mirror of
https://github.com/msberends/AMR.git
synced 2026-03-20 02:22:24 +01:00
Replace bare backticks with cli inline markup across all messaging calls
- {.arg} for argument names in stop_/warning_/message_ calls
- {.cls} after "of class" text in format_class() and elsewhere
- {.fun} for function names (replaces `fn()` pattern)
- {.pkg} for tidyverse package names (dplyr, ggplot2)
- {.code} for code literals (TRUE, FALSE, expressions)
- Rewrite print.ab: use cli named-vector with * bullets and code
highlighting when cli >= 3.0.0; keep plain-text fallback otherwise
- Fix typo in as.sir(): "of must be" -> "or must be"
- switch sir.R verbose notes from message() to message_()
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
This commit is contained in:
Claude
@@ -304,8 +304,8 @@ search_type_in_df <- function(x, type, info = TRUE, add_col_prefix = TRUE) {
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if (!is.null(found)) {
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# this column should contain logicals
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if (!is.logical(x[, found, drop = TRUE])) {
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message_("Column '", font_bold(found), "' found as input for `", ifelse(add_col_prefix, "col_", ""), type,
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"`, but this column does not contain 'logical' values (TRUE/FALSE) and was ignored."
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message_("Column '", font_bold(found), "' found as input for {.arg ", ifelse(add_col_prefix, "col_", ""), type,
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"}, but this column does not contain {.code TRUE}/{.code FALSE} values and was ignored."
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)
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found <- NULL
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}
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@@ -771,7 +771,7 @@ format_class <- function(class, plural = FALSE) {
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ifelse(plural, "s", "")
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)
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# exceptions
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class[class == "logical"] <- ifelse(plural, "a vector of `TRUE`/`FALSE`", "`TRUE` or `FALSE`")
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class[class == "logical"] <- ifelse(plural, "a vector of {.code TRUE}/{.code FALSE}", "{.code TRUE} or {.code FALSE}")
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class[class == "data.frame"] <- "a data set"
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if ("list" %in% class) {
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class <- "a list"
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@@ -780,12 +780,12 @@ format_class <- function(class, plural = FALSE) {
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class <- "a matrix"
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}
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if ("custom_eucast_rules" %in% class) {
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class <- "input created with `custom_eucast_rules()`"
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class <- "input created with {.fun custom_eucast_rules}"
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}
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if (any(c("mo", "ab", "sir") %in% class)) {
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class <- paste0("of class '", class[1L], "'")
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class <- paste0("of class {.cls ", class[1L], "}")
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}
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class[class == class.bak] <- paste0("of class '", class[class == class.bak], "'")
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class[class == class.bak] <- paste0("of class {.cls ", class[class == class.bak], "}")
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# output
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vector_or(class, quotes = FALSE, sort = FALSE)
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}
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@@ -820,11 +820,11 @@ meet_criteria <- function(object, # can be literally `list(...)` for `allow_argu
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AMR_env$meet_criteria_error_txt <- NULL
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if (is.null(object)) {
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stop_if(allow_NULL == FALSE, "argument `", obj_name, "` must not be NULL", call = call_depth)
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stop_if(allow_NULL == FALSE, "argument {.arg ", obj_name, "} must not be NULL", call = call_depth)
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return(invisible())
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}
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if (is.null(dim(object)) && length(object) == 1 && suppressWarnings(is.na(object))) { # suppressWarnings for functions
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stop_if(allow_NA == FALSE, "argument `", obj_name, "` must not be NA", call = call_depth)
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stop_if(allow_NA == FALSE, "argument {.arg ", obj_name, "} must not be NA", call = call_depth)
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return(invisible())
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}
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@@ -834,32 +834,32 @@ meet_criteria <- function(object, # can be literally `list(...)` for `allow_argu
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}
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if (!is.null(allow_class) && !(suppressWarnings(all(is.na(object))) && allow_NA == TRUE)) {
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stop_ifnot(inherits(object, allow_class), "argument `", obj_name,
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"` must be ", format_class(allow_class, plural = isTRUE(has_length > 1)),
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stop_ifnot(inherits(object, allow_class), "argument {.arg ", obj_name,
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"} must be ", format_class(allow_class, plural = isTRUE(has_length > 1)),
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", i.e. not be ", format_class(class(object), plural = isTRUE(has_length > 1)),
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call = call_depth
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)
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# check data.frames for data
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if (inherits(object, "data.frame")) {
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stop_if(any(dim(object) == 0),
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"the data provided in argument `", obj_name,
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"` must contain rows and columns (current dimensions: ",
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"the data provided in argument {.arg ", obj_name,
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"} must contain rows and columns (current dimensions: ",
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paste(dim(object), collapse = "x"), ")",
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call = call_depth
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)
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}
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}
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if (!is.null(has_length)) {
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stop_ifnot(length(object) %in% has_length, "argument `", obj_name,
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"` must ", # ifelse(allow_NULL, "be NULL or must ", ""),
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stop_ifnot(length(object) %in% has_length, "argument {.arg ", obj_name,
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"} must ", # ifelse(allow_NULL, "be NULL or must ", ""),
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"be of length ", vector_or(has_length, quotes = FALSE),
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", not ", length(object),
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call = call_depth
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)
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}
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if (!is.null(looks_like)) {
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stop_ifnot(object %like% looks_like, "argument `", obj_name,
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"` must ", # ifelse(allow_NULL, "be NULL or must ", ""),
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stop_ifnot(object %like% looks_like, "argument {.arg ", obj_name,
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"} must ", # ifelse(allow_NULL, "be NULL or must ", ""),
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"resemble the regular expression \"", looks_like, "\"",
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call = call_depth
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)
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@@ -877,7 +877,7 @@ meet_criteria <- function(object, # can be literally `list(...)` for `allow_argu
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if ("logical" %in% allow_class) {
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or_values <- paste0(or_values, ", or TRUE or FALSE")
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}
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stop_ifnot(all(object %in% is_in.bak, na.rm = TRUE), "argument `", obj_name, "` ",
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stop_ifnot(all(object %in% is_in.bak, na.rm = TRUE), "argument {.arg ", obj_name, "} ",
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ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
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"must be either ",
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"must only contain values "
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@@ -888,8 +888,8 @@ meet_criteria <- function(object, # can be literally `list(...)` for `allow_argu
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)
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}
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if (isTRUE(is_positive)) {
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stop_if(is.numeric(object) && !all(object > 0, na.rm = TRUE), "argument `", obj_name,
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"` must ",
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stop_if(is.numeric(object) && !all(object > 0, na.rm = TRUE), "argument {.arg ", obj_name,
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"} must ",
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ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
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"be a number higher than zero",
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"all be numbers higher than zero"
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@@ -898,8 +898,8 @@ meet_criteria <- function(object, # can be literally `list(...)` for `allow_argu
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)
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}
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if (isTRUE(is_positive_or_zero)) {
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stop_if(is.numeric(object) && !all(object >= 0, na.rm = TRUE), "argument `", obj_name,
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"` must ",
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stop_if(is.numeric(object) && !all(object >= 0, na.rm = TRUE), "argument {.arg ", obj_name,
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"} must ",
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ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
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"be zero or a positive number",
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"all be zero or numbers higher than zero"
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@@ -908,8 +908,8 @@ meet_criteria <- function(object, # can be literally `list(...)` for `allow_argu
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)
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}
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if (isTRUE(is_finite)) {
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stop_if(is.numeric(object) && !all(is.finite(object[!is.na(object)]), na.rm = TRUE), "argument `", obj_name,
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"` must ",
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stop_if(is.numeric(object) && !all(is.finite(object[!is.na(object)]), na.rm = TRUE), "argument {.arg ", obj_name,
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"} must ",
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ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
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"be a finite number",
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"all be finite numbers"
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@@ -943,8 +943,8 @@ ascertain_sir_classes <- function(x, obj_name) {
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sirs <- vapply(FUN.VALUE = logical(1), x, is.sir)
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if (!any(sirs, na.rm = TRUE)) {
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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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"the data provided in argument {.arg ", obj_name,
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"} should contain at least one column of class {.cls sir}. Eligible SIR columns were now guessed. ",
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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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@@ -1047,13 +1047,13 @@ get_current_data <- function(arg_name, call) {
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} else {
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examples <- ""
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}
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stop_("this function must be used inside a `dplyr` verb or `data.frame` call",
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stop_("this function must be used inside a {.pkg dplyr} verb or {.code data.frame} call",
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examples,
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call = call
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)
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} else {
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# mimic a base R error that the argument is missing
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stop_("argument `", arg_name, "` is missing with no default", call = call)
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stop_("argument {.arg ", arg_name, "} is missing with no default", call = call)
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}
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}
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@@ -1647,7 +1647,7 @@ if (!is.null(import_fn("where", "tidyselect", error_on_fail = FALSE))) {
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where <- function(fn) {
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# based on https://github.com/nathaneastwood/poorman/blob/52eb6947e0b4430cd588976ed8820013eddf955f/R/where.R#L17-L32
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if (!is.function(fn)) {
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stop_("`", deparse(substitute(fn)), "()` is not a valid predicate function.")
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stop_("{.fun ", deparse(substitute(fn)), "} is not a valid predicate function.")
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}
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df <- pm_select_env$.data
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cols <- pm_select_env$get_colnames()
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@@ -1662,7 +1662,7 @@ if (!is.null(import_fn("where", "tidyselect", error_on_fail = FALSE))) {
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},
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fn
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))
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if (!is.logical(preds)) stop_("`where()` must be used with functions that return `TRUE` or `FALSE`.")
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if (!is.logical(preds)) stop_("{.fun where} must be used with functions that return {.code TRUE} or {.code FALSE}.")
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data_cols <- cols
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cols <- data_cols[preds]
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which(data_cols %in% cols)
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