mirror of
https://github.com/msberends/AMR.git
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Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)
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
@@ -460,7 +460,11 @@ cli_to_plain <- function(msg, envir = parent.frame()) {
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msg <- apply_sub(msg, "\\{\\.pkg (\\{[^}]+\\}|[^}]+)\\}", function(c) resolve(c))
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msg <- apply_sub(msg, "\\{\\.strong (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("*", resolve(c), "*"))
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msg <- apply_sub(msg, "\\{\\.emph (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("*", resolve(c), "*"))
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msg <- apply_sub(msg, "\\{\\.help (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("`", resolve(c), "`"))
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msg <- apply_sub(msg, "\\{\\.help ([^}]+)\\}", function(c) {
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# Handle [display text](topic) markdown link format: extract just the display text
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m <- regmatches(c, regexec("^\\[(.*)\\]\\([^)]*\\)$", c, perl = TRUE))[[1L]]
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if (length(m) >= 2L) m[2L] else paste0("`", resolve(c), "`")
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})
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msg <- apply_sub(msg, "\\{\\.url (\\{[^}]+\\}|[^}]+)\\}", function(c) resolve(c))
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msg <- apply_sub(msg, "\\{\\.href ([^}]+)\\}", function(c) strsplit(resolve(c), " ", fixed = TRUE)[[1L]][1L])
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@@ -936,7 +940,7 @@ ascertain_sir_classes <- function(x, obj_name) {
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warning_(
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"the data provided in argument `", obj_name,
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"` should contain at least one column of class 'sir'. Eligible SIR column were now guessed. ",
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"See {.help AMR::as.sir}().",
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"See {.help [{.fun as.sir}](AMR::as.sir)}.",
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immediate = TRUE
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)
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sirs_eligible <- is_sir_eligible(x)
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2
R/ab.R
2
R/ab.R
@@ -210,7 +210,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
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progress <- progress_ticker(n = sum(!already_known), n_min = 25, print = info) # start if n >= 25
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on.exit(close(progress))
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if (any(x_new[!already_known & !is.na(x_new)] %in% unlist(AMR_env$AV_lookup$generalised_all, use.names = FALSE), na.rm = TRUE)) {
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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}().")
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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)}.")
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}
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}
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@@ -837,7 +837,7 @@ amr_select_exec <- function(function_name,
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#' @export
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#' @noRd
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print.amr_selector <- function(x, ...) {
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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}().",
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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)}.",
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immediate = TRUE
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)
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cat("Class 'amr_selector'\n")
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@@ -1062,7 +1062,7 @@ message_agent_names <- function(function_name, agents, ab_group = NULL, examples
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if (message_not_thrown_before(function_name, sort(agents))) {
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if (length(agents) == 0) {
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if (is.null(ab_group)) {
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message_("For {.help AMR::", function_name, "}() no antimicrobial drugs found", examples, ".")
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message_("For {.help [{.fun ", function_name, "}](AMR::", function_name, ")} no antimicrobial drugs found", examples, ".")
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} else if (ab_group == "administrable_per_os") {
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message_("No orally administrable drugs found", examples, ".")
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} else if (ab_group == "administrable_iv") {
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@@ -1198,7 +1198,7 @@ simulate_coverage <- function(params) {
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#' @param wisca_model The outcome of [wisca()] or [`antibiogram(..., wisca = TRUE)`][antibiogram()].
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#' @rdname antibiogram
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retrieve_wisca_parameters <- function(wisca_model, ...) {
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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.")
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stop_ifnot(isTRUE(attributes(wisca_model)$wisca), "This function only applies to WISCA models. Use {.help [{.fun wisca}](AMR::wisca)} or {.help [{.fun antibiogram}](AMR::antibiogram)} (with {.code wisca = TRUE}) to create a WISCA model.")
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attributes(wisca_model)$wisca_parameters
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}
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@@ -180,7 +180,7 @@ atc_online_property <- function(atc_code,
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colnames(out) <- gsub("^atc.*", "atc", tolower(colnames(out)))
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if (length(out) == 0) {
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message_("in {.help AMR::atc_online_property}(): no properties found for ATC ", atc_code[i], ". Please check {.href {atc_url} this WHOCC webpage}.")
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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}.")
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returnvalue[i] <- NA
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next
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}
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@@ -128,7 +128,7 @@ count_resistant <- function(...,
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# other arguments for meet_criteria are handled by sir_calc()
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meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
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if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_resistant", "eucast_default", entire_session = TRUE)) {
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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}.")
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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}.")
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message_("This message will be shown once per session.")
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}
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tryCatch(
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@@ -152,7 +152,7 @@ count_susceptible <- function(...,
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# other arguments for meet_criteria are handled by sir_calc()
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meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
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if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_susceptible", "eucast_default", entire_session = TRUE)) {
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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}.")
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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}.")
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message_("This message will be shown once per session.")
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}
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tryCatch(
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@@ -150,15 +150,15 @@ custom_eucast_rules <- function(...) {
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)
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stop_if(
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identical(dots, "error"),
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"rules must be a valid formula inputs (e.g., using '~'), see {.help AMR::custom_eucast_rules}()"
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"rules must be a valid formula inputs (e.g., using '~'), see {.help [{.fun custom_eucast_rules}](AMR::custom_eucast_rules)}"
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)
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n_dots <- length(dots)
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stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using {.help AMR::custom_eucast_rules}().")
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stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using {.help [{.fun custom_eucast_rules}](AMR::custom_eucast_rules)}.")
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out <- vector("list", n_dots)
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for (i in seq_len(n_dots)) {
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stop_ifnot(
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inherits(dots[[i]], "formula"),
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"rule ", i, " must be a valid formula input (e.g., using '~'), see {.help AMR::custom_eucast_rules}()"
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"rule ", i, " must be a valid formula input (e.g., using '~'), see {.help [{.fun custom_eucast_rules}](AMR::custom_eucast_rules)}"
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)
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# Query
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@@ -180,7 +180,7 @@ custom_eucast_rules <- function(...) {
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result <- dots[[i]][[3]]
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stop_ifnot(
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deparse(result) %like% "==",
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"the result of rule ", i, " (the part after the `~`) must contain `==`, such as in `... ~ ampicillin == \"R\"`, see {.help AMR::custom_eucast_rules}()"
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"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)}"
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)
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result_group <- as.character(result)[[2]]
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result_group <- as.character(str2lang(result_group))
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@@ -145,15 +145,15 @@ custom_mdro_guideline <- function(..., as_factor = TRUE) {
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)
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stop_if(
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identical(dots, "error"),
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"rules must be a valid formula inputs (e.g., using '~'), see {.help AMR::mdro}()"
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"rules must be a valid formula inputs (e.g., using '~'), see {.help [{.fun mdro}](AMR::mdro)}"
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)
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n_dots <- length(dots)
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stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using {.help AMR::mdro}().")
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stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using {.help [{.fun mdro}](AMR::mdro)}.")
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out <- vector("list", n_dots)
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for (i in seq_len(n_dots)) {
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stop_ifnot(
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inherits(dots[[i]], "formula"),
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"rule ", i, " must be a valid formula input (e.g., using '~'), see {.help AMR::mdro}()"
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"rule ", i, " must be a valid formula input (e.g., using '~'), see {.help [{.fun mdro}](AMR::mdro)}"
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)
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# Query
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@@ -202,7 +202,7 @@ c.custom_mdro_guideline <- function(x, ..., as_factor = NULL) {
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}
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for (g in list(...)) {
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stop_ifnot(inherits(g, "custom_mdro_guideline"),
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"for combining custom MDRO guidelines, all rules must be created with {.help AMR::custom_mdro_guideline}()",
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"for combining custom MDRO guidelines, all rules must be created with {.help [{.fun custom_mdro_guideline}](AMR::custom_mdro_guideline)}",
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call = FALSE
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)
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vals <- attributes(x)$values
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@@ -259,14 +259,14 @@ run_custom_mdro_guideline <- function(df, guideline, info) {
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}
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)
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if (identical(qry, "error")) {
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warning_("in {.help AMR::custom_mdro_guideline}(): rule ", i,
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warning_("in {.help [{.fun custom_mdro_guideline}](AMR::custom_mdro_guideline)}: rule ", i,
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" (`", as.character(guideline[[i]]$query), "`) was ignored because of this error message: ",
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AMR_env$err_msg,
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call = FALSE
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)
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next
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}
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stop_ifnot(is.logical(qry), "in {.help AMR::custom_mdro_guideline}(): rule ", i, " (`", guideline[[i]]$query,
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stop_ifnot(is.logical(qry), "in {.help [{.fun custom_mdro_guideline}](AMR::custom_mdro_guideline)}: rule ", i, " (`", guideline[[i]]$query,
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"`) must return {.code TRUE} or {.code FALSE}, not ",
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format_class(class(qry), plural = FALSE),
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call = FALSE
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@@ -210,7 +210,7 @@ get_column_abx <- function(x,
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newnames <- suppressWarnings(as.ab(names(dots), info = FALSE))
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if (anyNA(newnames)) {
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if (isTRUE(info)) {
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message_("WARNING: some columns returned NA for {.help AMR::as.ab}()", as_note = FALSE)
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message_("WARNING: some columns returned NA for {.help [{.fun as.ab}](AMR::as.ab)}", as_note = FALSE)
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}
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warning_("Invalid antibiotic reference(s): ", vector_and(names(dots)[is.na(newnames)], quotes = FALSE),
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call = FALSE,
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@@ -267,7 +267,7 @@ get_column_abx <- function(x,
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if (all_okay == TRUE) {
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message_(" OK.", as_note = FALSE)
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} else if (!isFALSE(dups)) {
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message_("WARNING: some results from {.help AMR::as.ab}() are duplicated: ", vector_and(dups, quotes = "`"), as_note = FALSE)
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message_("WARNING: some results from {.help [{.fun as.ab}](AMR::as.ab)} are duplicated: ", vector_and(dups, quotes = "`"), as_note = FALSE)
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} else {
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message_(" WARNING.", as_note = FALSE)
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}
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@@ -198,7 +198,7 @@ interpretive_rules <- function(x,
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add_MO_lookup_to_AMR_env()
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if ("custom" %in% rules && is.null(custom_rules)) {
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warning_("in {.help AMR::eucast_rules}(): no custom rules were set with the {.arg custom_rules} argument",
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warning_("in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: no custom rules were set with the {.arg custom_rules} argument",
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immediate = TRUE
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)
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rules <- rules[rules != "custom"]
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@@ -481,7 +481,7 @@ interpretive_rules <- function(x,
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"Rules by the ",
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font_bold(paste0("AMR package v", utils::packageDescription("AMR")$Version)),
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" (", format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y"),
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"), see {.help AMR::eucast_rules}()\n"
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"), see {.help [{.fun eucast_rules}](AMR::eucast_rules)}\n"
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)
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))
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cat("\n\n")
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@@ -1062,7 +1062,7 @@ interpretive_rules <- function(x,
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warn_lacking_sir_class <- warn_lacking_sir_class[order(colnames(x.bak))]
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warn_lacking_sir_class <- warn_lacking_sir_class[!is.na(warn_lacking_sir_class)]
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warning_(
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"in {.help AMR::eucast_rules}(): not all columns with antimicrobial results are of class 'sir'. Transform them on beforehand, with e.g.:\n",
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"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",
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" - ", highlight_code(paste0(x_deparsed, " %>% as.sir(", ifelse(length(warn_lacking_sir_class) == 1,
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warn_lacking_sir_class,
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paste0(warn_lacking_sir_class[1], ":", warn_lacking_sir_class[length(warn_lacking_sir_class)])
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@@ -1178,7 +1178,7 @@ edit_sir <- function(x,
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suppressWarnings(new_edits[rows, cols][non_SIR] <<- to)
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}
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warning_(
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"in {.help AMR::eucast_rules}(): value \"", to, "\" added to the factor levels of column",
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"in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: value \"", to, "\" added to the factor levels of column",
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ifelse(length(cols) == 1, "", "s"),
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" ", vector_and(cols, quotes = "`", sort = FALSE),
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" because this value was not an existing factor level."
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@@ -1186,7 +1186,7 @@ edit_sir <- function(x,
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txt_warning()
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warned <- FALSE
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} else {
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warning_("in {.help AMR::eucast_rules}(): ", w$message)
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warning_("in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: ", w$message)
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txt_warning()
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}
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},
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@@ -187,7 +187,7 @@ key_antimicrobials <- function(x = NULL,
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"No columns available ",
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paste0("Only using ", values_new_length, " out of ", values_old_length, " defined columns ")
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),
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"as key antimicrobials for ", name, "s. See {.help AMR::key_antimicrobials}()."
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"as key antimicrobials for ", name, "s. See {.help [{.fun key_antimicrobials}](AMR::key_antimicrobials)}."
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)
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}
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6
R/mdro.R
6
R/mdro.R
@@ -170,9 +170,9 @@ mdro <- function(x = NULL,
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meet_criteria(infer_from_combinations, allow_class = "logical", has_length = 1)
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if (isTRUE(only_sir_columns) && !any(is.sir(x))) {
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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.")
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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.")
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} else if (!isTRUE(only_sir_columns) && !any(is.sir(x)) && !any(is_sir_eligible(x))) {
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stop_("There were no eligible SIR columns found in the data set. Transform columns with {.help AMR::as.sir}() for valid antimicrobial interpretations.")
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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.")
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}
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# get gene values as TRUE/FALSE
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@@ -251,7 +251,7 @@ mdro <- function(x = NULL,
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guideline.bak <- guideline
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if (is.list(guideline)) {
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# Custom MDRO guideline ---------------------------------------------------
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stop_ifnot(inherits(guideline, "custom_mdro_guideline"), "use {.help AMR::custom_mdro_guideline}() to create custom guidelines")
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stop_ifnot(inherits(guideline, "custom_mdro_guideline"), "use {.help [{.fun custom_mdro_guideline}](AMR::custom_mdro_guideline)} to create custom guidelines")
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if (isTRUE(info)) {
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txt <- paste0(
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"Determining MDROs based on custom rules",
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8
R/mo.R
8
R/mo.R
@@ -483,7 +483,7 @@ as.mo <- function(x,
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}
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} else if (is.null(getOption("AMR_keep_synonyms")) && length(AMR_env$mo_renamed$old) > 0 && message_not_thrown_before("as.mo", "keep_synonyms_warning", entire_session = TRUE)) {
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# keep synonyms is TRUE, so check if any do have synonyms
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warning_("{.help AMR::as.mo}() returned ", nr2char(length(unique(AMR_env$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 ----
|
||||
@@ -907,14 +907,14 @@ rep.mo <- function(x, ...) {
|
||||
print.mo_uncertainties <- function(x, n = 10, ...) {
|
||||
more_than_50 <- FALSE
|
||||
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))
|
||||
} else if (NROW(x) > 50) {
|
||||
more_than_50 <- TRUE
|
||||
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()
|
||||
|
||||
@@ -1032,7 +1032,7 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
|
||||
#' @noRd
|
||||
print.mo_renamed <- function(x, extra_txt = "", n = 25, ...) {
|
||||
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))
|
||||
}
|
||||
|
||||
|
||||
@@ -1043,7 +1043,7 @@ find_mo_col <- function(fn) {
|
||||
)
|
||||
if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
|
||||
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])
|
||||
} else {
|
||||
|
||||
@@ -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 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$mo_source)) {
|
||||
AMR_env$mo_source <- readRDS_AMR(path.expand(destination))
|
||||
|
||||
@@ -412,7 +412,7 @@ create_scale_sir <- function(aesthetics, colours_SIR, language, eucast_I, ...) {
|
||||
|
||||
scale$labels <- function(x) {
|
||||
stop_ifnot(all(x %in% c(levels(NA_sir_), "SI", "IR", NA)),
|
||||
"Apply `scale_", aesthetics[1], "_sir()` to a variable of class 'sir', see {.help AMR::as.sir}().",
|
||||
"Apply `scale_", aesthetics[1], "_sir()` to a variable of class 'sir', see {.help [{.fun as.sir}](AMR::as.sir)}.",
|
||||
call = FALSE
|
||||
)
|
||||
x <- as.character(x)
|
||||
|
||||
@@ -238,7 +238,7 @@ resistance_predict <- function(x,
|
||||
prediction <- predictmodel$fit
|
||||
se <- predictmodel$se.fit
|
||||
} 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
|
||||
|
||||
26
R/sir.R
26
R/sir.R
@@ -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 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), ...))
|
||||
} 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), ...))
|
||||
}
|
||||
}
|
||||
@@ -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 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) {
|
||||
@@ -610,7 +610,7 @@ as.sir.default <- function(x,
|
||||
sort() %pm>%
|
||||
vector_and(quotes = TRUE)
|
||||
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(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 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 {
|
||||
# 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 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)
|
||||
|
||||
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)
|
||||
@@ -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 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 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
|
||||
@@ -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 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)
|
||||
@@ -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 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
|
||||
)
|
||||
}
|
||||
@@ -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 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)
|
||||
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 {.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)) {
|
||||
# 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 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))
|
||||
}
|
||||
class(x) <- class(x)[class(x) != "sir_log"]
|
||||
|
||||
Reference in New Issue
Block a user