P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 03:22:00 +02:00
Code Releases Activity

(v1.4.0.9011) message formatting

Browse Source
This commit is contained in:
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
Download Patch File Download Diff File Expand all files Collapse all files

50
R/first_isolate.R
View File

@ -201,7 +201,7 @@ first_isolate <- function(x,
# WHONET support
x$patient_id <- paste(x$`First name`, x$`Last name`, x$Sex)
col_patient_id <- "patient_id"
message(font_blue(paste0("NOTE: Using combined columns `", font_bold("First name"), "`, `", font_bold("Last name"), "` and `", font_bold("Sex"), "` as input for `col_patient_id`")))
message_("Using combined columns `", font_bold("First name"), "`, `", font_bold("Last name"), "` and `", font_bold("Sex"), "` as input for `col_patient_id`")
} else {
col_patient_id <- search_type_in_df(x = x, type = "patient_id")
}
@ -250,7 +250,9 @@ first_isolate <- function(x,
}
# remove testcodes
if (!is.null(testcodes_exclude) & info == TRUE) {
message(font_black(paste0("[Criterion] Exclude test codes: ", toString(paste0("'", testcodes_exclude, "'")))))
message_("[Criterion] Exclude test codes: ", toString(paste0("'", testcodes_exclude, "'")),
add_fn = font_black,
as_note = FALSE)
}
if (is.null(col_specimen)) {
@ -261,7 +263,9 @@ first_isolate <- function(x,
if (!is.null(specimen_group)) {
check_columns_existance(col_specimen, x)
if (info == TRUE) {
message(font_black(paste0("[Criterion] Exclude other than specimen group '", specimen_group, "'")))
message_("[Criterion] Exclude other than specimen group '", specimen_group, "'",
add_fn = font_black,
as_note = FALSE)
}
}
if (!is.null(col_keyantibiotics)) {
@ -298,7 +302,7 @@ first_isolate <- function(x,
# no isolates found
if (abs(row.start) == Inf | abs(row.end) == Inf) {
if (info == TRUE) {
message(paste("=> Found", font_bold("no isolates")))
message_("=> Found ", font_bold("no isolates"), as_note = FALSE)
}
return(rep(FALSE, nrow(x)))
}
@ -350,13 +354,17 @@ first_isolate <- function(x,
weighted.notice <- "weighted "
if (info == TRUE) {
if (type == "keyantibiotics") {
message(font_black(paste0("[Criterion] Base inclusion on key antibiotics, ",
ifelse(ignore_I == FALSE, "not ", ""),
"ignoring I")))
message_("[Criterion] Base inclusion on key antibiotics, ",
ifelse(ignore_I == FALSE, "not ", ""),
"ignoring I",
add_fn = font_black,
as_note = FALSE)
}
if (type == "points") {
message(font_black(paste0("[Criterion] Base inclusion on key antibiotics, using points threshold of "
, points_threshold)))
message_("[Criterion] Base inclusion on key antibiotics, using points threshold of "
, points_threshold,
add_fn = font_black,
as_note = FALSE)
}
}
type_param <- type
@ -393,10 +401,14 @@ first_isolate <- function(x,
}
if (!is.null(col_icu)) {
if (icu_exclude == TRUE) {
message(font_black("[Criterion] Exclude isolates from ICU.\n"))
message_("[Criterion] Exclude isolates from ICU.",
add_fn = font_black,
as_note = FALSE)
x[which(as.logical(x[, col_icu, drop = TRUE])), "newvar_first_isolate"] <- FALSE
} else {
message(font_black("[Criterion] Include isolates from ICU.\n"))
message_("[Criterion] Include isolates from ICU.",
add_fn = font_black,
as_note = FALSE)
}
}
@ -405,18 +417,18 @@ first_isolate <- function(x,
# handle empty microorganisms
if (any(x$newvar_mo == "UNKNOWN", na.rm = TRUE) & info == TRUE) {
message(font_blue(paste0("NOTE: ", ifelse(include_unknown == TRUE, "Included ", "Excluded "),
format(sum(x$newvar_mo == "UNKNOWN", na.rm = TRUE),
decimal.mark = decimal.mark, big.mark = big.mark),
" isolates with a microbial ID 'UNKNOWN' (column `", font_bold(col_mo), "`)")))
message_(ifelse(include_unknown == TRUE, "Included ", "Excluded "),
format(sum(x$newvar_mo == "UNKNOWN", na.rm = TRUE),
decimal.mark = decimal.mark, big.mark = big.mark),
" isolates with a microbial ID 'UNKNOWN' (column `", font_bold(col_mo), "`)")
}
x[which(x$newvar_mo == "UNKNOWN"), "newvar_first_isolate"] <- include_unknown
# exclude all NAs
if (any(is.na(x$newvar_mo)) & info == TRUE) {
message(font_blue(paste0("NOTE: Excluded ", format(sum(is.na(x$newvar_mo), na.rm = TRUE),
decimal.mark = decimal.mark, big.mark = big.mark),
" isolates with a microbial ID 'NA' (column `", font_bold(col_mo), "`)")))
message_("Excluded ", format(sum(is.na(x$newvar_mo), na.rm = TRUE),
decimal.mark = decimal.mark, big.mark = big.mark),
" isolates with a microbial ID 'NA' (column `", font_bold(col_mo), "`)")
}
x[which(is.na(x$newvar_mo)), "newvar_first_isolate"] <- FALSE
@ -445,7 +457,7 @@ first_isolate <- function(x,
font_bold(paste0(n_found, " first ", weighted.notice, "isolates")),
" (", p_found_total, " of total where a microbial ID was available)")
}
message(font_black(msg_txt))
message_(msg_txt, add_fn = font_black, as_note = FALSE)
}
x$newvar_first_isolate