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Fix {.topic} to use required pkg::topic format with display text

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{.topic} in cli requires a package-qualified topic reference to generate
a valid x-r-help:pkg::topic URI. Bare {.topic AMR-options} produced a
malformed x-r-help:AMR-options URI (no package prefix).

Use the [display_text](pkg::topic) form throughout:
  {.topic [AMR-options](AMR::AMR-options)}
  {.topic [AMR-deprecated](AMR::AMR-deprecated)}

The hyphen in the topic name is fine as a URI string even though
AMR::AMR-options is not a valid R symbol expression.

The fallback handler in format_message() already handles the [text](uri)
form by extracting the display text, so plain-text output is unchanged.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
This commit is contained in:
Claude
2026-03-18 22:47:38 +00:00
parent 8760c6d85a
commit 5ecbc9001e
4 changed files with 6 additions and 6 deletions
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4
R/count.R
View File

@@ -128,7 +128,7 @@ count_resistant <- function(...,
# other arguments for meet_criteria are handled by sir_calc() # other arguments for meet_criteria are handled by sir_calc()
meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1) meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_resistant", "eucast_default", entire_session = TRUE)) { if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_resistant", "eucast_default", entire_session = TRUE)) {
message_("{.help [{.fun count_resistant}](AMR::count_resistant)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic AMR-options}.") message_("{.help [{.fun count_resistant}](AMR::count_resistant)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
message_("This message will be shown once per session.") message_("This message will be shown once per session.")
} }
tryCatch( tryCatch(
@@ -152,7 +152,7 @@ count_susceptible <- function(...,
# other arguments for meet_criteria are handled by sir_calc() # other arguments for meet_criteria are handled by sir_calc()
meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1) meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_susceptible", "eucast_default", entire_session = TRUE)) { if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_susceptible", "eucast_default", entire_session = TRUE)) {
message_("{.help [{.fun count_susceptible}](AMR::count_susceptible)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic AMR-options}.") message_("{.help [{.fun count_susceptible}](AMR::count_susceptible)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
message_("This message will be shown once per session.") message_("This message will be shown once per session.")
} }
tryCatch( tryCatch(

2
R/interpretive_rules.R
View File

@@ -1097,7 +1097,7 @@ eucast_rules <- function(x,
rules = getOption("AMR_interpretive_rules", default = c("breakpoints", "expected_phenotypes")), rules = getOption("AMR_interpretive_rules", default = c("breakpoints", "expected_phenotypes")),
...) { ...) {
if (!is.null(getOption("AMR_eucastrules", default = NULL))) { if (!is.null(getOption("AMR_eucastrules", default = NULL))) {
warning_("The global option {.code AMR_eucastrules} that you have set is now invalid was ignored - set {.code AMR_interpretive_rules} instead. See {.topic AMR-options}.") warning_("The global option {.code AMR_eucastrules} that you have set is now invalid was ignored - set {.code AMR_interpretive_rules} instead. See {.topic [AMR-options](AMR::AMR-options)}.")
} }
interpretive_rules(x = x, col_mo = col_mo, info = info, rules = rules, guideline = "EUCAST", ...) interpretive_rules(x = x, col_mo = col_mo, info = info, rules = rules, guideline = "EUCAST", ...)
} }

4
R/proportion.R
View File

@@ -238,7 +238,7 @@ resistance <- function(...,
# other arguments for meet_criteria are handled by sir_calc() # other arguments for meet_criteria are handled by sir_calc()
meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1) meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("resistance", "eucast_default", entire_session = TRUE)) { if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("resistance", "eucast_default", entire_session = TRUE)) {
message_("{.help [{.fun resistance}](AMR::resistance)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic AMR-options}.") message_("{.help [{.fun resistance}](AMR::resistance)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
message_("This message will be shown once per session.") message_("This message will be shown once per session.")
} }
tryCatch( tryCatch(
@@ -266,7 +266,7 @@ susceptibility <- function(...,
# other arguments for meet_criteria are handled by sir_calc() # other arguments for meet_criteria are handled by sir_calc()
meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1) meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("susceptibility", "eucast_default", entire_session = TRUE)) { if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("susceptibility", "eucast_default", entire_session = TRUE)) {
message_("{.help [{.fun susceptibility}](AMR::susceptibility)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic AMR-options}.") message_("{.help [{.fun susceptibility}](AMR::susceptibility)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
message_("This message will be shown once per session.") message_("This message will be shown once per session.")
} }
tryCatch( tryCatch(

2
R/zz_deprecated.R
View File

@@ -124,7 +124,7 @@ deprecation_warning <- function(old = NULL, new = NULL, fn = NULL, extra_msg = N
". The old name will be removed in future version, so please update your code.", ". The old name will be removed in future version, so please update your code.",
ifelse(type == "argument", ifelse(type == "argument",
". While the old argument still works, it will be removed in a future version, so please update your code.", ". While the old argument still works, it will be removed in a future version, so please update your code.",
" and will be removed in a future version, see {.topic AMR-deprecated}." " and will be removed in a future version, see {.topic [AMR-deprecated](AMR::AMR-deprecated)}."
) )
), ),
ifelse(!is.null(extra_msg), ifelse(!is.null(extra_msg),