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Qualify all {.help} tags with AMR:: and convert backtick ?func references

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- Add AMR:: namespace prefix and trailing () to all {.help} cli markup
  so they render as clickable help links (e.g. {.help AMR::as.sir}())
- Convert `?funcname` backtick-quoted help references to {.help AMR::funcname}()
  in aa_helper_functions.R, custom_eucast_rules.R, interpretive_rules.R,
  key_antimicrobials.R, mo.R, plotting.R, resistance_predict.R, and sir.R
- Skipped `?proportion` in sir_calc.R as 'proportion' is not exported

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
This commit is contained in:
Claude
2026-03-18 20:06:52 +00:00
parent 4798d2c55e
commit 0cc154257a
14 changed files with 41 additions and 41 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 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 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 as.sir} for valid antimicrobial interpretations.")
stop_("There were no eligible SIR columns found in the data set. Transform columns with {.help 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 custom_mdro_guideline} to create custom guidelines")
stop_ifnot(inherits(guideline, "custom_mdro_guideline"), "use {.help AMR::custom_mdro_guideline}() to create custom guidelines")
if (isTRUE(info)) {
txt <- paste0(
"Determining MDROs based on custom rules",