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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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8
R/custom_eucast_rules.R
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@@ -150,15 +150,15 @@ custom_eucast_rules <- function(...) {
)
stop_if(
identical(dots, "error"),
"rules must be a valid formula inputs (e.g., using '~'), see {.help AMR::custom_eucast_rules}()"
"rules must be a valid formula inputs (e.g., using '~'), see {.help [{.fun custom_eucast_rules}](AMR::custom_eucast_rules)}"
)
n_dots <- length(dots)
stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using {.help AMR::custom_eucast_rules}().")
stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using {.help [{.fun custom_eucast_rules}](AMR::custom_eucast_rules)}.")
out <- vector("list", n_dots)
for (i in seq_len(n_dots)) {
stop_ifnot(
inherits(dots[[i]], "formula"),
"rule ", i, " must be a valid formula input (e.g., using '~'), see {.help AMR::custom_eucast_rules}()"
"rule ", i, " must be a valid formula input (e.g., using '~'), see {.help [{.fun custom_eucast_rules}](AMR::custom_eucast_rules)}"
)
# Query
@@ -180,7 +180,7 @@ custom_eucast_rules <- function(...) {
result <- dots[[i]][[3]]
stop_ifnot(
deparse(result) %like% "==",
"the result of rule ", i, " (the part after the `~`) must contain `==`, such as in `... ~ ampicillin == \"R\"`, see {.help AMR::custom_eucast_rules}()"
"the result of rule ", i, " (the part after the `~`) must contain `==`, such as in `... ~ ampicillin == \"R\"`, see {.help [{.fun custom_eucast_rules}](AMR::custom_eucast_rules)}"
)
result_group <- as.character(result)[[2]]
result_group <- as.character(str2lang(result_group))