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fix txt export of microorganisms
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17
R/rsi.R
17
R/rsi.R
@ -622,7 +622,7 @@ as.rsi.data.frame <- function(x,
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# only print message if class not already set
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message_("=> Assigning class 'rsi' to already clean column '", font_bold(ab), "' (",
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ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
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ab_name(ab_coerced, tolower = TRUE), ")... ",
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ab_name(ab_coerced, tolower = TRUE, language = NULL), ")... ",
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appendLF = FALSE,
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as_note = FALSE
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)
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@ -872,12 +872,13 @@ as_rsi_method <- function(method_short,
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lookup_lancefield[i],
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lookup_other[i]
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))
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if (NROW(get_record) == 0) {
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warning_("No ", method_param, " breakpoints available for ",
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font_italic(suppressMessages(suppressWarnings(mo_shortname(mo[i], language = NULL, keep_synonyms = FALSE)))),
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paste0(" / "),
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suppressMessages(suppressWarnings(ab_name(ab, language = NULL, tolower = TRUE))))
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suppressMessages(suppressWarnings(ab_name(ab_param, language = NULL, tolower = TRUE))),
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" (", ab_param, ")")
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rise_warning <- TRUE
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next
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}
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@ -899,18 +900,18 @@ as_rsi_method <- function(method_short,
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# uti not set as TRUE, but there are only a UTI breakpoints available, so throw warning
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warning_("in `as.rsi()`: interpretation of ", font_bold(ab_name(ab_param, tolower = TRUE)), " is only available for (uncomplicated) urinary tract infections (UTI) for some microorganisms, thus assuming `uti = TRUE`. See ?as.rsi.")
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rise_warning <- TRUE
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} else if (nrow(records_same_mo) > 1 && length(unique(records_same_mo$site)) > 1 && uti[i] == FALSE && all(c(TRUE, FALSE) %in% records_same_mo$uti, na.rm = TRUE) && message_not_thrown_before("as.rsi", "siteUTI", records_same_mo$mo[1], records_same_mo$ab[1])) {
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} else if (nrow(records_same_mo) > 1 && length(unique(records_same_mo$site)) > 1 && is.na(uti[i]) && all(c(TRUE, FALSE) %in% records_same_mo$uti, na.rm = TRUE) && message_not_thrown_before("as.rsi", "siteUTI", records_same_mo$mo[1], ab_param)) {
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# uti not set and both UTI and non-UTI breakpoints available, so throw warning
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warning_("in `as.rsi()`: breakpoints for UTI ", font_underline("and"), " non-UTI available for ",
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font_italic(suppressMessages(suppressWarnings(mo_shortname(records_same_mo$mo[1], language = NULL, keep_synonyms = FALSE)))),
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paste0(" / "),
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suppressMessages(suppressWarnings(ab_name(records_same_mo$ab[1], language = NULL, tolower = TRUE))),
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paste0(" - assuming non-UTI. Use argument `uti` to set which isolates are from urine. See ?as.rsi. '"),
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" / ",
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suppressMessages(suppressWarnings(ab_name(ab_param, language = NULL, tolower = TRUE))),
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" (", ab_param, ") - assuming non-UTI. Use argument `uti` to set which isolates are from urine. See ?as.rsi.",
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call = FALSE)
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get_record <- get_record %pm>%
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pm_filter(uti == FALSE)
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rise_warning <- TRUE
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} else if (nrow(records_same_mo) > 1 && length(unique(records_same_mo$site)) > 1 && all(records_same_mo$uti == FALSE, na.rm = TRUE) && message_not_thrown_before("as.rsi", "site", records_same_mo$mo[1], records_same_mo$ab[1])) {
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} else if (nrow(records_same_mo) > 1 && length(unique(records_same_mo$site)) > 1 && all(records_same_mo$uti == FALSE, na.rm = TRUE) && message_not_thrown_before("as.rsi", "siteOther", records_same_mo$mo[1], ab_param)) {
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# breakpoints for multiple body sites available, so throw warning
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site <- get_record[1L, "site", drop = FALSE]
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if (is.na(site)) {
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