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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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2
R/antibiogram.R
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@@ -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)$wisca), "This function only applies to WISCA models. Use {.help AMR::wisca}() or {.help AMR::antibiogram}() (with {.code wisca = TRUE}) to create a WISCA model.")
stop_ifnot(isTRUE(attributes(wisca_model)$wisca), "This function only applies to WISCA models. Use {.help [{.fun wisca}](AMR::wisca)} or {.help [{.fun antibiogram}](AMR::antibiogram)} (with {.code wisca = TRUE}) to create a WISCA model.")
attributes(wisca_model)$wisca_parameters
}