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(v1.5.0.9019) use functions without loading AMR pkg

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-02-17 10:58:13 +01:00
parent 2dd0656355
commit 601ea7377c
30 changed files with 90 additions and 74 deletions
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21
R/aa_helper_functions.R
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@ -82,20 +82,27 @@ check_dataset_integrity <- function() {
# exception for example_isolates
overwritten <- overwritten[overwritten != "example_isolates"]
if (length(overwritten) > 0) {
warning_(ifelse(length(overwritten) == 1,
"The following data set is overwritten by your global environment and prevents the AMR package from working correctly: ",
"The following data sets are overwritten by your global environment and prevent the AMR package from working correctly: "),
if (length(overwritten) > 1) {
plural <- c("s are", "", "s")
} else {
plural <- c(" is", "s", "")
}
warning_("The following data set", plural[1],
" overwritten by your global environment and prevent", plural[2],
" the AMR package from working correctly: ",
vector_and(overwritten, quotes = "'"),
".\nPlease rename your object(s).", call = FALSE)
".\nPlease rename your object", plural[3], ".", call = FALSE)
}
# check if other packages did not overwrite our data sets
valid_microorganisms <- TRUE
valid_antibiotics <- TRUE
tryCatch({
check_microorganisms <- all(c("mo", "fullname", "kingdom", "phylum",
valid_microorganisms <- all(c("mo", "fullname", "kingdom", "phylum",
"class", "order", "family", "genus",
"species", "subspecies", "rank",
"species_id", "source", "ref", "prevalence") %in% colnames(microorganisms),
na.rm = TRUE)
check_antibiotics <- all(c("ab", "atc", "cid", "name", "group",
valid_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),
@ -104,7 +111,7 @@ check_dataset_integrity <- function() {
# package not yet loaded
require("AMR")
})
stop_if(!check_microorganisms | !check_antibiotics,
stop_if(!valid_microorganisms | !valid_antibiotics,
"the data set `microorganisms` or `antibiotics` was overwritten in your environment because another package with the same object names was loaded _after_ the AMR package, preventing the AMR package from working correctly. Please load the AMR package last.")
invisible(TRUE)
}

2
R/ab_class_selectors.R
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@ -43,7 +43,7 @@
#' # See ?example_isolates.
#'
#' # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
#' example_isolates[, c(carbapenems())]
#' example_isolates[, carbapenems()]
#' # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
#' example_isolates[, c("mo", aminoglycosides())]
#'

4
R/mo.R
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@ -1806,7 +1806,9 @@ print.mo_uncertainties <- function(x, ...) {
candidates <- candidates[order(1 - scores)]
scores_formatted <- trimws(formatC(round(scores, 3), format = "f", digits = 3))
n_candidates <- length(candidates)
candidates <- vector_and(paste0(candidates, " (", scores_formatted[order(1 - scores)], ")"), quotes = FALSE)
candidates <- vector_and(paste0(candidates, " (", scores_formatted[order(1 - scores)], ")"),
quotes = FALSE,
sort = FALSE)
# align with input after arrow
candidates <- paste0("\n",
strwrap(paste0("Also matched",