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(v1.6.0.9015) italicise_taxonomy

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dr. M.S. (Matthijs) Berends
2021-05-03 10:47:32 +02:00
parent e405de079c
commit 12a8d59869
34 changed files with 625 additions and 126 deletions
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27
R/eucast_rules.R
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@ -65,7 +65,6 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#' @details
#' **Note:** This function does not translate MIC values to RSI values. Use [as.rsi()] for that. \cr
#' **Note:** When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. \cr
#'
#' The file containing all EUCAST rules is located here: <https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv>. **Note:** Old taxonomic names are replaced with the current taxonomy where applicable. For example, *Ochrobactrum anthropi* was renamed to *Brucella anthropi* in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this `AMR` package contains the taxonomy updated until [`r CATALOGUE_OF_LIFE$yearmonth_LPSN`][catalogue_of_life()].
#'
@ -322,17 +321,6 @@ eucast_rules <- function(x,
}
cols_ab[match(x_new, names(cols_ab))]
}
markup_italics_where_needed <- function(x) {
# returns names found in family, genus or species as italics
if (!has_colour()) {
return(x)
}
x <- unlist(strsplit(x, " "))
ind <- gsub("[)(:]", "", x) %in% c(MO_lookup[which(MO_lookup$rank %in% c("family", "genus")), ]$fullname,
MO_lookup[which(MO_lookup$rank == "species"), ]$species)
x[ind] <- font_italic(x[ind], collapse = NULL)
paste(x, collapse = " ")
}
get_antibiotic_names <- function(x) {
x <- x %pm>%
strsplit(",") %pm>%
@ -343,6 +331,7 @@ eucast_rules <- function(x,
paste(collapse = ", ")
x <- gsub("_", " ", x, fixed = TRUE)
x <- gsub("except CAZ", paste("except", ab_name("CAZ", language = NULL, tolower = TRUE)), x, fixed = TRUE)
x <- gsub("except TGC", paste("except", ab_name("TGC", language = NULL, tolower = TRUE)), x, fixed = TRUE)
x <- gsub("cephalosporins (1st|2nd|3rd|4th|5th)", "cephalosporins (\\1 gen.)", x)
x
}
@ -655,9 +644,10 @@ eucast_rules <- function(x,
# Print rule -------------------------------------------------------------
if (rule_current != rule_previous) {
# is new rule within group, print its name
cat(markup_italics_where_needed(word_wrap(rule_current,
width = getOption("width") - 30,
extra_indent = 6)))
cat(italicise_taxonomy(word_wrap(rule_current,
width = getOption("width") - 30,
extra_indent = 6),
type = "ansi"))
warned <- FALSE
}
}
@ -795,9 +785,10 @@ eucast_rules <- function(x,
get_antibiotic_names(cols))
if (info == TRUE) {
# print rule
cat(markup_italics_where_needed(word_wrap(format_custom_query_rule(rule$query, colours = FALSE),
width = getOption("width") - 30,
extra_indent = 6)))
cat(italicise_taxonomy(word_wrap(format_custom_query_rule(rule$query, colours = FALSE),
width = getOption("width") - 30,
extra_indent = 6),
type = "ansi"))
warned <- FALSE
}
run_changes <- edit_rsi(x = x,