# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Data Analysis for R # # # # SOURCE # # https://github.com/msberends/AMR # # # # LICENCE # # (c) 2018-2022 Berends MS, Luz CF et al. # # Developed at the University of Groningen, the Netherlands, in # # collaboration with non-profit organisations Certe Medical # # Diagnostics & Advice, and University Medical Center Groningen. # # # # This R package is free software; you can freely use and distribute # # it for both personal and commercial purposes under the terms of the # # GNU General Public License version 2.0 (GNU GPL-2), as published by # # the Free Software Foundation. # # We created this package for both routine data analysis and academic # # research and it was publicly released in the hope that it will be # # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # # # # Visit our website for the full manual and a complete tutorial about # # how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # ==================================================================== # # faster implementation of left_join than using merge() by poorman - we use match(): pm_left_join <- function(x, y, by = NULL, suffix = c(".x", ".y")) { if (is.null(by)) { by <- intersect(names(x), names(y))[1L] if (is.na(by)) { stop_("no common column found for pm_left_join()") } pm_join_message(by) } else if (!is.null(names(by))) { by <- unname(c(names(by), by)) } if (length(by) == 1) { by <- rep(by, 2) } int_x <- colnames(x) %in% colnames(y) & colnames(x) != by[1] int_y <- colnames(y) %in% colnames(x) & colnames(y) != by[2] colnames(x)[int_x] <- paste0(colnames(x)[int_x], suffix[1L]) colnames(y)[int_y] <- paste0(colnames(y)[int_y], suffix[2L]) merged <- cbind(x, y[match(x[, by[1], drop = TRUE], y[, by[2], drop = TRUE]), colnames(y)[!colnames(y) %in% colnames(x) & !colnames(y) == by[2]], drop = FALSE]) rownames(merged) <- NULL merged } # support where() like tidyverse: # adapted from https://github.com/nathaneastwood/poorman/blob/52eb6947e0b4430cd588976ed8820013eddf955f/R/where.R#L17-L32 where <- function(fn) { if (!is.function(fn)) { stop(pm_deparse_var(fn), " is not a valid predicate function.") } preds <- unlist(lapply( pm_select_env$.data, function(x, fn) { do.call("fn", list(x)) }, fn )) if (!is.logical(preds)) stop("`where()` must be used with functions that return `TRUE` or `FALSE`.") data_cols <- pm_select_env$get_colnames() cols <- data_cols[preds] which(data_cols %in% cols) } # copied and slightly rewritten from poorman under same license (2021-10-15) quick_case_when <- function (...) { fs <- list(...) lapply(fs, function(x) if (class(x) != "formula") stop("`case_when()` requires formula inputs.")) n <- length(fs) if (n == 0L) stop("No cases provided.") validate_case_when_length <- function (query, value, fs) { lhs_lengths <- lengths(query) rhs_lengths <- lengths(value) all_lengths <- unique(c(lhs_lengths, rhs_lengths)) if (length(all_lengths) <= 1L) return(all_lengths[[1L]]) non_atomic_lengths <- all_lengths[all_lengths != 1L] len <- non_atomic_lengths[[1L]] if (length(non_atomic_lengths) == 1L) return(len) inconsistent_lengths <- non_atomic_lengths[-1L] lhs_problems <- lhs_lengths %in% inconsistent_lengths rhs_problems <- rhs_lengths %in% inconsistent_lengths problems <- lhs_problems | rhs_problems if (any(problems)) { stop("The following formulas must be length ", len, " or 1, not ", paste(inconsistent_lengths, collapse = ", "), ".\n ", paste(fs[problems], collapse = "\n "), call. = FALSE) } } replace_with <- function (x, i, val, arg_name) { if (is.null(val)) return(x) i[is.na(i)] <- FALSE if (length(val) == 1L) { x[i] <- val } else { x[i] <- val[i] } x } query <- vector("list", n) value <- vector("list", n) default_env <- parent.frame() for (i in seq_len(n)) { query[[i]] <- eval(fs[[i]][[2]], envir = default_env) value[[i]] <- eval(fs[[i]][[3]], envir = default_env) if (!is.logical(query[[i]])) stop(fs[[i]][[2]], " does not return a `logical` vector.") } m <- validate_case_when_length(query, value, fs) out <- value[[1]][rep(NA_integer_, m)] replaced <- rep(FALSE, m) for (i in seq_len(n)) { out <- replace_with(out, query[[i]] & !replaced, value[[i]], NULL) replaced <- replaced | (query[[i]] & !is.na(query[[i]])) } out } # No export, no Rd addin_insert_in <- function() { import_fn("insertText", "rstudioapi")(" %in% ") } # No export, no Rd addin_insert_like <- function() { # we want Shift + Ctrl/Cmd + L to iterate over %like%, %unlike%, %like_case%, and %unlike_case% getActiveDocumentContext <- import_fn("getActiveDocumentContext", "rstudioapi") insertText <- import_fn("insertText", "rstudioapi") modifyRange <- import_fn("modifyRange", "rstudioapi") document_range <- import_fn("document_range", "rstudioapi") document_position <- import_fn("document_position", "rstudioapi") context <- getActiveDocumentContext() current_row <- context$selection[[1]]$range$end[1] current_col <- context$selection[[1]]$range$end[2] current_row_txt <- context$contents[current_row] if (is.null(current_row) || current_row_txt %unlike% "%(un)?like") { insertText(" %like% ") return(invisible()) } pos_preceded_by <- function(txt) { if (tryCatch(substr(current_row_txt, current_col - nchar(trimws(txt, which = "right")), current_col) == trimws(txt, which = "right"), error = function(e) FALSE)) { return(TRUE) } tryCatch(substr(current_row_txt, current_col - nchar(txt), current_col) %like% paste0("^", txt), error = function(e) FALSE) } replace_pos <- function(old, with) { modifyRange(document_range(document_position(current_row, current_col - nchar(old)), document_position(current_row, current_col)), text = with, id = context$id) } if (pos_preceded_by(" %like% ")) { replace_pos(" %like% ", with = " %unlike% ") } else if (pos_preceded_by(" %unlike% ")) { replace_pos(" %unlike% ", with = " %like_case% ") } else if (pos_preceded_by(" %like_case% ")) { replace_pos(" %like_case% ", with = " %unlike_case% ") } else if (pos_preceded_by(" %unlike_case% ")) { replace_pos(" %unlike_case% ", with = " %like% ") } else { insertText(" %like% ") } } check_dataset_integrity <- function() { # check if user overwrote our data sets in their global environment data_in_pkg <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item", drop = TRUE] data_in_globalenv <- ls(envir = globalenv()) overwritten <- data_in_pkg[data_in_pkg %in% data_in_globalenv] # exception for example_isolates overwritten <- overwritten[overwritten %unlike% "example_isolates"] if (length(overwritten) > 0) { if (length(overwritten) > 1) { plural <- c("s are", "", "s") } else { plural <- c(" is", "s", "") } if (message_not_thrown_before("check_dataset_integrity", overwritten)) { warning_("The following data set", plural[1], " overwritten by your global environment and prevent", plural[2], " the AMR package from working correctly: ", vector_and(overwritten, quotes = "'"), ".\nPlease rename your object", plural[3], ".", call = FALSE) } } # check if other packages did not overwrite our data sets valid_microorganisms <- TRUE valid_antibiotics <- TRUE tryCatch({ valid_microorganisms <- all(c("mo", "fullname", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "species_id", "source", "ref", "prevalence") %in% colnames(microorganisms), na.rm = TRUE) valid_antibiotics <- all(c("ab", "atc", "cid", "name", "group", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", "loinc") %in% colnames(antibiotics), na.rm = TRUE) }, error = function(e) { # package not yet loaded require("AMR") }) stop_if(!valid_microorganisms | !valid_antibiotics, "the data set `microorganisms` or `antibiotics` was overwritten in your environment because another package with the same object name(s) was loaded _after_ the AMR package, preventing the AMR package from working correctly. Please load the AMR package last.") invisible(TRUE) } search_type_in_df <- function(x, type, info = TRUE) { meet_criteria(x, allow_class = "data.frame") meet_criteria(type, allow_class = "character", has_length = 1) # try to find columns based on type found <- NULL # remove attributes from other packages x <- as.data.frame(x, stringsAsFactors = FALSE) colnames_formatted <- tolower(generalise_antibiotic_name(colnames(x))) # -- mo if (type == "mo") { if (any(vapply(FUN.VALUE = logical(1), x, is.mo))) { # take first column found <- colnames(x)[vapply(FUN.VALUE = logical(1), x, is.mo)] } else if ("mo" %in% colnames_formatted & suppressWarnings(all(x$mo %in% c(NA, microorganisms$mo)))) { found <- "mo" } else if (any(colnames_formatted %like_case% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$")) { found <- sort(colnames(x)[colnames_formatted %like_case% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$"]) } else if (any(colnames_formatted %like_case% "^(microorganism|organism|bacteria|ba[ck]terie)")) { found <- sort(colnames(x)[colnames_formatted %like_case% "^(microorganism|organism|bacteria|ba[ck]terie)"]) } else if (any(colnames_formatted %like_case% "species")) { found <- sort(colnames(x)[colnames_formatted %like_case% "species"]) } } # -- key antibiotics if (type %in% c("keyantibiotics", "keyantimicrobials")) { if (any(colnames_formatted %like_case% "^key.*(ab|antibiotics|antimicrobials)")) { found <- sort(colnames(x)[colnames_formatted %like_case% "^key.*(ab|antibiotics|antimicrobials)"]) } } # -- date if (type == "date") { if (any(colnames_formatted %like_case% "^(specimen date|specimen_date|spec_date)")) { # WHONET support found <- sort(colnames(x)[colnames_formatted %like_case% "^(specimen date|specimen_date|spec_date)"]) if (!any(class(pm_pull(x, found)) %in% c("Date", "POSIXct"))) { stop(font_red(paste0("Found column '", font_bold(found), "' to be used as input for `col_", type, "`, but this column contains no valid dates. Transform its values to valid dates first.")), call. = FALSE) } } else if (any(vapply(FUN.VALUE = logical(1), x, function(x) inherits(x, c("Date", "POSIXct"))))) { # take first column found <- colnames(x)[vapply(FUN.VALUE = logical(1), x, function(x) inherits(x, c("Date", "POSIXct")))] } } # -- patient id if (type == "patient_id") { crit1 <- colnames_formatted %like_case% "^(patient|patid)" if (any(crit1)) { found <- colnames(x)[crit1] } else { crit2 <- colnames_formatted %like_case% "(identification |patient|pat.*id)" if (any(crit2)) { found <- colnames(x)[crit2] } } } # -- specimen if (type == "specimen") { if (any(colnames_formatted %like_case% "(specimen type|spec_type)")) { found <- sort(colnames(x)[colnames_formatted %like_case% "(specimen type|spec_type)"]) } else if (any(colnames_formatted %like_case% "^(specimen)")) { found <- sort(colnames(x)[colnames_formatted %like_case% "^(specimen)"]) } } # -- UTI (urinary tract infection) if (type == "uti") { if (any(colnames_formatted == "uti")) { found <- colnames(x)[colnames_formatted == "uti"] } else if (any(colnames_formatted %like_case% "(urine|urinary)")) { found <- sort(colnames(x)[colnames_formatted %like_case% "(urine|urinary)"]) } if (!is.null(found)) { # this column should contain logicals if (!is.logical(x[, found, drop = TRUE])) { message_("Column '", font_bold(found), "' found as input for `col_", type, "`, but this column does not contain 'logical' values (TRUE/FALSE) and was ignored.", add_fn = font_red) found <- NULL } } } found <- found[1] if (!is.null(found) & info == TRUE) { if (message_not_thrown_before("search_in_type", type)) { msg <- paste0("Using column '", font_bold(found), "' as input for `col_", type, "`.") if (type %in% c("keyantibiotics", "keyantimicrobials", "specimen")) { msg <- paste(msg, "Use", font_bold(paste0("col_", type), "= FALSE"), "to prevent this.") } message_(msg) } } found } is_valid_regex <- function(x) { regex_at_all <- tryCatch(vapply(FUN.VALUE = logical(1), X = strsplit(x, ""), FUN = function(y) any(y %in% c("$", "(", ")", "*", "+", "-", ".", "?", "[", "]", "^", "{", "|", "}", "\\"), na.rm = TRUE), USE.NAMES = FALSE), error = function(e) rep(TRUE, length(x))) regex_valid <- vapply(FUN.VALUE = logical(1), X = x, FUN = function(y) !"try-error" %in% class(try(grepl(y, "", perl = TRUE), silent = TRUE)), USE.NAMES = FALSE) regex_at_all & regex_valid } stop_ifnot_installed <- function(package) { # no "utils::installed.packages()" since it requires non-staged install since R 3.6.0 # https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html vapply(FUN.VALUE = character(1), package, function(pkg) tryCatch(get(".packageName", envir = asNamespace(pkg)), error = function(e) { if (pkg == "rstudioapi") { stop("This function only works in RStudio when using R >= 3.2.", call. = FALSE) } else if (pkg != "base") { stop("This requires the '", pkg, "' package.", "\nTry to install it with: install.packages(\"", pkg, "\")", call. = FALSE) } })) return(invisible()) } pkg_is_available <- function(pkg, also_load = TRUE, min_version = NULL) { if (also_load == TRUE) { out <- suppressWarnings(require(pkg, character.only = TRUE, warn.conflicts = FALSE)) } else { out <- requireNamespace(pkg, quietly = TRUE) } if (!is.null(min_version)) { out <- out && utils::packageVersion(pkg) >= min_version } isTRUE(out) } import_fn <- function(name, pkg, error_on_fail = TRUE) { if (isTRUE(error_on_fail)) { stop_ifnot_installed(pkg) } tryCatch( # don't use get() to avoid fetching non-API functions getExportedValue(name = name, ns = asNamespace(pkg)), error = function(e) { if (isTRUE(error_on_fail)) { stop_("function ", name, "() is not an exported object from package '", pkg, "'. Please create an issue at https://github.com/msberends/AMR/issues. Many thanks!", call = FALSE) } else { return(NULL) } }) } # this alternative wrapper to the message(), warning() and stop() functions: # - wraps text to never break lines within words # - ignores formatted text while wrapping # - adds indentation dependent on the type of message (such as NOTE) # - can add additional formatting functions like blue or bold text word_wrap <- function(..., add_fn = list(), as_note = FALSE, width = 0.95 * getOption("width"), extra_indent = 0) { msg <- paste0(c(...), collapse = "") if (isTRUE(as_note)) { msg <- paste0(pkg_env$info_icon, " ", gsub("^note:? ?", "", msg, ignore.case = TRUE)) } if (msg %like% "\n") { # run word_wraps() over every line here, bind them and return again return(paste0(vapply(FUN.VALUE = character(1), trimws(unlist(strsplit(msg, "\n")), which = "right"), word_wrap, add_fn = add_fn, as_note = FALSE, width = width, extra_indent = extra_indent), collapse = "\n")) } # correct for operators (will add the space later on) ops <- "([,./><\\]\\[])" msg <- gsub(paste0(ops, " ", ops), "\\1\\2", msg, perl = TRUE) # we need to correct for already applied style, that adds text like "\033[31m\" msg_stripped <- font_stripstyle(msg) # where are the spaces now? msg_stripped_wrapped <- paste0(strwrap(msg_stripped, simplify = TRUE, width = width), collapse = "\n") msg_stripped_wrapped <- paste0(unlist(strsplit(msg_stripped_wrapped, "(\n|\\*\\|\\*)")), collapse = "\n") msg_stripped_spaces <- which(unlist(strsplit(msg_stripped, "")) == " ") msg_stripped_wrapped_spaces <- which(unlist(strsplit(msg_stripped_wrapped, "")) != "\n") # so these are the indices of spaces that need to be replaced replace_spaces <- which(!msg_stripped_spaces %in% msg_stripped_wrapped_spaces) # put it together msg <- unlist(strsplit(msg, " ")) msg[replace_spaces] <- paste0(msg[replace_spaces], "\n") # add space around operators again msg <- gsub(paste0(ops, ops), "\\1 \\2", msg, perl = TRUE) msg <- paste0(msg, collapse = " ") msg <- gsub("\n ", "\n", msg, fixed = TRUE) if (msg_stripped %like% "\u2139 ") { indentation <- 2 + extra_indent } else if (msg_stripped %like% "^=> ") { indentation <- 3 + extra_indent } else { indentation <- 0 + extra_indent } msg <- gsub("\n", paste0("\n", strrep(" ", indentation)), msg, fixed = TRUE) # remove trailing empty characters msg <- gsub("(\n| )+$", "", msg) if (length(add_fn) > 0) { if (!is.list(add_fn)) { add_fn <- list(add_fn) } for (i in seq_len(length(add_fn))) { msg <- add_fn[[i]](msg) } } # format backticks msg <- gsub("(`.+?`)", font_grey_bg("\\1"), msg) # clean introduced whitespace between fullstops msg <- gsub("[.] +[.]", "..", msg) msg } message_ <- function(..., appendLF = TRUE, add_fn = list(font_blue), as_note = TRUE) { message(word_wrap(..., add_fn = add_fn, as_note = as_note), appendLF = appendLF) } warning_ <- function(..., add_fn = list(), immediate = FALSE, call = TRUE) { warning(word_wrap(..., add_fn = add_fn, as_note = FALSE), immediate. = immediate, call. = call) } # this alternative to the stop() function: # - adds the function name where the error was thrown # - wraps text to never break lines within words stop_ <- function(..., call = TRUE) { msg <- paste0(c(...), collapse = "") if (!isFALSE(call)) { if (isTRUE(call)) { call <- as.character(sys.call(-1)[1]) } else { # so you can go back more than 1 call, as used in rsi_calc(), that now throws a reference to e.g. n_rsi() call <- as.character(sys.call(call)[1]) } msg <- paste0("in ", call, "(): ", msg) } msg <- word_wrap(msg, add_fn = list(), as_note = FALSE) stop(msg, call. = FALSE) } stop_if <- function(expr, ..., call = TRUE) { if (isTRUE(expr)) { if (isTRUE(call)) { call <- -1 } if (!isFALSE(call)) { # since we're calling stop_(), which is another call call <- call - 1 } stop_(..., call = call) } } stop_ifnot <- function(expr, ..., call = TRUE) { if (isFALSE(expr)) { if (isTRUE(call)) { call <- -1 } if (!isFALSE(call)) { # since we're calling stop_(), which is another call call <- call - 1 } stop_(..., call = call) } } "%or%" <- function(x, y) { if (is.null(x) | is.null(y)) { if (is.null(x)) { return(y) } else { return(x) } } ifelse(!is.na(x), x, ifelse(!is.na(y), y, NA)) } return_after_integrity_check <- function(value, type, check_vector) { if (!all(value[!is.na(value)] %in% check_vector)) { warning_(paste0("invalid ", type, ", NA generated"), call = FALSE) value[!value %in% check_vector] <- NA } value } # transforms data set to data.frame with only ASCII values, to comply with CRAN policies dataset_UTF8_to_ASCII <- function(df) { trans <- function(vect) { iconv(vect, from = "UTF-8", to = "ASCII//TRANSLIT") } df <- as.data.frame(df, stringsAsFactors = FALSE) for (i in seq_len(NCOL(df))) { col <- df[, i] if (is.list(col)) { col <- lapply(col, function(j) trans(j)) df[, i] <- list(col) } else { if (is.factor(col)) { levels(col) <- trans(levels(col)) } else if (is.character(col)) { col <- trans(col) } else { col } df[, i] <- col } } df } # for eucast_rules() and mdro(), creates markdown output with URLs and names create_eucast_ab_documentation <- function() { x <- trimws(unique(toupper(unlist(strsplit(EUCAST_RULES_DF$then_change_these_antibiotics, ","))))) ab <- character() for (val in x) { if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) { # antibiotic group names, as defined in data-raw/_internals.R, such as `CARBAPENEMS` val <- eval(parse(text = paste0("AB_", val)), envir = asNamespace("AMR")) } else if (val %in% AB_lookup$ab) { # separate drugs, such as `AMX` val <- as.ab(val) } else { val <- as.rsi(NA) } ab <- c(ab, val) } ab <- unique(ab) atcs <- ab_atc(ab, only_first = TRUE) # only keep ABx with an ATC code: ab <- ab[!is.na(atcs)] ab_names <- ab_name(ab, language = NULL, tolower = TRUE) ab <- ab[order(ab_names)] ab_names <- ab_names[order(ab_names)] atc_txt <- paste0("[", atcs[!is.na(atcs)], "](", ab_url(ab), ")") out <- paste0(ab_names, " (`", ab, "`, ", atc_txt, ")", collapse = ", ") substr(out, 1, 1) <- toupper(substr(out, 1, 1)) out } vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE, last_sep = " or ") { # makes unique and sorts, and this also removed NAs v <- unique(v) if (isTRUE(sort)) { v <- sort(v) } if (isTRUE(reverse)) { v <- rev(v) } if (isTRUE(quotes)) { quotes <- '"' } else if (isFALSE(quotes)) { quotes <- "" } else { quotes <- quotes[1L] } if (isTRUE(initial_captital)) { v[1] <- gsub("^([a-z])", "\\U\\1", v[1], perl = TRUE) } if (length(v) == 1) { return(paste0(quotes, v, quotes)) } if (identical(v, c("I", "R", "S"))) { # class should be sorted like this v <- c("R", "S", "I") } # all commas except for last item, so will become '"val1", "val2", "val3" or "val4"' paste0(paste0(quotes, v[seq_len(length(v) - 1)], quotes, collapse = ", "), last_sep, paste0(quotes, v[length(v)], quotes)) } vector_and <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE) { vector_or(v = v, quotes = quotes, reverse = reverse, sort = sort, initial_captital = initial_captital, last_sep = " and ") } format_class <- function(class, plural = FALSE) { class.bak <- class class[class == "numeric"] <- "number" class[class == "integer"] <- "whole number" if (all(c("numeric", "integer") %in% class.bak, na.rm = TRUE)) { class[class %in% c("number", "whole number")] <- "(whole) number" } class[class == "character"] <- "text string" class[class %in% c("Date", "POSIXt")] <- "date" class[class != class.bak] <- paste0(ifelse(plural, "", "a "), class[class != class.bak], ifelse(plural, "s", "")) # exceptions class[class == "logical"] <- ifelse(plural, "a vector of `TRUE`/`FALSE`", "`TRUE` or `FALSE`") class[class == "data.frame"] <- "a data set" if ("list" %in% class) { class <- "a list" } if ("matrix" %in% class) { class <- "a matrix" } if ("custom_eucast_rules" %in% class) { class <- "input created with `custom_eucast_rules()`" } if (any(c("mo", "ab", "rsi") %in% class)) { class <- paste0("of class <", class[1L], ">") } class[class == class.bak] <- paste0("of class <", class[class == class.bak], ">") # output vector_or(class, quotes = FALSE, sort = FALSE) } # a check for every single argument in all functions meet_criteria <- function(object, allow_class = NULL, has_length = NULL, looks_like = NULL, is_in = NULL, is_positive = NULL, is_positive_or_zero = NULL, is_finite = NULL, contains_column_class = NULL, allow_NULL = FALSE, allow_NA = FALSE, ignore.case = FALSE, .call_depth = 0) { # depth in calling obj_name <- deparse(substitute(object)) call_depth <- -2 - abs(.call_depth) # if object is missing, or another error: tryCatch(invisible(object), error = function(e) pkg_env$meet_criteria_error_txt <- e$message) if (!is.null(pkg_env$meet_criteria_error_txt)) { error_txt <- pkg_env$meet_criteria_error_txt pkg_env$meet_criteria_error_txt <- NULL stop(error_txt, call. = FALSE) # don't use stop_() here, pkg may not be loaded yet } pkg_env$meet_criteria_error_txt <- NULL if (is.null(object)) { stop_if(allow_NULL == FALSE, "argument `", obj_name, "` must not be NULL", call = call_depth) return(invisible()) } if (is.null(dim(object)) && length(object) == 1 && suppressWarnings(is.na(object))) { # suppressWarnings for functions stop_if(allow_NA == FALSE, "argument `", obj_name, "` must not be NA", call = call_depth) return(invisible()) } if (!is.null(allow_class)) { stop_ifnot(inherits(object, allow_class), "argument `", obj_name, "` must be ", format_class(allow_class, plural = isTRUE(has_length > 1)), ", i.e. not be ", format_class(class(object), plural = isTRUE(has_length > 1)), call = call_depth) # check data.frames for data if (inherits(object, "data.frame")) { stop_if(any(dim(object) == 0), "the data provided in argument `", obj_name, "` must contain rows and columns (current dimensions: ", paste(dim(object), collapse = "x"), ")", call = call_depth) } } if (!is.null(has_length)) { stop_ifnot(length(object) %in% has_length, "argument `", obj_name, "` must ", # ifelse(allow_NULL, "be NULL or must ", ""), "be of length ", vector_or(has_length, quotes = FALSE), ", not ", length(object), call = call_depth) } if (!is.null(looks_like)) { stop_ifnot(object %like% looks_like, "argument `", obj_name, "` must ", # ifelse(allow_NULL, "be NULL or must ", ""), "resemble the regular expression \"", looks_like, "\"", call = call_depth) } if (!is.null(is_in)) { if (ignore.case == TRUE) { object <- tolower(object) is_in <- tolower(is_in) } stop_ifnot(all(object %in% is_in, na.rm = TRUE), "argument `", obj_name, "` ", ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1, "must be either ", "must only contain values "), vector_or(is_in, quotes = !isTRUE(any(c("double", "numeric", "integer") %in% allow_class))), ifelse(allow_NA == TRUE, ", or NA", ""), call = call_depth) } if (isTRUE(is_positive)) { stop_if(is.numeric(object) && !all(object > 0, na.rm = TRUE), "argument `", obj_name, "` must ", ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1, "be a number higher than zero", "all be numbers higher than zero"), call = call_depth) } if (isTRUE(is_positive_or_zero)) { stop_if(is.numeric(object) && !all(object >= 0, na.rm = TRUE), "argument `", obj_name, "` must ", ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1, "be zero or a positive number", "all be zero or numbers higher than zero"), call = call_depth) } if (isTRUE(is_finite)) { stop_if(is.numeric(object) && !all(is.finite(object[!is.na(object)]), na.rm = TRUE), "argument `", obj_name, "` must ", ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1, "be a finite number", "all be finite numbers"), " (i.e. not be infinite)", call = call_depth) } if (!is.null(contains_column_class)) { stop_ifnot(any(vapply(FUN.VALUE = logical(1), object, function(col, columns_class = contains_column_class) { inherits(col, columns_class) }), na.rm = TRUE), "the data provided in argument `", obj_name, "` must contain at least one column of class <", contains_column_class, ">. ", "See ?as.", contains_column_class, ".", call = call_depth) } return(invisible()) } get_current_data <- function(arg_name, call) { valid_df <- function(x) { !is.null(x) && is.data.frame(x) } # try dplyr::cur_data_all() first to support dplyr groups # only useful for e.g. dplyr::filter(), dplyr::mutate() and dplyr::summarise() # not useful (throws error) with e.g. dplyr::select() - but that will be caught later in this function cur_data_all <- import_fn("cur_data_all", "dplyr", error_on_fail = FALSE) if (!is.null(cur_data_all)) { out <- tryCatch(cur_data_all(), error = function(e) NULL) if (valid_df(out)) { return(out) } } # try a manual (base R) method, by going over all underlying environments with sys.frames() for (env in sys.frames()) { if (!is.null(env$`.Generic`)) { # don't check `".Generic" %in% names(env)`, because in R < 3.2, `names(env)` is always NULL if (valid_df(env$`.data`)) { # an element `.data` will be in the environment when using `dplyr::select()` # (but not when using `dplyr::filter()`, `dplyr::mutate()` or `dplyr::summarise()`) return(env$`.data`) } else if (valid_df(env$xx)) { # an element `xx` will be in the environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]` return(env$xx) } else if (valid_df(env$x)) { # an element `x` will be in the environment for only cols, e.g. `example_isolates[, carbapenems()]` return(env$x) } } } # no data.frame found, so an error must be returned: if (is.na(arg_name)) { if (isTRUE(is.numeric(call))) { fn <- as.character(sys.call(call + 1)[1]) examples <- paste0(", e.g.:\n", " your_data %>% select(", fn, "())\n", " your_data %>% select(column_a, column_b, ", fn, "())\n", " your_data[, ", fn, "()]\n", ' your_data[, c("column_a", "column_b", ', fn, "())]") } else { examples <- "" } stop_("this function must be used inside a `dplyr` verb or `data.frame` call", examples, call = call) } else { # mimic a base R error that the argument is missing stop_("argument `", arg_name, "` is missing with no default", call = call) } } get_current_column <- function() { # try dplyr::cur_columns() first cur_column <- import_fn("cur_column", "dplyr", error_on_fail = FALSE) if (!is.null(cur_column)) { out <- tryCatch(cur_column(), error = function(e) NULL) if (!is.null(out)) { return(out) } } # cur_column() doesn't always work (only allowed for certain conditions set by dplyr), but it's probably still possible: frms <- lapply(sys.frames(), function(env) { if (!is.null(env$i)) { if (!is.null(env$tibble_vars)) { # for mutate_if() env$tibble_vars[env$i] } else { # for mutate(across()) df <- tryCatch(get_current_data(NA, 0), error = function(e) NULL) if (is.data.frame(df)) { colnames(df)[env$i] } else { env$i } } } else { NULL } }) vars <- unlist(frms) if (length(vars) > 0) { vars[length(vars)] } else { # not found, so: NULL } } is_null_or_grouped_tbl <- function(x) { # class "grouped_df" might change at one point, so only set in one place; here. is.null(x) || inherits(x, "grouped_df") } unique_call_id <- function(entire_session = FALSE, match_fn = NULL) { if (entire_session == TRUE) { return(c(envir = "session", call = "session")) } # combination of environment ID (such as "0x7fed4ee8c848") # and relevant system call (where 'match_fn' is being called in) calls <- sys.calls() if (!identical(Sys.getenv("R_RUN_TINYTEST"), "true") && !any(as.character(calls[[1]]) %like_case% "run_test_dir|run_test_file|test_all|tinytest|test_package|testthat")) { for (i in seq_len(length(calls))) { call_clean <- gsub("[^a-zA-Z0-9_().-]", "", as.character(calls[[i]]), perl = TRUE) if (any(call_clean %like% paste0(match_fn, "\\("), na.rm = TRUE)) { return(c(envir = gsub("", "\\1", utils::capture.output(sys.frames()[[1]]), perl = TRUE), call = paste0(deparse(calls[[i]]), collapse = ""))) } } } c(envir = paste0(sample(c(c(0:9), letters[1:6]), size = 32, replace = TRUE), collapse = ""), call = paste0(sample(c(c(0:9), letters[1:6]), size = 32, replace = TRUE), collapse = "")) } #' @noRd #' @param fn name of the function as a character #' @param ... character elements to be pasted together as a 'salt' #' @param entire_session show message once per session message_not_thrown_before <- function(fn, ..., entire_session = FALSE) { # this is to prevent that messages/notes will be printed for every dplyr group or more than once per session # e.g. this would show a msg 4 times: example_isolates %>% group_by(hospital_id) %>% filter(mo_is_gram_negative()) salt <- gsub("[^a-zA-Z0-9|_-]", "?", paste(c(...), sep = "|", collapse = "|"), perl = TRUE) not_thrown_before <- is.null(pkg_env[[paste0("thrown_msg.", fn, ".", salt)]]) || !identical(pkg_env[[paste0("thrown_msg.", fn, ".", salt)]], unique_call_id(entire_session = entire_session, match_fn = fn)) if (isTRUE(not_thrown_before)) { # message was not thrown before - remember this so on the next run it will return FALSE: assign(x = paste0("thrown_msg.", fn, ".", salt), value = unique_call_id(entire_session = entire_session, match_fn = fn), envir = pkg_env) } not_thrown_before } has_colour <- function() { # this is a base R version of crayon::has_color, but disables colours on emacs if (Sys.getenv("EMACS") != "" || Sys.getenv("INSIDE_EMACS") != "") { # disable on emacs, which only supports 8 colours return(FALSE) } enabled <- getOption("crayon.enabled") if (!is.null(enabled)) { return(isTRUE(enabled)) } rstudio_with_ansi_support <- function(x) { if (Sys.getenv("RSTUDIO", "") == "") { return(FALSE) } if ((cols <- Sys.getenv("RSTUDIO_CONSOLE_COLOR", "")) != "" && !is.na(as.double(cols))) { return(TRUE) } tryCatch(get("isAvailable", envir = asNamespace("rstudioapi"))(), error = function(e) return(FALSE)) && tryCatch(get("hasFun", envir = asNamespace("rstudioapi"))("getConsoleHasColor"), error = function(e) return(FALSE)) } if (rstudio_with_ansi_support() && sink.number() == 0) { return(TRUE) } if (!isatty(stdout())) { return(FALSE) } if (tolower(Sys.info()["sysname"]) == "windows") { if (Sys.getenv("ConEmuANSI") == "ON") { return(TRUE) } if (Sys.getenv("CMDER_ROOT") != "") { return(TRUE) } return(FALSE) } if ("COLORTERM" %in% names(Sys.getenv())) { return(TRUE) } if (Sys.getenv("TERM") == "dumb") { return(FALSE) } grepl(pattern = "^screen|^xterm|^vt100|color|ansi|cygwin|linux", x = Sys.getenv("TERM"), ignore.case = TRUE, perl = TRUE) } # set colours if console has_colour() try_colour <- function(..., before, after, collapse = " ") { txt <- paste0(unlist(list(...)), collapse = collapse) if (isTRUE(has_colour())) { if (is.null(collapse)) { paste0(before, txt, after, collapse = NULL) } else { paste0(before, txt, after, collapse = "") } } else { txt } } font_black <- function(..., collapse = " ") { try_colour(..., before = "\033[38;5;232m", after = "\033[39m", collapse = collapse) } font_blue <- function(..., collapse = " ") { try_colour(..., before = "\033[34m", after = "\033[39m", collapse = collapse) } font_green <- function(..., collapse = " ") { try_colour(..., before = "\033[32m", after = "\033[39m", collapse = collapse) } font_magenta <- function(..., collapse = " ") { try_colour(..., before = "\033[35m", after = "\033[39m", collapse = collapse) } font_red <- function(..., collapse = " ") { try_colour(..., before = "\033[31m", after = "\033[39m", collapse = collapse) } font_silver <- function(..., collapse = " ") { try_colour(..., before = "\033[90m", after = "\033[39m", collapse = collapse) } font_white <- function(..., collapse = " ") { try_colour(..., before = "\033[37m", after = "\033[39m", collapse = collapse) } font_yellow <- function(..., collapse = " ") { try_colour(..., before = "\033[33m", after = "\033[39m", collapse = collapse) } font_subtle <- function(..., collapse = " ") { try_colour(..., before = "\033[38;5;246m", after = "\033[39m", collapse = collapse) } font_grey <- function(..., collapse = " ") { try_colour(..., before = "\033[38;5;249m", after = "\033[39m", collapse = collapse) } font_grey_bg <- function(..., collapse = " ") { if (tryCatch(import_fn("getThemeInfo", "rstudioapi", error_on_fail = FALSE)()$dark, error = function(e) FALSE)) { # similar to HTML #444444 try_colour(..., before = "\033[48;5;238m", after = "\033[49m", collapse = collapse) } else { # similar to HTML #f0f0f0 try_colour(..., before = "\033[48;5;255m", after = "\033[49m", collapse = collapse) } } font_green_bg <- function(..., collapse = " ") { try_colour(..., before = "\033[42m", after = "\033[49m", collapse = collapse) } font_rsi_R_bg <- function(..., collapse = " ") { #ED553B try_colour(..., before = "\033[48;5;203m", after = "\033[49m", collapse = collapse) } font_rsi_S_bg <- function(..., collapse = " ") { #3CAEA3 try_colour(..., before = "\033[48;5;79m", after = "\033[49m", collapse = collapse) } font_rsi_I_bg <- function(..., collapse = " ") { #F6D55C try_colour(..., before = "\033[48;5;222m", after = "\033[49m", collapse = collapse) } font_red_bg <- function(..., collapse = " ") { try_colour(..., before = "\033[41m", after = "\033[49m", collapse = collapse) } font_yellow_bg <- function(..., collapse = " ") { try_colour(..., before = "\033[43m", after = "\033[49m", collapse = collapse) } font_na <- function(..., collapse = " ") { font_red(..., collapse = collapse) } font_bold <- function(..., collapse = " ") { try_colour(..., before = "\033[1m", after = "\033[22m", collapse = collapse) } font_italic <- function(..., collapse = " ") { try_colour(..., before = "\033[3m", after = "\033[23m", collapse = collapse) } font_underline <- function(..., collapse = " ") { try_colour(..., before = "\033[4m", after = "\033[24m", collapse = collapse) } font_stripstyle <- function(x) { # from crayon:::ansi_regex gsub("(?:(?:\\x{001b}\\[)|\\x{009b})(?:(?:[0-9]{1,3})?(?:(?:;[0-9]{0,3})*)?[A-M|f-m])|\\x{001b}[A-M]", "", x, perl = TRUE) } progress_ticker <- function(n = 1, n_min = 0, print = TRUE, ...) { if (print == FALSE || n < n_min) { pb <- list() pb$tick <- function() { invisible() } pb$kill <- function() { invisible() } set_clean_class(pb, new_class = "txtProgressBar") } else if (n >= n_min) { # rely on the progress package if it is available - it has a more verbose output progress_bar <- import_fn("progress_bar", "progress", error_on_fail = FALSE) if (!is.null(progress_bar)) { # so we use progress::progress_bar # a close() method was also added, see below this function pb <- progress_bar$new(format = "[:bar] :percent (:current/:total)", total = n) } else { pb <- utils::txtProgressBar(max = n, style = 3) pb$tick <- function() { pb$up(pb$getVal() + 1) } } pb } } #' @method close progress_bar #' @export #' @noRd close.progress_bar <- function(con, ...) { con$terminate() } set_clean_class <- function(x, new_class) { # return the object with only the new class and no additional attributes where possible if (is.null(x)) { x <- NA_character_ } if (is.factor(x)) { # keep only levels and remove all other attributes lvls <- levels(x) attributes(x) <- NULL levels(x) <- lvls } else if (!is.list(x) && !is.function(x)) { attributes(x) <- NULL } class(x) <- new_class x } formatted_filesize <- function(...) { size_kb <- file.size(...) / 1024 if (size_kb < 1) { paste(round(size_kb, 1), "kB") } else if (size_kb < 100) { paste(round(size_kb, 0), "kB") } else { paste(round(size_kb / 1024, 1), "MB") } } create_pillar_column <- function(x, ...) { new_pillar_shaft_simple <- import_fn("new_pillar_shaft_simple", "pillar") new_pillar_shaft_simple(x, ...) } # copied from vctrs::s3_register by their permission: # https://github.com/r-lib/vctrs/blob/05968ce8e669f73213e3e894b5f4424af4f46316/R/register-s3.R s3_register <- function(generic, class, method = NULL) { stopifnot(is.character(generic), length(generic) == 1) stopifnot(is.character(class), length(class) == 1) pieces <- strsplit(generic, "::")[[1]] stopifnot(length(pieces) == 2) package <- pieces[[1]] generic <- pieces[[2]] caller <- parent.frame() get_method_env <- function() { top <- topenv(caller) if (isNamespace(top)) { asNamespace(environmentName(top)) } else { caller } } get_method <- function(method, env) { if (is.null(method)) { get(paste0(generic, ".", class), envir = get_method_env()) } else { method } } method_fn <- get_method(method) stopifnot(is.function(method_fn)) setHook(packageEvent(package, "onLoad"), function(...) { ns <- asNamespace(package) method_fn <- get_method(method) registerS3method(generic, class, method_fn, envir = ns) }) if (!isNamespaceLoaded(package)) { return(invisible()) } envir <- asNamespace(package) if (exists(generic, envir)) { registerS3method(generic, class, method_fn, envir = envir) } invisible() } # works exactly like round(), but rounds `round2(44.55, 1)` to 44.6 instead of 44.5 # and adds decimal zeroes until `digits` is reached when force_zero = TRUE round2 <- function(x, digits = 1, force_zero = TRUE) { x <- as.double(x) # https://stackoverflow.com/a/12688836/4575331 val <- (trunc((abs(x) * 10 ^ digits) + 0.5) / 10 ^ digits) * sign(x) if (digits > 0 & force_zero == TRUE) { values_trans <- val[val != as.integer(val) & !is.na(val)] val[val != as.integer(val) & !is.na(val)] <- paste0(values_trans, strrep("0", max(0, digits - nchar( format( as.double( gsub(".*[.](.*)$", "\\1", values_trans)), scientific = FALSE))))) } as.double(val) } # percentage from our other package: 'cleaner' percentage <- function(x, digits = NULL, ...) { # getdecimalplaces() function getdecimalplaces <- function(x, minimum = 0, maximum = 3) { if (maximum < minimum) { maximum <- minimum } if (minimum > maximum) { minimum <- maximum } max_places <- max(unlist(lapply(strsplit(sub("0+$", "", as.character(x * 100)), ".", fixed = TRUE), function(y) ifelse(length(y) == 2, nchar(y[2]), 0))), na.rm = TRUE) max(min(max_places, maximum, na.rm = TRUE), minimum, na.rm = TRUE) } # format_percentage() function format_percentage <- function(x, digits = NULL, ...) { if (is.null(digits)) { digits <- getdecimalplaces(x) } if (is.null(digits) || is.na(digits) || !is.numeric(digits)) { digits <- 2 } # round right: percentage(0.4455) and format(as.percentage(0.4455), 1) should return "44.6%", not "44.5%" x_formatted <- format(round2(as.double(x), digits = digits + 2) * 100, scientific = FALSE, digits = max(1, digits), nsmall = digits, ...) x_formatted <- paste0(x_formatted, "%") x_formatted[!grepl(pattern = "^[0-9.,e-]+$", x = x)] <- NA_character_ x_formatted } # the actual working part x <- as.double(x) if (is.null(digits)) { # max one digit if undefined digits <- getdecimalplaces(x, minimum = 0, maximum = 1) } format_percentage(structure(.Data = as.double(x), class = c("percentage", "numeric")), digits = digits, ...) } time_start_tracking <- function() { pkg_env$time_start <- round(as.double(Sys.time()) * 1000) } time_track <- function(name = NULL) { paste("(until now:", trimws(round(as.double(Sys.time()) * 1000) - pkg_env$time_start), "ms)") } # prevent dependency on package 'backports' ---- # these functions were not available in previous versions of R (last checked: R 4.1.0) # see here for the full list: https://github.com/r-lib/backports strrep <- function(x, times) { x <- as.character(x) if (length(x) == 0L) return(x) unlist(.mapply(function(x, times) { if (is.na(x) || is.na(times)) return(NA_character_) if (times <= 0L) return("") paste0(replicate(times, x), collapse = "") }, list(x = x, times = times), MoreArgs = list()), use.names = FALSE) } trimws <- function(x, which = c("both", "left", "right"), whitespace = "[ \t\r\n]") { which <- match.arg(which) mysub <- function(re, x) sub(re, "", x, perl = TRUE) switch(which, left = mysub(paste0("^", whitespace, "+"), x), right = mysub(paste0(whitespace, "+$"), x), both = mysub(paste0(whitespace, "+$"), mysub(paste0("^", whitespace, "+"), x))) } isFALSE <- function(x) { is.logical(x) && length(x) == 1L && !is.na(x) && !x } deparse1 <- function(expr, collapse = " ", width.cutoff = 500L, ...) { paste(deparse(expr, width.cutoff, ...), collapse = collapse) } file.size <- function(...) { file.info(...)$size } file.mtime <- function(...) { file.info(...)$mtime } str2lang <- function(s) { stopifnot(length(s) == 1L) ex <- parse(text = s, keep.source = FALSE) stopifnot(length(ex) == 1L) ex[[1L]] } isNamespaceLoaded <- function(pkg) { pkg %in% loadedNamespaces() } lengths <- function(x, use.names = TRUE) { vapply(x, length, FUN.VALUE = NA_integer_, USE.NAMES = use.names) } if (getRversion() < "3.1") { # R-3.0 does not contain these functions, set them here to prevent installation failure # (required for extension of the class) cospi <- function(...) 1 sinpi <- function(...) 1 tanpi <- function(...) 1 } dir.exists <- function (paths) { x = base::file.info(paths)$isdir !is.na(x) & x }