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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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20
R/mdro.R
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@ -114,7 +114,7 @@ mdro <- function(x,
q_continue <- utils::menu(choices = c("OK", "Cancel"), graphics = FALSE, title = txt)
}
if (q_continue %in% c(FALSE, 2)) {
message("Cancelled, returning original data")
message_("Cancelled, returning original data", add_fn = font_red, as_note = FALSE)
return(x)
}
}
@ -162,10 +162,10 @@ mdro <- function(x,
col_mo <- search_type_in_df(x = x, type = "mo", info = info)
}
if (is.null(col_mo) & guideline$code == "tb") {
message(font_blue("NOTE: No column found as input for `col_mo`,",
font_bold("assuming all records contain", font_italic("Mycobacterium tuberculosis."))))
x$mo <- as.mo("Mycobacterium tuberculosis")
col_mo <- "mo"
message_("No column found as input for `col_mo`, ",
font_bold("assuming all records contain", font_italic("Mycobacterium tuberculosis.")))
x$mo <- as.mo("Mycobacterium tuberculosis")
col_mo <- "mo"
}
stop_if(is.null(col_mo), "`col_mo` must be set")
stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found")
@ -599,7 +599,7 @@ mdro <- function(x,
}
trans_tbl2 <- function(txt, rows, lst) {
if (info == TRUE) {
message(font_blue(txt, "..."), appendLF = FALSE)
message_(txt, "...", appendLF = FALSE, as_note = FALSE)
}
if (length(rows) > 0) {
# function specific for the CMI paper of 2012 (Magiorakos et al.)
@ -633,7 +633,7 @@ mdro <- function(x,
}
if (info == TRUE) {
message(font_blue(" OK"))
message_(" OK", as_note = FALSE)
}
}
@ -653,20 +653,20 @@ mdro <- function(x,
# take amoxicillin if ampicillin is unavailable
if (is.na(AMP) & !is.na(AMX)) {
if (verbose == TRUE) {
message(font_blue("NOTE: Filling ampicillin (AMP) results with amoxicillin (AMX) results"))
message_("Filling ampicillin (AMP) results with amoxicillin (AMX) results")
}
AMP <- AMX
}
# take ceftriaxone if cefotaxime is unavailable and vice versa
if (is.na(CRO) & !is.na(CTX)) {
if (verbose == TRUE) {
message(font_blue("NOTE: Filling ceftriaxone (CRO) results with cefotaxime (CTX) results"))
message_("Filling ceftriaxone (CRO) results with cefotaxime (CTX) results")
}
CRO <- CTX
}
if (is.na(CTX) & !is.na(CRO)) {
if (verbose == TRUE) {
message(font_blue("NOTE: Filling cefotaxime (CTX) results with ceftriaxone (CRO) results"))
message_("Filling cefotaxime (CTX) results with ceftriaxone (CRO) results")
}
CTX <- CRO
}