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mirror of https://github.com/msberends/AMR.git synced 2026-03-19 19:02:27 +01:00

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

- 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

View File

@@ -1198,7 +1198,7 @@ simulate_coverage <- function(params) {
#' @param wisca_model The outcome of [wisca()] or [`antibiogram(..., wisca = TRUE)`][antibiogram()].
#' @rdname antibiogram
retrieve_wisca_parameters <- function(wisca_model, ...) {
stop_ifnot(isTRUE(attributes(wisca_model)$wisca), "This function only applies to WISCA models. Use {.help wisca} or {.help antibiogram} (with {.code wisca = TRUE}) to create a WISCA model.")
stop_ifnot(isTRUE(attributes(wisca_model)$wisca), "This function only applies to WISCA models. Use {.help AMR::wisca}() or {.help AMR::antibiogram}() (with {.code wisca = TRUE}) to create a WISCA model.")
attributes(wisca_model)$wisca_parameters
}