global environment and prevents the AMR package from working correctly. Please rename your object before using this function.", call. = FALSE)
}
data_in_pkg <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item"]
data_in_globalenv <- ls(envir = globalenv())
overwritten <- data_in_pkg[data_in_pkg %in% data_in_globalenv]
stop_if(length(overwritten) > 0,
"the following data set is overwritten by your global environment and prevents the AMR package from working correctly:\n",
paste0("'", overwritten, "'", collapse = ", "),
".\nPlease rename your object before using this function.", call = FALSE)
invisible(TRUE)
}
@ -198,7 +202,9 @@ stop_ifnot_installed <- function(package) {
import_fn <- function(name, pkg) {
stop_ifnot_installed(pkg)
get(name, envir = asNamespace(pkg))
tryCatch(
get(name, envir = asNamespace(pkg)),
error = function(e) stop_("an error occurred in import_fn() while using this function", call = FALSE))
}
stop_ <- function(..., call = TRUE) {