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(v1.4.0.9011) message formatting

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dr. M.S. (Matthijs) Berends
2020-10-27 15:56:51 +01:00
parent 98773aa859
commit 5a607abb36
27 changed files with 187 additions and 157 deletions
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37
R/guess_ab_col.R
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@ -94,14 +94,16 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE) {
if (length(ab_result) == 0) {
if (verbose == TRUE) {
message(paste0("No column found as input for `", search_string,
"` (", ab_name(search_string, language = NULL, tolower = TRUE), ")."))
message_("No column found as input for `", search_string,
"` (", ab_name(search_string, language = NULL, tolower = TRUE), ").",
add_fn = font_black,
as_note = FALSE)
}
return(NULL)
} else {
if (verbose == TRUE) {
message(font_blue(paste0("NOTE: Using column `", font_bold(ab_result), "` as input for `", search_string,
"` (", ab_name(search_string, language = NULL, tolower = TRUE), ").")))
message_("Using column `", font_bold(ab_result), "` as input for `", search_string,
"` (", ab_name(search_string, language = NULL, tolower = TRUE), ").")
}
return(ab_result)
}
@ -120,18 +122,20 @@ get_column_abx <- function(x,
meet_criteria(info, allow_class = "logical", has_length = 1)
if (info == TRUE) {
message(font_blue("NOTE: Auto-guessing columns suitable for analysis"), appendLF = FALSE)
message_("Auto-guessing columns suitable for analysis", appendLF = FALSE)
}
x <- as.data.frame(x, stringsAsFactors = FALSE)
if (NROW(x) > 10000) {
# only test maximum of 10,000 values per column
if (info == TRUE) {
message(font_blue(paste0(" (using only ", font_bold("the first 10,000 rows"), ")...")), appendLF = FALSE)
message_(" (using only ", font_bold("the first 10,000 rows"), ")...",
appendLF = FALSE,
as_note = FALSE)
}
x <- x[1:10000, , drop = FALSE]
} else if (info == TRUE) {
message(font_blue("..."), appendLF = FALSE)
message_("...", appendLF = FALSE, as_note = FALSE)
}
x_bak <- x
# only check columns that are a valid AB code, ATC code, name, abbreviation or synonym,
@ -178,7 +182,7 @@ get_column_abx <- function(x,
if (length(x) == 0) {
if (info == TRUE) {
message(font_blue("No columns found."))
message_("No columns found.")
}
return(x)
}
@ -192,13 +196,13 @@ get_column_abx <- function(x,
# succeeded with auto-guessing
if (info == TRUE) {
message(font_blue("OK."))
message_("OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
}
for (i in seq_len(length(x))) {
if (info == TRUE & verbose == TRUE & !names(x[i]) %in% names(duplicates)) {
message(font_blue(paste0("NOTE: Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE, language = NULL), ").")))
message_("Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE, language = NULL), ").")
}
if (info == TRUE & names(x[i]) %in% names(duplicates)) {
warning(font_red(paste0("Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
@ -225,15 +229,10 @@ get_column_abx <- function(x,
# missing a soft dependency may lower the reliability
missing <- soft_dependencies[!soft_dependencies %in% names(x)]
missing_msg <- paste(paste0(ab_name(missing, tolower = TRUE, language = NULL),
" (", missing, ")"),
" (", font_bold(missing, collapse = NULL), ")"),
collapse = ", ")
missing_msg <- paste("NOTE: Reliability would be improved if these antimicrobial results would be available too:",
missing_msg)
wrapped <- strwrap(missing_msg,
width = 0.95 * getOption("width"),
exdent = 6)
wrapped <- gsub("\\((.*?)\\)", paste0("(", font_bold("\\1"), ")"), wrapped) # add bold abbreviations
message(font_blue(wrapped, collapse = "\n"))
message_("Reliability would be improved if these antimicrobial results would be available too: ",
missing_msg)
}
}
x