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Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)

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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
2026-03-18 22:37:46 +00:00
parent 10c00ff606
commit 3928a3de55
18 changed files with 55 additions and 51 deletions
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6
R/mdro.R
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@@ -170,9 +170,9 @@ mdro <- function(x = NULL,
meet_criteria(infer_from_combinations, allow_class = "logical", has_length = 1)
if (isTRUE(only_sir_columns) && !any(is.sir(x))) {
stop_("There were no SIR columns found in the data set, despite {.arg only_sir_columns} being {.code TRUE}. Transform columns with {.help AMR::as.sir}() for valid antimicrobial interpretations.")
stop_("There were no SIR columns found in the data set, despite {.arg only_sir_columns} being {.code TRUE}. Transform columns with {.help [{.fun as.sir}](AMR::as.sir)} for valid antimicrobial interpretations.")
} else if (!isTRUE(only_sir_columns) && !any(is.sir(x)) && !any(is_sir_eligible(x))) {
stop_("There were no eligible SIR columns found in the data set. Transform columns with {.help AMR::as.sir}() for valid antimicrobial interpretations.")
stop_("There were no eligible SIR columns found in the data set. Transform columns with {.help [{.fun as.sir}](AMR::as.sir)} for valid antimicrobial interpretations.")
}
# get gene values as TRUE/FALSE
@@ -251,7 +251,7 @@ mdro <- function(x = NULL,
guideline.bak <- guideline
if (is.list(guideline)) {
# Custom MDRO guideline ---------------------------------------------------
stop_ifnot(inherits(guideline, "custom_mdro_guideline"), "use {.help AMR::custom_mdro_guideline}() to create custom guidelines")
stop_ifnot(inherits(guideline, "custom_mdro_guideline"), "use {.help [{.fun custom_mdro_guideline}](AMR::custom_mdro_guideline)} to create custom guidelines")
if (isTRUE(info)) {
txt <- paste0(
"Determining MDROs based on custom rules",