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Replace {.fun} with {.help} for all exported functions in messaging

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All function names referenced via {.fun …} in cli-style messages are
exported in NAMESPACE, so {.help …} is the appropriate markup — it
renders as a clickable help link rather than plain function styling.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
This commit is contained in:
Claude
2026-03-18 16:06:30 +00:00
parent ad31fba556
commit 4798d2c55e
8 changed files with 30 additions and 30 deletions
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8
R/interpretive_rules.R
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@@ -198,7 +198,7 @@ interpretive_rules <- function(x,
add_MO_lookup_to_AMR_env()
if ("custom" %in% rules && is.null(custom_rules)) {
warning_("in {.fun eucast_rules}: no custom rules were set with the {.arg custom_rules} argument",
warning_("in {.help eucast_rules}: no custom rules were set with the {.arg custom_rules} argument",
immediate = TRUE
)
rules <- rules[rules != "custom"]
@@ -1062,7 +1062,7 @@ interpretive_rules <- function(x,
warn_lacking_sir_class <- warn_lacking_sir_class[order(colnames(x.bak))]
warn_lacking_sir_class <- warn_lacking_sir_class[!is.na(warn_lacking_sir_class)]
warning_(
"in {.fun eucast_rules}: not all columns with antimicrobial results are of class 'sir'. Transform them on beforehand, with e.g.:\n",
"in {.help eucast_rules}: not all columns with antimicrobial results are of class 'sir'. Transform them on beforehand, with e.g.:\n",
" - ", x_deparsed, " %>% as.sir(", ifelse(length(warn_lacking_sir_class) == 1,
warn_lacking_sir_class,
paste0(warn_lacking_sir_class[1], ":", warn_lacking_sir_class[length(warn_lacking_sir_class)])
@@ -1178,7 +1178,7 @@ edit_sir <- function(x,
suppressWarnings(new_edits[rows, cols][non_SIR] <<- to)
}
warning_(
"in {.fun eucast_rules}: value \"", to, "\" added to the factor levels of column",
"in {.help eucast_rules}: value \"", to, "\" added to the factor levels of column",
ifelse(length(cols) == 1, "", "s"),
" ", vector_and(cols, quotes = "`", sort = FALSE),
" because this value was not an existing factor level."
@@ -1186,7 +1186,7 @@ edit_sir <- function(x,
txt_warning()
warned <- FALSE
} else {
warning_("in {.fun eucast_rules}: ", w$message)
warning_("in {.help eucast_rules}: ", w$message)
txt_warning()
}
},