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Replace {.fun} with {.help} for all exported functions in messaging

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All function names referenced via {.fun …} in cli-style messages are
exported in NAMESPACE, so {.help …} is the appropriate markup — it
renders as a clickable help link rather than plain function styling.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
This commit is contained in:
Claude
2026-03-18 16:06:30 +00:00
parent ad31fba556
commit 4798d2c55e
8 changed files with 30 additions and 30 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 {.fun 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 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 {.fun as.sir} for valid antimicrobial interpretations.")
stop_("There were no eligible SIR columns found in the data set. Transform columns with {.help 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 {.fun custom_mdro_guideline} to create custom guidelines")
stop_ifnot(inherits(guideline, "custom_mdro_guideline"), "use {.help custom_mdro_guideline} to create custom guidelines")
if (isTRUE(info)) {
txt <- paste0(
"Determining MDROs based on custom rules",