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