mirror of
https://github.com/msberends/AMR.git
synced 2026-03-19 15:42:27 +01:00
Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)
Replace all instances of {.help AMR::fn}() (incorrect format with manual
parentheses outside the link) with {.help [{.fun fn}](AMR::fn)} which is
the correct cli hyperlink syntax: the display text [{.fun fn}] renders the
function name with parentheses automatically, and (AMR::fn) is the link target.
Also update the plain-text fallback handler in aa_helper_functions.R to
extract the display text from the [text](topic) markdown link format,
so that non-cli environments show just the function name (e.g. `fn()`),
not the raw link markup.
Dynamic cases in amr_selectors.R and mo_property.R also updated.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
This commit is contained in:
Claude
26
R/sir.R
26
R/sir.R
@@ -529,10 +529,10 @@ as.sir.default <- function(x,
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if (all(x %unlike% "(S|I|R)", na.rm = TRUE) && !all(x %in% c(1, 2, 3, 4, 5), na.rm = TRUE)) {
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# check if they are actually MICs or disks
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if (all_valid_mics(x)) {
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warning_("in {.help AMR::as.sir}(): input values were guessed to be MIC values - preferably transform them with {.help AMR::as.mic}() before running {.help AMR::as.sir}().")
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warning_("in {.help [{.fun as.sir}](AMR::as.sir)}: input values were guessed to be MIC values - preferably transform them with {.help [{.fun as.mic}](AMR::as.mic)} before running {.help [{.fun as.sir}](AMR::as.sir)}.")
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return(as.sir(as.mic(x), ...))
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} else if (all_valid_disks(x)) {
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warning_("in {.help AMR::as.sir}(): input values were guessed to be disk diffusion values - preferably transform them with {.help AMR::as.disk}() before running {.help AMR::as.sir}().")
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warning_("in {.help [{.fun as.sir}](AMR::as.sir)}: input values were guessed to be disk diffusion values - preferably transform them with {.help [{.fun as.disk}](AMR::as.disk)} before running {.help [{.fun as.sir}](AMR::as.sir)}.")
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return(as.sir(as.disk(x), ...))
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}
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}
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@@ -601,7 +601,7 @@ as.sir.default <- function(x,
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ifelse(length(out7) > 0, paste0("7 as \"", out7, "\""), NA_character_),
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ifelse(length(out8) > 0, paste0("8 as \"", out8, "\""), NA_character_)
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)
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message_("in {.help AMR::as.sir}(): Interpreting input value ", vector_and(out[!is.na(out)], quotes = FALSE, sort = FALSE))
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message_("in {.help [{.fun as.sir}](AMR::as.sir)}: Interpreting input value ", vector_and(out[!is.na(out)], quotes = FALSE, sort = FALSE))
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}
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if (na_before != na_after) {
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@@ -610,7 +610,7 @@ as.sir.default <- function(x,
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sort() %pm>%
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vector_and(quotes = TRUE)
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cur_col <- get_current_column()
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warning_("in {.help AMR::as.sir}(): ", na_after - na_before, " result",
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warning_("in {.help [{.fun as.sir}](AMR::as.sir)}: ", na_after - na_before, " result",
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ifelse(na_after - na_before > 1, "s", ""),
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ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
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" truncated (",
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@@ -1029,7 +1029,7 @@ as.sir.data.frame <- function(x,
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if (isTRUE(info)) {
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message_(font_green_bg(" DONE "), as_note = FALSE)
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message()
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message_("Run {.help AMR::sir_interpretation_history}() to retrieve a logbook with all details of the breakpoint interpretations.")
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message_("Run {.help [{.fun sir_interpretation_history}](AMR::sir_interpretation_history)} to retrieve a logbook with all details of the breakpoint interpretations.")
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}
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} else {
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# sequential mode (non-parallel)
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@@ -1168,13 +1168,13 @@ as_sir_method <- function(method_short,
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dots <- list(...)
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dots <- dots[which(!names(dots) %in% c("warn", "mo.bak", "is_data.frame"))]
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if (length(dots) != 0) {
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warning_("These arguments in {.help AMR::as.sir}() are no longer used: ", vector_and(names(dots), quotes = "`"), ".", call = FALSE)
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warning_("These arguments in {.help [{.fun as.sir}](AMR::as.sir)} are no longer used: ", vector_and(names(dots), quotes = "`"), ".", call = FALSE)
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}
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current_sir_interpretation_history <- NROW(AMR_env$sir_interpretation_history)
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if (isTRUE(info) && message_not_thrown_before("as.sir", "sir_interpretation_history")) {
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message_("Run {.help AMR::sir_interpretation_history}() afterwards to retrieve a logbook with all details of the breakpoint interpretations.\n\n")
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message_("Run {.help [{.fun sir_interpretation_history}](AMR::sir_interpretation_history)} afterwards to retrieve a logbook with all details of the breakpoint interpretations.\n\n")
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}
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current_df <- tryCatch(get_current_data(NA, 0), error = function(e) NULL)
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@@ -1276,7 +1276,7 @@ as_sir_method <- function(method_short,
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mo_var_found <- ""
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}
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if (is.null(mo)) {
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stop_("No information was supplied about the microorganisms (missing argument {.arg mo} and no column of class 'mo' found). See {.help AMR::as.sir}().\n\n",
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stop_("No information was supplied about the microorganisms (missing argument {.arg mo} and no column of class 'mo' found). See {.help [{.fun as.sir}](AMR::as.sir)}.\n\n",
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"To transform certain columns with e.g. mutate(), use ", highlight_code("data %>% mutate(across(..., as.sir, mo = x))"), ", where x is your column with microorganisms.\n",
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"To transform all ", method_long, " in a data set, use ", highlight_code("data %>% as.sir()"), " or ", highlight_code(paste0("data %>% mutate_if(is.", method_short, ", as.sir)")), ".",
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call = FALSE
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@@ -1312,7 +1312,7 @@ as_sir_method <- function(method_short,
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if (length(ab) == 1 && ab %like% paste0("as.", method_short)) {
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stop_("No unambiguous name was supplied about the antibiotic (argument {.arg ab}). See {.help AMR::as.sir}().", call = FALSE)
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stop_("No unambiguous name was supplied about the antibiotic (argument {.arg ab}). See {.help [{.fun as.sir}](AMR::as.sir)}.", call = FALSE)
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}
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ab.bak <- trimws2(ab)
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@@ -1328,7 +1328,7 @@ as_sir_method <- function(method_short,
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if (all(is.na(ab))) {
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if (isTRUE(info)) {
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message_("Returning NAs for unknown antibiotic: ", vector_and(ab.bak, sort = FALSE, quotes = TRUE),
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". Rename this column to a valid name or code, and check the output with {.help AMR::as.ab}().",
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". Rename this column to a valid name or code, and check the output with {.help [{.fun as.ab}](AMR::as.ab)}.",
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as_note = FALSE
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)
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}
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@@ -1352,7 +1352,7 @@ as_sir_method <- function(method_short,
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}
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if (isTRUE(add_intrinsic_resistance) && guideline_coerced %unlike% "EUCAST") {
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if (isTRUE(info) && message_not_thrown_before("as.sir", "intrinsic")) {
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message_("in {.help AMR::as.sir}(): using {.arg add_intrinsic_resistance} is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.")
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message_("in {.help [{.fun as.sir}](AMR::as.sir)}: using {.arg add_intrinsic_resistance} is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.")
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}
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}
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@@ -1721,7 +1721,7 @@ as_sir_method <- function(method_short,
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pm_filter(uti == FALSE)
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notes_current <- paste0(
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notes_current, "\n",
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paste0("Breakpoints for UTI ", font_bold("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument `uti` to set which isolates are from urine. See {.help AMR::as.sir}().")
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paste0("Breakpoints for UTI ", font_bold("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument `uti` to set which isolates are from urine. See {.help [{.fun as.sir}](AMR::as.sir)}.")
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)
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} else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && all(breakpoints_current$uti == FALSE, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteOther", mo_current, ab_current)) {
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# breakpoints for multiple body sites available
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@@ -1988,7 +1988,7 @@ sir_interpretation_history <- function(clean = FALSE) {
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#' @noRd
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print.sir_log <- function(x, ...) {
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if (NROW(x) == 0) {
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message_("No results to print. First run {.help AMR::as.sir}() on MIC values or disk diffusion zones (or on a {.cls data.frame} containing any of these) to print a 'logbook' data set here.")
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message_("No results to print. First run {.help [{.fun as.sir}](AMR::as.sir)} on MIC values or disk diffusion zones (or on a {.cls data.frame} containing any of these) to print a 'logbook' data set here.")
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return(invisible(NULL))
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}
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class(x) <- class(x)[class(x) != "sir_log"]
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