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(v1.7.1.9019) Morganella MIC in EUCAST 2021

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-07-12 12:28:41 +02:00
parent 5ccb330b42
commit fc946564d1
30 changed files with 112 additions and 74 deletions
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3
R/aa_helper_functions.R
View File

@ -400,6 +400,9 @@ word_wrap <- function(...,
# format backticks
msg <- gsub("(`.+?`)", font_grey_bg("\\1"), msg)
# clean introduced whitespace between fullstops
msg <- gsub("[.] +[.]", "..", msg)
msg
}

3
R/plot.R
View File

@ -684,6 +684,7 @@ plot_prepare_table <- function(x, expand) {
if (is.mic(x)) {
if (expand == TRUE) {
# expand range for MIC by adding factors of 2 from lowest to highest so all MICs in between also print
valid_lvls <- levels(x)
extra_range <- max(x) / 2
while (min(extra_range) / 2 > min(x)) {
extra_range <- c(min(extra_range) / 2, extra_range)
@ -692,7 +693,7 @@ plot_prepare_table <- function(x, expand) {
extra_range <- rep(0, length(extra_range))
names(extra_range) <- nms
x <- table(droplevels(x, as.mic = FALSE))
extra_range <- extra_range[!names(extra_range) %in% names(x)]
extra_range <- extra_range[!names(extra_range) %in% names(x) & names(extra_range) %in% valid_lvls]
x <- as.table(c(x, extra_range))
} else {
x <- table(droplevels(x, as.mic = FALSE))

26
R/rsi.R
View File

@ -411,13 +411,18 @@ as.rsi.mic <- function(x,
uti <- rep(uti, length(x))
}
message_("=> Interpreting MIC values of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""), "'", font_bold(ab), "' (",
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
ab_name(ab_coerced, tolower = TRUE), ")", mo_var_found,
agent_formatted <- paste0("'", font_bold(ab), "'")
agent_name <- ab_name(ab_coerced, tolower = TRUE, language = NULL)
if (generalise_antibiotic_name(ab) != generalise_antibiotic_name(agent_name)) {
agent_formatted <- paste0(agent_formatted, " (", ab_coerced, ", ", agent_name, ")")
}
message_("=> Interpreting MIC values of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
agent_formatted,
mo_var_found,
" according to ", ifelse(identical(reference_data, AMR::rsi_translation),
font_bold(guideline_coerced),
"manually defined 'reference_data'"),
" ... ",
"... ",
appendLF = FALSE,
as_note = FALSE)
@ -500,13 +505,18 @@ as.rsi.disk <- function(x,
uti <- rep(uti, length(x))
}
message_("=> Interpreting disk zones of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""), "'", font_bold(ab), "' (",
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
ab_name(ab_coerced, tolower = TRUE), ")", mo_var_found,
agent_formatted <- paste0("'", font_bold(ab), "'")
agent_name <- ab_name(ab_coerced, tolower = TRUE, language = NULL)
if (generalise_antibiotic_name(ab) != generalise_antibiotic_name(agent_name)) {
agent_formatted <- paste0(agent_formatted, " (", ab_coerced, ", ", agent_name, ")")
}
message_("=> Interpreting disk zones of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
agent_formatted,
mo_var_found,
" according to ", ifelse(identical(reference_data, AMR::rsi_translation),
font_bold(guideline_coerced),
"manually defined 'reference_data'"),
" ... ",
"... ",
appendLF = FALSE,
as_note = FALSE)