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Qualify all {.help} tags with AMR:: and convert backtick ?func references

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- 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
This commit is contained in:
Claude
2026-03-18 20:06:52 +00:00
parent 4798d2c55e
commit 0cc154257a
14 changed files with 41 additions and 41 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
R/aa_helper_functions.R
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@@ -928,7 +928,7 @@ ascertain_sir_classes <- function(x, obj_name) {
warning_(
"the data provided in argument `", obj_name,
"` should contain at least one column of class 'sir'. Eligible SIR column were now guessed. ",
"See `?as.sir`.",
"See {.help AMR::as.sir}().",
immediate = TRUE
)
sirs_eligible <- is_sir_eligible(x)

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

2
R/atc_online.R
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@@ -180,7 +180,7 @@ atc_online_property <- function(atc_code,
colnames(out) <- gsub("^atc.*", "atc", tolower(colnames(out)))
if (length(out) == 0) {
message_("in {.help atc_online_property}: no properties found for ATC ", atc_code[i], ". Please check {.href {atc_url} this WHOCC webpage}.")
message_("in {.help AMR::atc_online_property}(): no properties found for ATC ", atc_code[i], ". Please check {.href {atc_url} this WHOCC webpage}.")
returnvalue[i] <- NA
next
}

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 `?custom_eucast_rules`"
"rules must be a valid formula inputs (e.g., using '~'), see {.help AMR::custom_eucast_rules}()"
)
n_dots <- length(dots)
stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using `?custom_eucast_rules`.")
stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using {.help 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 `?custom_eucast_rules`"
"rule ", i, " must be a valid formula input (e.g., using '~'), see {.help 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 `?custom_eucast_rules`"
"the result of rule ", i, " (the part after the `~`) must contain `==`, such as in `... ~ ampicillin == \"R\"`, see {.help AMR::custom_eucast_rules}()"
)
result_group <- as.character(result)[[2]]
result_group <- as.character(str2lang(result_group))

12
R/custom_mdro_guideline.R
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@@ -145,15 +145,15 @@ custom_mdro_guideline <- function(..., as_factor = TRUE) {
)
stop_if(
identical(dots, "error"),
"rules must be a valid formula inputs (e.g., using '~'), see {.help mdro}"
"rules must be a valid formula inputs (e.g., using '~'), see {.help AMR::mdro}()"
)
n_dots <- length(dots)
stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using {.help mdro}.")
stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using {.help AMR::mdro}().")
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 mdro}"
"rule ", i, " must be a valid formula input (e.g., using '~'), see {.help AMR::mdro}()"
)
# Query
@@ -202,7 +202,7 @@ c.custom_mdro_guideline <- function(x, ..., as_factor = NULL) {
}
for (g in list(...)) {
stop_ifnot(inherits(g, "custom_mdro_guideline"),
"for combining custom MDRO guidelines, all rules must be created with {.help custom_mdro_guideline}",
"for combining custom MDRO guidelines, all rules must be created with {.help AMR::custom_mdro_guideline}()",
call = FALSE
)
vals <- attributes(x)$values
@@ -259,14 +259,14 @@ run_custom_mdro_guideline <- function(df, guideline, info) {
}
)
if (identical(qry, "error")) {
warning_("in {.help custom_mdro_guideline}: rule ", i,
warning_("in {.help AMR::custom_mdro_guideline}(): rule ", i,
" (`", as.character(guideline[[i]]$query), "`) was ignored because of this error message: ",
AMR_env$err_msg,
call = FALSE
)
next
}
stop_ifnot(is.logical(qry), "in {.help custom_mdro_guideline}: rule ", i, " (`", guideline[[i]]$query,
stop_ifnot(is.logical(qry), "in {.help AMR::custom_mdro_guideline}(): rule ", i, " (`", guideline[[i]]$query,
"`) must return {.code TRUE} or {.code FALSE}, not ",
format_class(class(qry), plural = FALSE),
call = FALSE

4
R/guess_ab_col.R
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@@ -210,7 +210,7 @@ get_column_abx <- function(x,
newnames <- suppressWarnings(as.ab(names(dots), info = FALSE))
if (anyNA(newnames)) {
if (isTRUE(info)) {
message_("WARNING: some columns returned NA for {.help as.ab}", as_note = FALSE)
message_("WARNING: some columns returned NA for {.help AMR::as.ab}()", as_note = FALSE)
}
warning_("Invalid antibiotic reference(s): ", vector_and(names(dots)[is.na(newnames)], quotes = FALSE),
call = FALSE,
@@ -267,7 +267,7 @@ get_column_abx <- function(x,
if (all_okay == TRUE) {
message_(" OK.", as_note = FALSE)
} else if (!isFALSE(dups)) {
message_("WARNING: some results from {.help as.ab} are duplicated: ", vector_and(dups, quotes = "`"), as_note = FALSE)
message_("WARNING: some results from {.help AMR::as.ab}() are duplicated: ", vector_and(dups, quotes = "`"), as_note = FALSE)
} else {
message_(" WARNING.", as_note = FALSE)
}

10
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 {.help eucast_rules}: no custom rules were set with the {.arg custom_rules} argument",
warning_("in {.help AMR::eucast_rules}(): no custom rules were set with the {.arg custom_rules} argument",
immediate = TRUE
)
rules <- rules[rules != "custom"]
@@ -481,7 +481,7 @@ interpretive_rules <- function(x,
"Rules by the ",
font_bold(paste0("AMR package v", utils::packageDescription("AMR")$Version)),
" (", format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y"),
"), see `?eucast_rules`\n"
"), see {.help AMR::eucast_rules}()\n"
)
))
cat("\n\n")
@@ -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 {.help eucast_rules}: not all columns with antimicrobial results are of class 'sir'. Transform them on beforehand, with e.g.:\n",
"in {.help AMR::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 {.help eucast_rules}: value \"", to, "\" added to the factor levels of column",
"in {.help AMR::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 {.help eucast_rules}: ", w$message)
warning_("in {.help AMR::eucast_rules}(): ", w$message)
txt_warning()
}
},

2
R/key_antimicrobials.R
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@@ -187,7 +187,7 @@ key_antimicrobials <- function(x = NULL,
"No columns available ",
paste0("Only using ", values_new_length, " out of ", values_old_length, " defined columns ")
),
"as key antimicrobials for ", name, "s. See `?key_antimicrobials`."
"as key antimicrobials for ", name, "s. See {.help AMR::key_antimicrobials}()."
)
}

6
R/mdro.R
View File

@@ -170,9 +170,9 @@ mdro <- function(x = NULL,
meet_criteria(infer_from_combinations, allow_class = "logical", has_length = 1)
if (isTRUE(only_sir_columns) && !any(is.sir(x))) {
stop_("There were no SIR columns found in the data set, despite {.arg only_sir_columns} being {.code TRUE}. Transform columns with {.help as.sir} for valid antimicrobial interpretations.")
stop_("There were no SIR columns found in the data set, despite {.arg only_sir_columns} being {.code TRUE}. Transform columns with {.help AMR::as.sir}() for valid antimicrobial interpretations.")
} else if (!isTRUE(only_sir_columns) && !any(is.sir(x)) && !any(is_sir_eligible(x))) {
stop_("There were no eligible SIR columns found in the data set. Transform columns with {.help as.sir} for valid antimicrobial interpretations.")
stop_("There were no eligible SIR columns found in the data set. Transform columns with {.help AMR::as.sir}() for valid antimicrobial interpretations.")
}
# get gene values as TRUE/FALSE
@@ -251,7 +251,7 @@ mdro <- function(x = NULL,
guideline.bak <- guideline
if (is.list(guideline)) {
# Custom MDRO guideline ---------------------------------------------------
stop_ifnot(inherits(guideline, "custom_mdro_guideline"), "use {.help custom_mdro_guideline} to create custom guidelines")
stop_ifnot(inherits(guideline, "custom_mdro_guideline"), "use {.help AMR::custom_mdro_guideline}() to create custom guidelines")
if (isTRUE(info)) {
txt <- paste0(
"Determining MDROs based on custom rules",

2
R/mo.R
View File

@@ -914,7 +914,7 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
x <- x[1:50, , drop = FALSE]
}
cat(font_blue(word_wrap("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See `?mo_matching_score`.\n\n")))
cat(font_blue(word_wrap("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See {.help AMR::mo_matching_score}().\n\n")))
add_MO_lookup_to_AMR_env()

2
R/mo_source.R
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@@ -249,7 +249,7 @@ get_mo_source <- function(destination = getOption("AMR_mo_source", "~/mo_source.
current_ext <- regexpr("\\.([[:alnum:]]+)$", destination)
current_ext <- ifelse(current_ext > -1L, substring(destination, current_ext + 1L), "")
vowel <- ifelse(current_ext %like% "^[AEFHILMNORSX]", "n", "")
stop_("The AMR mo source must be an RDS file, not a{vowel} {toupper(current_ext)} file. If \"{basename(destination)}\" was meant as your input file, use {.help set_mo_source} on this file. In any case, the option {.code AMR_mo_source} must be set to another path.")
stop_("The AMR mo source must be an RDS file, not a{vowel} {toupper(current_ext)} file. If \"{basename(destination)}\" was meant as your input file, use {.help AMR::set_mo_source}() on this file. In any case, the option {.code AMR_mo_source} must be set to another path.")
}
if (is.null(AMR_env$mo_source)) {
AMR_env$mo_source <- readRDS_AMR(path.expand(destination))

2
R/plotting.R
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@@ -412,7 +412,7 @@ create_scale_sir <- function(aesthetics, colours_SIR, language, eucast_I, ...) {
scale$labels <- function(x) {
stop_ifnot(all(x %in% c(levels(NA_sir_), "SI", "IR", NA)),
"Apply `scale_", aesthetics[1], "_sir()` to a variable of class 'sir', see `?as.sir`.",
"Apply `scale_", aesthetics[1], "_sir()` to a variable of class 'sir', see {.help AMR::as.sir}().",
call = FALSE
)
x <- as.character(x)

2
R/resistance_predict.R
View File

@@ -238,7 +238,7 @@ resistance_predict <- function(x,
prediction <- predictmodel$fit
se <- predictmodel$se.fit
} else {
stop("no valid model selected. See `?resistance_predict`.")
stop("no valid model selected. See {.help AMR::resistance_predict}().")
}
# prepare the output dataframe

26
R/sir.R
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@@ -529,10 +529,10 @@ as.sir.default <- function(x,
if (all(x %unlike% "(S|I|R)", na.rm = TRUE) && !all(x %in% c(1, 2, 3, 4, 5), na.rm = TRUE)) {
# check if they are actually MICs or disks
if (all_valid_mics(x)) {
warning_("in {.help as.sir}: input values were guessed to be MIC values - preferably transform them with {.help as.mic} before running {.help as.sir}.")
warning_("in {.help AMR::as.sir}(): input values were guessed to be MIC values - preferably transform them with {.help AMR::as.mic}() before running {.help AMR::as.sir}().")
return(as.sir(as.mic(x), ...))
} else if (all_valid_disks(x)) {
warning_("in {.help as.sir}: input values were guessed to be disk diffusion values - preferably transform them with {.help as.disk} before running {.help as.sir}.")
warning_("in {.help AMR::as.sir}(): input values were guessed to be disk diffusion values - preferably transform them with {.help AMR::as.disk}() before running {.help AMR::as.sir}().")
return(as.sir(as.disk(x), ...))
}
}
@@ -601,7 +601,7 @@ as.sir.default <- function(x,
ifelse(length(out7) > 0, paste0("7 as \"", out7, "\""), NA_character_),
ifelse(length(out8) > 0, paste0("8 as \"", out8, "\""), NA_character_)
)
message_("in {.help as.sir}: Interpreting input value ", vector_and(out[!is.na(out)], quotes = FALSE, sort = FALSE))
message_("in {.help AMR::as.sir}(): Interpreting input value ", vector_and(out[!is.na(out)], quotes = FALSE, sort = FALSE))
}
if (na_before != na_after) {
@@ -610,7 +610,7 @@ as.sir.default <- function(x,
sort() %pm>%
vector_and(quotes = TRUE)
cur_col <- get_current_column()
warning_("in {.help as.sir}: ", na_after - na_before, " result",
warning_("in {.help AMR::as.sir}(): ", na_after - na_before, " result",
ifelse(na_after - na_before > 1, "s", ""),
ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
" truncated (",
@@ -1029,7 +1029,7 @@ as.sir.data.frame <- function(x,
if (isTRUE(info)) {
message_(font_green_bg(" DONE "), as_note = FALSE)
message()
message_("Run {.help sir_interpretation_history} to retrieve a logbook with all details of the breakpoint interpretations.")
message_("Run {.help AMR::sir_interpretation_history}() to retrieve a logbook with all details of the breakpoint interpretations.")
}
} else {
# sequential mode (non-parallel)
@@ -1168,13 +1168,13 @@ as_sir_method <- function(method_short,
dots <- list(...)
dots <- dots[which(!names(dots) %in% c("warn", "mo.bak", "is_data.frame"))]
if (length(dots) != 0) {
warning_("These arguments in {.help as.sir} are no longer used: ", vector_and(names(dots), quotes = "`"), ".", call = FALSE)
warning_("These arguments in {.help AMR::as.sir}() are no longer used: ", vector_and(names(dots), quotes = "`"), ".", call = FALSE)
}
current_sir_interpretation_history <- NROW(AMR_env$sir_interpretation_history)
if (isTRUE(info) && message_not_thrown_before("as.sir", "sir_interpretation_history")) {
message_("Run {.help sir_interpretation_history} afterwards to retrieve a logbook with all details of the breakpoint interpretations.\n\n")
message_("Run {.help AMR::sir_interpretation_history}() afterwards to retrieve a logbook with all details of the breakpoint interpretations.\n\n")
}
current_df <- tryCatch(get_current_data(NA, 0), error = function(e) NULL)
@@ -1276,7 +1276,7 @@ as_sir_method <- function(method_short,
mo_var_found <- ""
}
if (is.null(mo)) {
stop_("No information was supplied about the microorganisms (missing argument {.arg mo} and no column of class 'mo' found). See {.help as.sir}.\n\n",
stop_("No information was supplied about the microorganisms (missing argument {.arg mo} and no column of class 'mo' found). See {.help AMR::as.sir}().\n\n",
"To transform certain columns with e.g. mutate(), use `data %>% mutate(across(..., as.sir, mo = x))`, where x is your column with microorganisms.\n",
"To transform all ", method_long, " in a data set, use `data %>% as.sir()` or `data %>% mutate_if(is.", method_short, ", as.sir)`.",
call = FALSE
@@ -1312,7 +1312,7 @@ as_sir_method <- function(method_short,
if (length(ab) == 1 && ab %like% paste0("as.", method_short)) {
stop_("No unambiguous name was supplied about the antibiotic (argument {.arg ab}). See {.help as.sir}.", call = FALSE)
stop_("No unambiguous name was supplied about the antibiotic (argument {.arg ab}). See {.help AMR::as.sir}().", call = FALSE)
}
ab.bak <- trimws2(ab)
@@ -1328,7 +1328,7 @@ as_sir_method <- function(method_short,
if (all(is.na(ab))) {
if (isTRUE(info)) {
message_("Returning NAs for unknown antibiotic: ", vector_and(ab.bak, sort = FALSE, quotes = TRUE),
". Rename this column to a valid name or code, and check the output with {.help as.ab}.",
". Rename this column to a valid name or code, and check the output with {.help AMR::as.ab}().",
as_note = FALSE
)
}
@@ -1352,7 +1352,7 @@ as_sir_method <- function(method_short,
}
if (isTRUE(add_intrinsic_resistance) && guideline_coerced %unlike% "EUCAST") {
if (isTRUE(info) && message_not_thrown_before("as.sir", "intrinsic")) {
message_("in {.help as.sir}: using {.arg add_intrinsic_resistance} is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.")
message_("in {.help AMR::as.sir}(): using {.arg add_intrinsic_resistance} is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.")
}
}
@@ -1721,7 +1721,7 @@ as_sir_method <- function(method_short,
pm_filter(uti == FALSE)
notes_current <- paste0(
notes_current, "\n",
paste0("Breakpoints for UTI ", font_bold("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument `uti` to set which isolates are from urine. See `?as.sir`.")
paste0("Breakpoints for UTI ", font_bold("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument `uti` to set which isolates are from urine. See {.help AMR::as.sir}().")
)
} else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && all(breakpoints_current$uti == FALSE, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteOther", mo_current, ab_current)) {
# breakpoints for multiple body sites available
@@ -1988,7 +1988,7 @@ sir_interpretation_history <- function(clean = FALSE) {
#' @noRd
print.sir_log <- function(x, ...) {
if (NROW(x) == 0) {
message_("No results to print. First run {.help as.sir} on MIC values or disk diffusion zones (or on a {.cls data.frame} containing any of these) to print a 'logbook' data set here.")
message_("No results to print. First run {.help AMR::as.sir}() on MIC values or disk diffusion zones (or on a {.cls data.frame} containing any of these) to print a 'logbook' data set here.")
return(invisible(NULL))
}
class(x) <- class(x)[class(x) != "sir_log"]