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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/aa_helper_functions.R
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@@ -460,7 +460,11 @@ cli_to_plain <- function(msg, envir = parent.frame()) {
msg <- apply_sub(msg, "\\{\\.pkg (\\{[^}]+\\}|[^}]+)\\}", function(c) resolve(c)) msg <- apply_sub(msg, "\\{\\.pkg (\\{[^}]+\\}|[^}]+)\\}", function(c) resolve(c))
msg <- apply_sub(msg, "\\{\\.strong (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("*", resolve(c), "*")) msg <- apply_sub(msg, "\\{\\.strong (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("*", resolve(c), "*"))
msg <- apply_sub(msg, "\\{\\.emph (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("*", resolve(c), "*")) msg <- apply_sub(msg, "\\{\\.emph (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("*", resolve(c), "*"))
msg <- apply_sub(msg, "\\{\\.help (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("`", resolve(c), "`")) msg <- apply_sub(msg, "\\{\\.help ([^}]+)\\}", function(c) {
# Handle [display text](topic) markdown link format: extract just the display text
m <- regmatches(c, regexec("^\\[(.*)\\]\\([^)]*\\)$", c, perl = TRUE))[[1L]]
if (length(m) >= 2L) m[2L] else paste0("`", resolve(c), "`")
})
msg <- apply_sub(msg, "\\{\\.url (\\{[^}]+\\}|[^}]+)\\}", function(c) resolve(c)) msg <- apply_sub(msg, "\\{\\.url (\\{[^}]+\\}|[^}]+)\\}", function(c) resolve(c))
msg <- apply_sub(msg, "\\{\\.href ([^}]+)\\}", function(c) strsplit(resolve(c), " ", fixed = TRUE)[[1L]][1L]) msg <- apply_sub(msg, "\\{\\.href ([^}]+)\\}", function(c) strsplit(resolve(c), " ", fixed = TRUE)[[1L]][1L])
@@ -936,7 +940,7 @@ ascertain_sir_classes <- function(x, obj_name) {
warning_( warning_(
"the data provided in argument `", obj_name, "the data provided in argument `", obj_name,
"` should contain at least one column of class 'sir'. Eligible SIR column were now guessed. ", "` should contain at least one column of class 'sir'. Eligible SIR column were now guessed. ",
"See {.help AMR::as.sir}().", "See {.help [{.fun as.sir}](AMR::as.sir)}.",
immediate = TRUE immediate = TRUE
) )
sirs_eligible <- is_sir_eligible(x) sirs_eligible <- is_sir_eligible(x)

2
R/ab.R
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@@ -210,7 +210,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
progress <- progress_ticker(n = sum(!already_known), n_min = 25, print = info) # start if n >= 25 progress <- progress_ticker(n = sum(!already_known), n_min = 25, print = info) # start if n >= 25
on.exit(close(progress)) on.exit(close(progress))
if (any(x_new[!already_known & !is.na(x_new)] %in% unlist(AMR_env$AV_lookup$generalised_all, use.names = FALSE), na.rm = TRUE)) { if (any(x_new[!already_known & !is.na(x_new)] %in% unlist(AMR_env$AV_lookup$generalised_all, use.names = FALSE), na.rm = TRUE)) {
warning_("in {.help AMR::as.ab}(): some input seems to resemble antiviral drugs - use {.help AMR::as.av}() or e.g. {.help AMR::av_name}() for these, not {.help AMR::as.ab}() or e.g. {.help AMR::ab_name}().") warning_("in {.help [{.fun as.ab}](AMR::as.ab)}: some input seems to resemble antiviral drugs - use {.help [{.fun as.av}](AMR::as.av)} or e.g. {.help [{.fun av_name}](AMR::av_name)} for these, not {.help [{.fun as.ab}](AMR::as.ab)} or e.g. {.help [{.fun ab_name}](AMR::ab_name)}.")
} }
} }

4
R/amr_selectors.R
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@@ -837,7 +837,7 @@ amr_select_exec <- function(function_name,
#' @export #' @export
#' @noRd #' @noRd
print.amr_selector <- function(x, ...) { print.amr_selector <- function(x, ...) {
warning_("It should never be needed to print an antimicrobial selector class. Are you using {.pkg data.table}? Then add the argument {.code with = FALSE}, see our examples at {.help AMR::amr_selector}().", warning_("It should never be needed to print an antimicrobial selector class. Are you using {.pkg data.table}? Then add the argument {.code with = FALSE}, see our examples at {.help [{.fun amr_selector}](AMR::amr_selector)}.",
immediate = TRUE immediate = TRUE
) )
cat("Class 'amr_selector'\n") cat("Class 'amr_selector'\n")
@@ -1062,7 +1062,7 @@ message_agent_names <- function(function_name, agents, ab_group = NULL, examples
if (message_not_thrown_before(function_name, sort(agents))) { if (message_not_thrown_before(function_name, sort(agents))) {
if (length(agents) == 0) { if (length(agents) == 0) {
if (is.null(ab_group)) { if (is.null(ab_group)) {
message_("For {.help AMR::", function_name, "}() no antimicrobial drugs found", examples, ".") message_("For {.help [{.fun ", function_name, "}](AMR::", function_name, ")} no antimicrobial drugs found", examples, ".")
} else if (ab_group == "administrable_per_os") { } else if (ab_group == "administrable_per_os") {
message_("No orally administrable drugs found", examples, ".") message_("No orally administrable drugs found", examples, ".")
} else if (ab_group == "administrable_iv") { } else if (ab_group == "administrable_iv") {

2
R/antibiogram.R
View File

@@ -1198,7 +1198,7 @@ simulate_coverage <- function(params) {
#' @param wisca_model The outcome of [wisca()] or [`antibiogram(..., wisca = TRUE)`][antibiogram()]. #' @param wisca_model The outcome of [wisca()] or [`antibiogram(..., wisca = TRUE)`][antibiogram()].
#' @rdname antibiogram #' @rdname antibiogram
retrieve_wisca_parameters <- function(wisca_model, ...) { 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)$wisca_parameters attributes(wisca_model)$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))) colnames(out) <- gsub("^atc.*", "atc", tolower(colnames(out)))
if (length(out) == 0) { if (length(out) == 0) {
message_("in {.help AMR::atc_online_property}(): no properties found for ATC ", atc_code[i], ". Please check {.href {atc_url} this WHOCC webpage}.") message_("in {.help [{.fun atc_online_property}](AMR::atc_online_property)}: no properties found for ATC ", atc_code[i], ". Please check {.href {atc_url} this WHOCC webpage}.")
returnvalue[i] <- NA returnvalue[i] <- NA
next next
} }

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 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 {.code ?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 {.code ?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 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 {.code ?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 {.code ?AMR-options}.")
message_("This message will be shown once per session.") message_("This message will be shown once per session.")
} }
tryCatch( tryCatch(

8
R/custom_eucast_rules.R
View File

@@ -150,15 +150,15 @@ custom_eucast_rules <- function(...) {
) )
stop_if( stop_if(
identical(dots, "error"), 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) 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) out <- vector("list", n_dots)
for (i in seq_len(n_dots)) { for (i in seq_len(n_dots)) {
stop_ifnot( stop_ifnot(
inherits(dots[[i]], "formula"), 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 # Query
@@ -180,7 +180,7 @@ custom_eucast_rules <- function(...) {
result <- dots[[i]][[3]] result <- dots[[i]][[3]]
stop_ifnot( stop_ifnot(
deparse(result) %like% "==", 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(result)[[2]]
result_group <- as.character(str2lang(result_group)) result_group <- as.character(str2lang(result_group))

12
R/custom_mdro_guideline.R
View File

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

4
R/guess_ab_col.R
View File

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

10
R/interpretive_rules.R
View File

@@ -198,7 +198,7 @@ interpretive_rules <- function(x,
add_MO_lookup_to_AMR_env() add_MO_lookup_to_AMR_env()
if ("custom" %in% rules && is.null(custom_rules)) { if ("custom" %in% rules && is.null(custom_rules)) {
warning_("in {.help AMR::eucast_rules}(): no custom rules were set with the {.arg custom_rules} argument", warning_("in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: no custom rules were set with the {.arg custom_rules} argument",
immediate = TRUE immediate = TRUE
) )
rules <- rules[rules != "custom"] rules <- rules[rules != "custom"]
@@ -481,7 +481,7 @@ interpretive_rules <- function(x,
"Rules by the ", "Rules by the ",
font_bold(paste0("AMR package v", utils::packageDescription("AMR")$Version)), font_bold(paste0("AMR package v", utils::packageDescription("AMR")$Version)),
" (", format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y"), " (", format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y"),
"), see {.help AMR::eucast_rules}()\n" "), see {.help [{.fun eucast_rules}](AMR::eucast_rules)}\n"
) )
)) ))
cat("\n\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[order(colnames(x.bak))]
warn_lacking_sir_class <- warn_lacking_sir_class[!is.na(warn_lacking_sir_class)] warn_lacking_sir_class <- warn_lacking_sir_class[!is.na(warn_lacking_sir_class)]
warning_( warning_(
"in {.help AMR::eucast_rules}(): not all columns with antimicrobial results are of class 'sir'. Transform them on beforehand, with e.g.:\n", "in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: not all columns with antimicrobial results are of class 'sir'. Transform them on beforehand, with e.g.:\n",
" - ", highlight_code(paste0(x_deparsed, " %>% as.sir(", ifelse(length(warn_lacking_sir_class) == 1, " - ", highlight_code(paste0(x_deparsed, " %>% as.sir(", ifelse(length(warn_lacking_sir_class) == 1,
warn_lacking_sir_class, warn_lacking_sir_class,
paste0(warn_lacking_sir_class[1], ":", warn_lacking_sir_class[length(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) suppressWarnings(new_edits[rows, cols][non_SIR] <<- to)
} }
warning_( warning_(
"in {.help AMR::eucast_rules}(): value \"", to, "\" added to the factor levels of column", "in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: value \"", to, "\" added to the factor levels of column",
ifelse(length(cols) == 1, "", "s"), ifelse(length(cols) == 1, "", "s"),
" ", vector_and(cols, quotes = "`", sort = FALSE), " ", vector_and(cols, quotes = "`", sort = FALSE),
" because this value was not an existing factor level." " because this value was not an existing factor level."
@@ -1186,7 +1186,7 @@ edit_sir <- function(x,
txt_warning() txt_warning()
warned <- FALSE warned <- FALSE
} else { } else {
warning_("in {.help AMR::eucast_rules}(): ", w$message) warning_("in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: ", w$message)
txt_warning() txt_warning()
} }
}, },

2
R/key_antimicrobials.R
View File

@@ -187,7 +187,7 @@ key_antimicrobials <- function(x = NULL,
"No columns available ", "No columns available ",
paste0("Only using ", values_new_length, " out of ", values_old_length, " defined columns ") paste0("Only using ", values_new_length, " out of ", values_old_length, " defined columns ")
), ),
"as key antimicrobials for ", name, "s. See {.help AMR::key_antimicrobials}()." "as key antimicrobials for ", name, "s. See {.help [{.fun key_antimicrobials}](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) meet_criteria(infer_from_combinations, allow_class = "logical", has_length = 1)
if (isTRUE(only_sir_columns) && !any(is.sir(x))) { 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 AMR::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 [{.fun as.sir}](AMR::as.sir)} for valid antimicrobial interpretations.")
} else if (!isTRUE(only_sir_columns) && !any(is.sir(x)) && !any(is_sir_eligible(x))) { } 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 AMR::as.sir}() for valid antimicrobial interpretations.") stop_("There were no eligible SIR columns found in the data set. Transform columns with {.help [{.fun as.sir}](AMR::as.sir)} for valid antimicrobial interpretations.")
} }
# get gene values as TRUE/FALSE # get gene values as TRUE/FALSE
@@ -251,7 +251,7 @@ mdro <- function(x = NULL,
guideline.bak <- guideline guideline.bak <- guideline
if (is.list(guideline)) { if (is.list(guideline)) {
# Custom MDRO guideline --------------------------------------------------- # Custom MDRO guideline ---------------------------------------------------
stop_ifnot(inherits(guideline, "custom_mdro_guideline"), "use {.help AMR::custom_mdro_guideline}() to create custom guidelines") stop_ifnot(inherits(guideline, "custom_mdro_guideline"), "use {.help [{.fun custom_mdro_guideline}](AMR::custom_mdro_guideline)} to create custom guidelines")
if (isTRUE(info)) { if (isTRUE(info)) {
txt <- paste0( txt <- paste0(
"Determining MDROs based on custom rules", "Determining MDROs based on custom rules",

8
R/mo.R
View File

@@ -483,7 +483,7 @@ as.mo <- function(x,
} }
} else if (is.null(getOption("AMR_keep_synonyms")) && length(AMR_env$mo_renamed$old) > 0 && message_not_thrown_before("as.mo", "keep_synonyms_warning", entire_session = TRUE)) { } else if (is.null(getOption("AMR_keep_synonyms")) && length(AMR_env$mo_renamed$old) > 0 && message_not_thrown_before("as.mo", "keep_synonyms_warning", entire_session = TRUE)) {
# keep synonyms is TRUE, so check if any do have synonyms # keep synonyms is TRUE, so check if any do have synonyms
warning_("{.help AMR::as.mo}() returned ", nr2char(length(unique(AMR_env$mo_renamed$old))), " outdated taxonomic name", ifelse(length(unique(AMR_env$mo_renamed$old)) > 1, "s", ""), ". Use ", highlight_code("as.mo(..., keep_synonyms = FALSE)"), " to clean the input to currently accepted taxonomic names, or set the R option {.code AMR_keep_synonyms} to {.code FALSE}. This warning will be shown once per session.", call = FALSE) warning_("{.help [{.fun as.mo}](AMR::as.mo)} returned ", nr2char(length(unique(AMR_env$mo_renamed$old))), " outdated taxonomic name", ifelse(length(unique(AMR_env$mo_renamed$old)) > 1, "s", ""), ". Use ", highlight_code("as.mo(..., keep_synonyms = FALSE)"), " to clean the input to currently accepted taxonomic names, or set the R option {.code AMR_keep_synonyms} to {.code FALSE}. This warning will be shown once per session.", call = FALSE)
} }
# Apply Becker ---- # Apply Becker ----
@@ -907,14 +907,14 @@ rep.mo <- function(x, ...) {
print.mo_uncertainties <- function(x, n = 10, ...) { print.mo_uncertainties <- function(x, n = 10, ...) {
more_than_50 <- FALSE more_than_50 <- FALSE
if (NROW(x) == 0) { if (NROW(x) == 0) {
cat(font_blue(word_wrap("No uncertainties to show. Only uncertainties of the last call to {.help AMR::as.mo}() or any mo_*() function are stored.\n\n"))) cat(font_blue(word_wrap("No uncertainties to show. Only uncertainties of the last call to {.help [{.fun as.mo}](AMR::as.mo)} or any mo_*() function are stored.\n\n")))
return(invisible(NULL)) return(invisible(NULL))
} else if (NROW(x) > 50) { } else if (NROW(x) > 50) {
more_than_50 <- TRUE more_than_50 <- TRUE
x <- x[1:50, , drop = FALSE] 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 {.help AMR::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 [{.fun mo_matching_score}](AMR::mo_matching_score)}.\n\n")))
add_MO_lookup_to_AMR_env() add_MO_lookup_to_AMR_env()
@@ -1032,7 +1032,7 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
#' @noRd #' @noRd
print.mo_renamed <- function(x, extra_txt = "", n = 25, ...) { print.mo_renamed <- function(x, extra_txt = "", n = 25, ...) {
if (NROW(x) == 0) { if (NROW(x) == 0) {
cat(font_blue(word_wrap("No renamed taxonomy to show. Only renamed taxonomy of the last call of {.help AMR::as.mo}() or any mo_*() function are stored.\n"))) cat(font_blue(word_wrap("No renamed taxonomy to show. Only renamed taxonomy of the last call of {.help [{.fun as.mo}](AMR::as.mo)} or any mo_*() function are stored.\n")))
return(invisible(NULL)) return(invisible(NULL))
} }

2
R/mo_property.R
View File

@@ -1043,7 +1043,7 @@ find_mo_col <- function(fn) {
) )
if (!is.null(df) && !is.null(mo) && is.data.frame(df)) { if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
if (message_not_thrown_before(fn = fn)) { if (message_not_thrown_before(fn = fn)) {
message_("Using column '", font_bold(mo), "' as input for {.help AMR::", fn, "}()") message_("Using column '", font_bold(mo), "' as input for {.help [{.fun ", fn, "}](AMR::", fn, ")}")
} }
return(df[, mo, drop = TRUE]) return(df[, mo, drop = TRUE])
} else { } else {

2
R/mo_source.R
View File

@@ -249,7 +249,7 @@ get_mo_source <- function(destination = getOption("AMR_mo_source", "~/mo_source.
current_ext <- regexpr("\\.([[:alnum:]]+)$", destination) current_ext <- regexpr("\\.([[:alnum:]]+)$", destination)
current_ext <- ifelse(current_ext > -1L, substring(destination, current_ext + 1L), "") current_ext <- ifelse(current_ext > -1L, substring(destination, current_ext + 1L), "")
vowel <- ifelse(current_ext %like% "^[AEFHILMNORSX]", "n", "") 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 AMR::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 [{.fun set_mo_source}](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$mo_source)) { if (is.null(AMR_env$mo_source)) {
AMR_env$mo_source <- readRDS_AMR(path.expand(destination)) AMR_env$mo_source <- readRDS_AMR(path.expand(destination))

2
R/plotting.R
View File

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

2
R/resistance_predict.R
View File

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

26
R/sir.R
View File

@@ -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)) { 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 # check if they are actually MICs or disks
if (all_valid_mics(x)) { if (all_valid_mics(x)) {
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}().") warning_("in {.help [{.fun as.sir}](AMR::as.sir)}: input values were guessed to be MIC values - preferably transform them with {.help [{.fun as.mic}](AMR::as.mic)} before running {.help [{.fun as.sir}](AMR::as.sir)}.")
return(as.sir(as.mic(x), ...)) return(as.sir(as.mic(x), ...))
} else if (all_valid_disks(x)) { } else if (all_valid_disks(x)) {
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}().") warning_("in {.help [{.fun as.sir}](AMR::as.sir)}: input values were guessed to be disk diffusion values - preferably transform them with {.help [{.fun as.disk}](AMR::as.disk)} before running {.help [{.fun as.sir}](AMR::as.sir)}.")
return(as.sir(as.disk(x), ...)) 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(out7) > 0, paste0("7 as \"", out7, "\""), NA_character_),
ifelse(length(out8) > 0, paste0("8 as \"", out8, "\""), NA_character_) ifelse(length(out8) > 0, paste0("8 as \"", out8, "\""), NA_character_)
) )
message_("in {.help AMR::as.sir}(): Interpreting input value ", vector_and(out[!is.na(out)], quotes = FALSE, sort = FALSE)) message_("in {.help [{.fun as.sir}](AMR::as.sir)}: Interpreting input value ", vector_and(out[!is.na(out)], quotes = FALSE, sort = FALSE))
} }
if (na_before != na_after) { if (na_before != na_after) {
@@ -610,7 +610,7 @@ as.sir.default <- function(x,
sort() %pm>% sort() %pm>%
vector_and(quotes = TRUE) vector_and(quotes = TRUE)
cur_col <- get_current_column() cur_col <- get_current_column()
warning_("in {.help AMR::as.sir}(): ", na_after - na_before, " result", warning_("in {.help [{.fun as.sir}](AMR::as.sir)}: ", na_after - na_before, " result",
ifelse(na_after - na_before > 1, "s", ""), ifelse(na_after - na_before > 1, "s", ""),
ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")), ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
" truncated (", " truncated (",
@@ -1029,7 +1029,7 @@ as.sir.data.frame <- function(x,
if (isTRUE(info)) { if (isTRUE(info)) {
message_(font_green_bg(" DONE "), as_note = FALSE) message_(font_green_bg(" DONE "), as_note = FALSE)
message() message()
message_("Run {.help AMR::sir_interpretation_history}() to retrieve a logbook with all details of the breakpoint interpretations.") message_("Run {.help [{.fun sir_interpretation_history}](AMR::sir_interpretation_history)} to retrieve a logbook with all details of the breakpoint interpretations.")
} }
} else { } else {
# sequential mode (non-parallel) # sequential mode (non-parallel)
@@ -1168,13 +1168,13 @@ as_sir_method <- function(method_short,
dots <- list(...) dots <- list(...)
dots <- dots[which(!names(dots) %in% c("warn", "mo.bak", "is_data.frame"))] dots <- dots[which(!names(dots) %in% c("warn", "mo.bak", "is_data.frame"))]
if (length(dots) != 0) { if (length(dots) != 0) {
warning_("These arguments in {.help AMR::as.sir}() are no longer used: ", vector_and(names(dots), quotes = "`"), ".", call = FALSE) warning_("These arguments in {.help [{.fun as.sir}](AMR::as.sir)} are no longer used: ", vector_and(names(dots), quotes = "`"), ".", call = FALSE)
} }
current_sir_interpretation_history <- NROW(AMR_env$sir_interpretation_history) current_sir_interpretation_history <- NROW(AMR_env$sir_interpretation_history)
if (isTRUE(info) && message_not_thrown_before("as.sir", "sir_interpretation_history")) { if (isTRUE(info) && message_not_thrown_before("as.sir", "sir_interpretation_history")) {
message_("Run {.help AMR::sir_interpretation_history}() afterwards to retrieve a logbook with all details of the breakpoint interpretations.\n\n") message_("Run {.help [{.fun sir_interpretation_history}](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) 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 <- "" mo_var_found <- ""
} }
if (is.null(mo)) { 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 AMR::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 [{.fun as.sir}](AMR::as.sir)}.\n\n",
"To transform certain columns with e.g. mutate(), use ", highlight_code("data %>% mutate(across(..., as.sir, mo = x))"), ", where x is your column with microorganisms.\n", "To transform certain columns with e.g. mutate(), use ", highlight_code("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 ", highlight_code("data %>% as.sir()"), " or ", highlight_code(paste0("data %>% mutate_if(is.", method_short, ", as.sir)")), ".", "To transform all ", method_long, " in a data set, use ", highlight_code("data %>% as.sir()"), " or ", highlight_code(paste0("data %>% mutate_if(is.", method_short, ", as.sir)")), ".",
call = FALSE call = FALSE
@@ -1312,7 +1312,7 @@ as_sir_method <- function(method_short,
if (length(ab) == 1 && ab %like% paste0("as.", 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 AMR::as.sir}().", call = FALSE) stop_("No unambiguous name was supplied about the antibiotic (argument {.arg ab}). See {.help [{.fun as.sir}](AMR::as.sir)}.", call = FALSE)
} }
ab.bak <- trimws2(ab) ab.bak <- trimws2(ab)
@@ -1328,7 +1328,7 @@ as_sir_method <- function(method_short,
if (all(is.na(ab))) { if (all(is.na(ab))) {
if (isTRUE(info)) { if (isTRUE(info)) {
message_("Returning NAs for unknown antibiotic: ", vector_and(ab.bak, sort = FALSE, quotes = TRUE), 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 AMR::as.ab}().", ". Rename this column to a valid name or code, and check the output with {.help [{.fun as.ab}](AMR::as.ab)}.",
as_note = FALSE as_note = FALSE
) )
} }
@@ -1352,7 +1352,7 @@ as_sir_method <- function(method_short,
} }
if (isTRUE(add_intrinsic_resistance) && guideline_coerced %unlike% "EUCAST") { if (isTRUE(add_intrinsic_resistance) && guideline_coerced %unlike% "EUCAST") {
if (isTRUE(info) && message_not_thrown_before("as.sir", "intrinsic")) { if (isTRUE(info) && message_not_thrown_before("as.sir", "intrinsic")) {
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.") message_("in {.help [{.fun as.sir}](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) pm_filter(uti == FALSE)
notes_current <- paste0( notes_current <- paste0(
notes_current, "\n", 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 {.help AMR::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 [{.fun as.sir}](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)) { } 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 # breakpoints for multiple body sites available
@@ -1988,7 +1988,7 @@ sir_interpretation_history <- function(clean = FALSE) {
#' @noRd #' @noRd
print.sir_log <- function(x, ...) { print.sir_log <- function(x, ...) {
if (NROW(x) == 0) { if (NROW(x) == 0) {
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.") message_("No results to print. First run {.help [{.fun as.sir}](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)) return(invisible(NULL))
} }
class(x) <- class(x)[class(x) != "sir_log"] class(x) <- class(x)[class(x) != "sir_log"]