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(v1.1.0.9004) lose dependencies

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dr. M.S. (Matthijs) Berends
2020-05-16 13:05:47 +02:00
parent 9fce546901
commit 7f3da74b17
111 changed files with 3211 additions and 2345 deletions
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28
R/guess_ab_col.R
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@ -27,8 +27,6 @@
#' @param search_string a text to search `x` for, will be checked with [as.ab()] if this value is not a column in `x`
#' @param verbose a logical to indicate whether additional info should be printed
#' @details You can look for an antibiotic (trade) name or abbreviation and it will search `x` and the [antibiotics] data set for any column containing a name or code of that antibiotic. **Longer columns names take precendence over shorter column names.**
#' @importFrom dplyr %>% select filter_all any_vars
#' @importFrom crayon blue
#' @return A column name of `x`, or `NULL` when no result is found.
#' @export
#' @inheritSection AMR Read more on our website!
@ -103,23 +101,20 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE) {
return(NULL)
} else {
if (verbose == TRUE) {
message(blue(paste0("NOTE: Using column `", bold(ab_result), "` as input for `", search_string,
message(font_blue(paste0("NOTE: Using column `", font_bold(ab_result), "` as input for `", search_string,
"` (", ab_name(search_string, language = "en", tolower = TRUE), ").")))
}
return(ab_result)
}
}
#' @importFrom crayon blue bold
#' @importFrom dplyr %>% mutate arrange pull
get_column_abx <- function(x,
soft_dependencies = NULL,
hard_dependencies = NULL,
verbose = FALSE,
...) {
message(blue("NOTE: Auto-guessing columns suitable for analysis..."), appendLF = FALSE)
message(font_blue("NOTE: Auto-guessing columns suitable for analysis..."), appendLF = FALSE)
x <- as.data.frame(x, stringsAsFactors = FALSE)
x_bak <- x
@ -173,15 +168,15 @@ get_column_abx <- function(x,
x <- x[order(names(x), x)]
# succeeded with aut-guessing
message(blue("OK."))
message(font_blue("OK."))
for (i in seq_len(length(x))) {
if (verbose == TRUE & !names(x[i]) %in% names(duplicates)) {
message(blue(paste0("NOTE: Using column `", bold(x[i]), "` as input for `", names(x)[i],
message(font_blue(paste0("NOTE: Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE), ").")))
}
if (names(x[i]) %in% names(duplicates)) {
warning(red(paste0("Using column `", bold(x[i]), "` as input for `", names(x)[i],
warning(font_red(paste0("Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE),
"), although it was matched for multiple antibiotics or columns.")),
call. = FALSE,
@ -204,14 +199,11 @@ get_column_abx <- function(x,
if (!all(soft_dependencies %in% names(x))) {
# missing a soft dependency may lower the reliability
missing <- soft_dependencies[!soft_dependencies %in% names(x)]
missing_txt <- data.frame(missing = missing,
missing_names = ab_name(missing, tolower = TRUE),
stringsAsFactors = FALSE) %>%
mutate(txt = paste0(bold(missing), " (", missing_names, ")")) %>%
arrange(missing_names) %>%
pull(txt)
message(blue("NOTE: Reliability will be improved if these antimicrobial results would be available too:",
paste(missing_txt, collapse = ", ")))
missing_txt <- paste(paste0(ab_name(missing, tolower = TRUE, language = NULL),
" (", font_bold(missing, collapse = NULL), ")"),
collapse = ", ")
message(font_blue("NOTE: Reliability would be improved if these antimicrobial results would be available too:",
missing_txt))
}
}
x