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(v1.4.0.9044) mo tibble printing, mo_shortname() fix

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dr. M.S. (Matthijs) Berends
2020-12-24 23:29:10 +01:00
parent 128ebcfd62
commit df37584189
96 changed files with 1039 additions and 2847 deletions
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18
R/mdro.R
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@ -192,7 +192,7 @@ mdro <- function(x,
if (guideline$code == "cmi2012") {
guideline$name <- "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance."
guideline$author <- "Magiorakos AP, Srinivasan A, Carey RB, ..., Vatopoulos A, Weber JT, Monnet DL"
guideline$version <- "N/A"
guideline$version <- NA
guideline$source <- "Clinical Microbiology and Infection 18:3, 2012. DOI: 10.1111/j.1469-0691.2011.03570.x"
guideline$type <- "MDRs/XDRs/PDRs"
@ -221,7 +221,7 @@ mdro <- function(x,
} else if (guideline$code == "mrgn") {
guideline$name <- "Cross-border comparison of the Dutch and German guidelines on multidrug-resistant Gram-negative microorganisms"
guideline$author <- "M\u00fcller J, Voss A, K\u00f6ck R, ..., Kern WV, Wendt C, Friedrich AW"
guideline$version <- "N/A"
guideline$version <- NA
guideline$source <- "Antimicrobial Resistance and Infection Control 4:7, 2015. DOI: 10.1186/s13756-015-0047-6"
guideline$type <- "MRGNs"
@ -568,11 +568,13 @@ mdro <- function(x,
} else {
cat(font_red("\nResults with 'R' or 'I' are considered as resistance. Use `combine_SI = TRUE` to only consider 'R' as resistance.\n"))
}
cat("\nDetermining multidrug-resistant organisms (MDRO), according to:\n",
font_bold("Guideline: "), font_italic(guideline$name), "\n",
font_bold("Version: "), guideline$version, "\n",
font_bold("Author: "), guideline$author, "\n",
font_bold("Source: "), guideline$source, "\n",
cat("\n", word_wrap("Determining multidrug-resistant organisms (MDRO), according to:"), "\n",
word_wrap(paste0(font_bold("Guideline: "), font_italic(guideline$name)), extra_indent = 11, as_note = FALSE), "\n",
word_wrap(paste0(font_bold("Author(s): "), guideline$author), extra_indent = 11, as_note = FALSE), "\n",
ifelse(!is.na(guideline$version),
paste0(word_wrap(paste0(font_bold("Version: "), guideline$version), extra_indent = 11, as_note = FALSE), "\n"),
""),
word_wrap(paste0(font_bold("Source: "), guideline$source), extra_indent = 11, as_note = FALSE), "\n",
"\n", sep = "")
}
@ -1237,7 +1239,7 @@ mdro <- function(x,
if (guideline$code == "cmi2012") {
if (any(x$MDRO == -1, na.rm = TRUE)) {
warning_("NA introduced for isolates where the available percentage of antimicrobial classes was below ",
percentage(pct_required_classes), " (set with `pct_required_classes`)")
percentage(pct_required_classes), " (set with `pct_required_classes`)", call = FALSE)
# set these -1s to NA
x[which(x$MDRO == -1), "MDRO"] <- NA_integer_
}