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New mo algorithm, prepare for 2.0
This commit is contained in:
Dr. Matthijs Berends
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GitHub
GitHub
parent
63fe160322
commit
cd2acc4a29
@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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@ -81,7 +85,7 @@ where <- function(fn) {
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quick_case_when <- function(...) {
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fs <- list(...)
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lapply(fs, function(x) {
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if (class(x) != "formula") {
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if (!inherits(x, "formula")) {
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stop("`case_when()` requires formula inputs.")
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}
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})
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@ -208,63 +212,6 @@ addin_insert_like <- function() {
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}
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}
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check_dataset_integrity <- function() {
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# check if user overwrote our data sets in their global environment
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data_in_pkg <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item", drop = TRUE]
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data_in_globalenv <- ls(envir = globalenv())
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overwritten <- data_in_pkg[data_in_pkg %in% data_in_globalenv]
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# exception for example_isolates
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overwritten <- overwritten[overwritten %unlike% "example_isolates"]
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if (length(overwritten) > 0) {
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if (length(overwritten) > 1) {
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plural <- c("s are", "", "s")
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} else {
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plural <- c(" is", "s", "")
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}
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if (message_not_thrown_before("check_dataset_integrity", overwritten)) {
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warning_(
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"The following data set", plural[1],
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" overwritten by your global environment and prevent", plural[2],
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" the AMR package from working correctly: ",
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vector_and(overwritten, quotes = "'"),
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".\nPlease rename your object", plural[3], "."
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)
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}
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}
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# check if other packages did not overwrite our data sets
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valid_microorganisms <- TRUE
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valid_antibiotics <- TRUE
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tryCatch(
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{
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valid_microorganisms <- all(c(
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"mo", "fullname", "kingdom", "phylum",
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"class", "order", "family", "genus",
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"species", "subspecies", "rank",
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"species_id", "source", "ref", "prevalence"
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) %in% colnames(microorganisms),
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na.rm = TRUE
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)
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valid_antibiotics <- all(c(
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"ab", "atc", "cid", "name", "group",
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"atc_group1", "atc_group2", "abbreviations",
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"synonyms", "oral_ddd", "oral_units",
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"iv_ddd", "iv_units", "loinc"
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) %in% colnames(antibiotics),
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na.rm = TRUE
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)
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},
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error = function(e) {
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# package not yet loaded
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require("AMR")
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}
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)
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stop_if(
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!valid_microorganisms | !valid_antibiotics,
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"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."
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)
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invisible(TRUE)
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}
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search_type_in_df <- function(x, type, info = TRUE) {
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meet_criteria(x, allow_class = "data.frame")
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meet_criteria(type, allow_class = "character", has_length = 1)
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@ -281,8 +228,8 @@ search_type_in_df <- function(x, type, info = TRUE) {
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if (any(vapply(FUN.VALUE = logical(1), x, is.mo))) {
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# take first <mo> column
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found <- colnames(x)[vapply(FUN.VALUE = logical(1), x, is.mo)]
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} else if ("mo" %in% colnames_formatted &
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suppressWarnings(all(x$mo %in% c(NA, microorganisms$mo)))) {
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} else if ("mo" %in% colnames_formatted &&
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suppressWarnings(all(x$mo %in% c(NA, AMR::microorganisms$mo)))) {
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found <- "mo"
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} else if (any(colnames_formatted %like_case% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$")) {
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found <- sort(colnames(x)[colnames_formatted %like_case% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$"])
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@ -303,7 +250,7 @@ search_type_in_df <- function(x, type, info = TRUE) {
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if (any(colnames_formatted %like_case% "^(specimen date|specimen_date|spec_date)")) {
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# WHONET support
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found <- sort(colnames(x)[colnames_formatted %like_case% "^(specimen date|specimen_date|spec_date)"])
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if (!any(class(pm_pull(x, found)) %in% c("Date", "POSIXct"))) {
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if (!inherits(pm_pull(x, found), c("Date", "POSIXct"))) {
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stop(font_red(paste0(
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"Found column '", font_bold(found), "' to be used as input for `col_", type,
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"`, but this column contains no valid dates. Transform its values to valid dates first."
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@ -357,7 +304,7 @@ search_type_in_df <- function(x, type, info = TRUE) {
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found <- found[1]
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if (!is.null(found) & info == TRUE) {
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if (!is.null(found) && info == TRUE) {
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if (message_not_thrown_before("search_in_type", type)) {
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msg <- paste0("Using column '", font_bold(found), "' as input for `col_", type, "`.")
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if (type %in% c("keyantibiotics", "keyantimicrobials", "specimen")) {
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@ -372,7 +319,7 @@ search_type_in_df <- function(x, type, info = TRUE) {
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is_valid_regex <- function(x) {
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regex_at_all <- tryCatch(vapply(
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FUN.VALUE = logical(1),
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X = strsplit(x, ""),
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X = strsplit(x, "", fixed = TRUE),
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FUN = function(y) {
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any(y %in% c(
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"$", "(", ")", "*", "+", "-",
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@ -390,9 +337,7 @@ is_valid_regex <- function(x) {
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FUN.VALUE = logical(1),
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X = x,
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FUN = function(y) {
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!"try-error" %in% class(try(grepl(y, "", perl = TRUE),
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silent = TRUE
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))
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!inherits(try(grepl(y, "", perl = TRUE), silent = TRUE), "try-error")
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},
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USE.NAMES = FALSE
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)
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@ -464,14 +409,14 @@ word_wrap <- function(...,
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msg <- paste0(c(...), collapse = "")
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if (isTRUE(as_note)) {
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msg <- paste0(pkg_env$info_icon, " ", gsub("^note:? ?", "", msg, ignore.case = TRUE))
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msg <- paste0(AMR_env$info_icon, " ", gsub("^note:? ?", "", msg, ignore.case = TRUE))
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}
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if (msg %like% "\n") {
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# run word_wraps() over every line here, bind them and return again
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return(paste0(vapply(
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FUN.VALUE = character(1),
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trimws(unlist(strsplit(msg, "\n")), which = "right"),
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trimws(unlist(strsplit(msg, "\n", fixed = TRUE)), which = "right"),
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word_wrap,
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add_fn = add_fn,
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as_note = FALSE,
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@ -497,12 +442,12 @@ word_wrap <- function(...,
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msg_stripped_wrapped <- paste0(unlist(strsplit(msg_stripped_wrapped, "(\n|\\*\\|\\*)")),
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collapse = "\n"
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)
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msg_stripped_spaces <- which(unlist(strsplit(msg_stripped, "")) == " ")
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msg_stripped_wrapped_spaces <- which(unlist(strsplit(msg_stripped_wrapped, "")) != "\n")
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msg_stripped_spaces <- which(unlist(strsplit(msg_stripped, "", fixed = TRUE)) == " ")
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msg_stripped_wrapped_spaces <- which(unlist(strsplit(msg_stripped_wrapped, "", fixed = TRUE)) != "\n")
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# so these are the indices of spaces that need to be replaced
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replace_spaces <- which(!msg_stripped_spaces %in% msg_stripped_wrapped_spaces)
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# put it together
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msg <- unlist(strsplit(msg, " "))
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msg <- unlist(strsplit(msg, " ", fixed = TRUE))
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msg[replace_spaces] <- paste0(msg[replace_spaces], "\n")
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# add space around operators again
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msg <- gsub(paste0(ops, ops), "\\1 \\2", msg, perl = TRUE)
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@ -534,6 +479,8 @@ word_wrap <- function(...,
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# clean introduced whitespace between fullstops
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msg <- gsub("[.] +[.]", "..", msg)
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# remove extra space that was introduced (case: "Smith et al., 2022")
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msg <- gsub(". ,", ".,", msg, fixed = TRUE)
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msg
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}
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@ -608,17 +555,14 @@ stop_ifnot <- function(expr, ..., call = TRUE) {
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}
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"%or%" <- function(x, y) {
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if (is.null(x) | is.null(y)) {
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if (is.null(x) || is.null(y)) {
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if (is.null(x)) {
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return(y)
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} else {
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return(x)
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}
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}
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ifelse(!is.na(x),
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x,
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ifelse(!is.na(y), y, NA)
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)
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ifelse(is.na(x), y, x)
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}
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return_after_integrity_check <- function(value, type, check_vector) {
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@ -654,9 +598,29 @@ dataset_UTF8_to_ASCII <- function(df) {
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import_fn("as_tibble", "tibble")(df)
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}
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documentation_date <- function(d) {
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paste0(trimws(format(d, "%e")), " ", month.name[as.integer(format(d, "%m"))], ", ", format(d, "%Y"))
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}
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format_included_data_number <- function(data) {
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if (is.data.frame(data)) {
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n <- nrow(data)
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} else {
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n <- length(unique(data))
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}
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if (n > 10000) {
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rounder <- -3 # round on thousands
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} else if (n > 1000) {
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rounder <- -2 # round on hundreds
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} else {
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rounder <- -1 # round on tens
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}
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paste0("~", format(round(n, rounder), decimal.mark = ".", big.mark = ","))
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}
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# for eucast_rules() and mdro(), creates markdown output with URLs and names
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create_eucast_ab_documentation <- function() {
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x <- trimws(unique(toupper(unlist(strsplit(EUCAST_RULES_DF$then_change_these_antibiotics, ",")))))
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x <- trimws(unique(toupper(unlist(strsplit(EUCAST_RULES_DF$then_change_these_antibiotics, ",", fixed = TRUE)))))
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ab <- character()
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for (val in x) {
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if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
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@ -731,7 +695,8 @@ format_class <- function(class, plural = FALSE) {
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class[class %in% c("number", "whole number")] <- "(whole) number"
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}
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class[class == "character"] <- "text string"
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class[class %in% c("Date", "POSIXt")] <- "date"
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class[class == "Date"] <- "date"
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class[class %in% c("POSIXt", "POSIXct", "POSIXlt")] <- "date/time"
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class[class != class.bak] <- paste0(
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ifelse(plural, "", "a "),
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class[class != class.bak],
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@ -777,14 +742,14 @@ meet_criteria <- function(object,
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# if object is missing, or another error:
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tryCatch(invisible(object),
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error = function(e) pkg_env$meet_criteria_error_txt <- e$message
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error = function(e) AMR_env$meet_criteria_error_txt <- e$message
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)
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if (!is.null(pkg_env$meet_criteria_error_txt)) {
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error_txt <- pkg_env$meet_criteria_error_txt
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pkg_env$meet_criteria_error_txt <- NULL
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if (!is.null(AMR_env$meet_criteria_error_txt)) {
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error_txt <- AMR_env$meet_criteria_error_txt
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AMR_env$meet_criteria_error_txt <- NULL
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stop(error_txt, call. = FALSE) # don't use stop_() here, our pkg may not be loaded yet
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}
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pkg_env$meet_criteria_error_txt <- NULL
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AMR_env$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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@ -999,8 +964,8 @@ unique_call_id <- function(entire_session = FALSE, match_fn = NULL) {
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# combination of environment ID (such as "0x7fed4ee8c848")
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# and relevant system call (where 'match_fn' is being called in)
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calls <- sys.calls()
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if (!identical(Sys.getenv("R_RUN_TINYTEST"), "true") &&
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!any(as.character(calls[[1]]) %like_case% "run_test_dir|run_test_file|test_all|tinytest|test_package|testthat")) {
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in_test <- any(as.character(calls[[1]]) %like_case% "run_test_dir|run_test_file|test_all|tinytest|test_package|testthat", na.rm = TRUE)
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if (!isTRUE(in_test)) {
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for (i in seq_len(length(calls))) {
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call_clean <- gsub("[^a-zA-Z0-9_().-]", "", as.character(calls[[i]]), perl = TRUE)
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if (any(call_clean %like% paste0(match_fn, "\\("), na.rm = TRUE)) {
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@ -1012,8 +977,8 @@ unique_call_id <- function(entire_session = FALSE, match_fn = NULL) {
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}
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}
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c(
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envir = paste0(sample(c(c(0:9), letters[1:6]), size = 32, replace = TRUE), collapse = ""),
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call = paste0(sample(c(c(0:9), letters[1:6]), size = 32, replace = TRUE), collapse = "")
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envir = paste0(sample(c(0:9, letters[1:6]), size = 32, replace = TRUE), collapse = ""),
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call = paste0(sample(c(0:9, letters[1:6]), size = 32, replace = TRUE), collapse = "")
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)
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}
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@ -1024,10 +989,10 @@ unique_call_id <- function(entire_session = FALSE, match_fn = NULL) {
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message_not_thrown_before <- function(fn, ..., entire_session = FALSE) {
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# this is to prevent that messages/notes will be printed for every dplyr group or more than once per session
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# e.g. this would show a msg 4 times: example_isolates %>% group_by(ward) %>% filter(mo_is_gram_negative())
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salt <- gsub("[^a-zA-Z0-9|_-]", "?", paste(c(...), sep = "|", collapse = "|"), perl = TRUE)
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not_thrown_before <- is.null(pkg_env[[paste0("thrown_msg.", fn, ".", salt)]]) ||
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salt <- gsub("[^a-zA-Z0-9|_-]", "?", substr(paste(c(...), sep = "|", collapse = "|"), 1, 512), perl = TRUE)
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not_thrown_before <- is.null(AMR_env[[paste0("thrown_msg.", fn, ".", salt)]]) ||
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!identical(
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pkg_env[[paste0("thrown_msg.", fn, ".", salt)]],
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AMR_env[[paste0("thrown_msg.", fn, ".", salt)]],
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unique_call_id(
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entire_session = entire_session,
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match_fn = fn
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@ -1038,7 +1003,7 @@ message_not_thrown_before <- function(fn, ..., entire_session = FALSE) {
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assign(
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x = paste0("thrown_msg.", fn, ".", salt),
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value = unique_call_id(entire_session = entire_session, match_fn = fn),
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envir = pkg_env
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envir = AMR_env
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)
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}
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not_thrown_before
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@ -1100,7 +1065,10 @@ has_colour <- function() {
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# set colours if console has_colour()
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try_colour <- function(..., before, after, collapse = " ") {
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txt <- paste0(unlist(list(...)), collapse = collapse)
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if (length(c(...)) == 0) {
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return(character(0))
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}
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txt <- paste0(c(...), collapse = collapse)
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if (isTRUE(has_colour())) {
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if (is.null(collapse)) {
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paste0(before, txt, after, collapse = NULL)
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@ -1166,26 +1134,26 @@ font_grey_bg <- function(..., collapse = " ") {
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try_colour(..., before = "\033[48;5;255m", after = "\033[49m", collapse = collapse)
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}
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}
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font_green_bg <- function(..., collapse = " ") {
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try_colour(..., before = "\033[42m", after = "\033[49m", collapse = collapse)
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}
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font_rsi_R_bg <- function(..., collapse = " ") {
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# ED553B
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try_colour(..., before = "\033[48;5;203m", after = "\033[49m", collapse = collapse)
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}
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font_rsi_S_bg <- function(..., collapse = " ") {
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# 3CAEA3
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try_colour(..., before = "\033[48;5;79m", after = "\033[49m", collapse = collapse)
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}
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font_rsi_I_bg <- function(..., collapse = " ") {
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# F6D55C
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try_colour(..., before = "\033[48;5;222m", after = "\033[49m", collapse = collapse)
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}
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font_red_bg <- function(..., collapse = " ") {
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try_colour(..., before = "\033[41m", after = "\033[49m", collapse = collapse)
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# this is #ed553b (picked to be colourblind-safe with other RSI colours)
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try_colour(font_black(..., collapse = collapse), before = "\033[48;5;203m", after = "\033[49m", collapse = collapse)
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}
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font_orange_bg <- function(..., collapse = " ") {
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# this is #f6d55c (picked to be colourblind-safe with other RSI colours)
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try_colour(font_black(..., collapse = collapse), before = "\033[48;5;222m", after = "\033[49m", collapse = collapse)
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}
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font_yellow_bg <- function(..., collapse = " ") {
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try_colour(..., before = "\033[43m", after = "\033[49m", collapse = collapse)
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try_colour(font_black(..., collapse = collapse), before = "\033[48;5;228m", after = "\033[49m", collapse = collapse)
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}
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font_green_bg <- function(..., collapse = " ") {
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# this is #3caea3 (picked to be colourblind-safe with other RSI colours)
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try_colour(font_black(..., collapse = collapse), before = "\033[48;5;79m", after = "\033[49m", collapse = collapse)
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}
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font_purple_bg <- function(..., collapse = " ") {
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||||
try_colour(font_black(..., collapse = collapse), before = "\033[48;5;89m", after = "\033[49m", collapse = collapse)
|
||||
}
|
||||
font_rose_bg <- function(..., collapse = " ") {
|
||||
try_colour(font_black(..., collapse = collapse), before = "\033[48;5;217m", after = "\033[49m", collapse = collapse)
|
||||
}
|
||||
font_na <- function(..., collapse = " ") {
|
||||
font_red(..., collapse = collapse)
|
||||
@ -1281,61 +1249,21 @@ as_original_data_class <- function(df, old_class = NULL) {
|
||||
fn <- import_fn("as_tsibble", "tsibble")
|
||||
} else if ("data.table" %in% old_class && pkg_is_available("data.table", also_load = FALSE)) {
|
||||
fn <- import_fn("as.data.table", "data.table")
|
||||
} else if ("tabyl" %in% old_class && pkg_is_available("janitor", also_load = FALSE)) {
|
||||
fn <- import_fn("as_tabyl", "janitor")
|
||||
} else {
|
||||
fn <- base::as.data.frame
|
||||
}
|
||||
fn(df)
|
||||
}
|
||||
|
||||
# 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) {
|
||||
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,
|
||||
@ -1426,73 +1354,167 @@ percentage <- function(x, digits = NULL, ...) {
|
||||
}
|
||||
|
||||
time_start_tracking <- function() {
|
||||
pkg_env$time_start <- round(as.double(Sys.time()) * 1000)
|
||||
AMR_env$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$time_start), "ms)")
|
||||
paste("(until now:", trimws(round(as.double(Sys.time()) * 1000) - AMR_env$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)
|
||||
trimws2 <- function(..., whitespace = "[\u0009\u000A\u000B\u000C\u000D\u0020\u0085\u00A0\u1680\u180E\u2000\u2001\u2002\u2003\u2004\u2005\u2006\u2007\u2008\u2009\u200A\u200B\u200C\u200D\u2028\u2029\u202F\u205F\u2060\u3000\uFEFF]") {
|
||||
# this is even faster than trimws() itself which sets " \t\n\r".
|
||||
trimws(..., whitespace = whitespace)
|
||||
}
|
||||
|
||||
|
||||
# Faster data.table implementations ----
|
||||
|
||||
match <- function(x, table, ...) {
|
||||
if (isTRUE(AMR_env$has_data.table) && is.character(x) && is.character(table)) {
|
||||
# data.table::chmatch() is 35% faster than base::match() for character
|
||||
getExportedValue(name = "chmatch", ns = asNamespace("data.table"))(x, table, ...)
|
||||
} else {
|
||||
base::match(x, table, ...)
|
||||
}
|
||||
unlist(.mapply(function(x, times) {
|
||||
if (is.na(x) || is.na(times)) {
|
||||
return(NA_character_)
|
||||
}
|
||||
if (times <= 0L) {
|
||||
return("")
|
||||
}
|
||||
paste0(replicate(times, x), collapse = "")
|
||||
}, list(x = x, times = times), MoreArgs = list()), use.names = FALSE)
|
||||
}
|
||||
trimws <- function(x, which = c("both", "left", "right"), whitespace = "[ \t\r\n]") {
|
||||
which <- match.arg(which)
|
||||
mysub <- function(re, x) sub(re, "", x, perl = TRUE)
|
||||
switch(which,
|
||||
left = mysub(paste0("^", whitespace, "+"), x),
|
||||
right = mysub(paste0(whitespace, "+$"), 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(...)$mtime
|
||||
}
|
||||
str2lang <- function(s) {
|
||||
stopifnot(length(s) == 1L)
|
||||
ex <- parse(text = s, keep.source = FALSE)
|
||||
stopifnot(length(ex) == 1L)
|
||||
ex[[1L]]
|
||||
}
|
||||
isNamespaceLoaded <- function(pkg) {
|
||||
pkg %in% loadedNamespaces()
|
||||
}
|
||||
lengths <- function(x, use.names = TRUE) {
|
||||
vapply(x, length, FUN.VALUE = NA_integer_, USE.NAMES = use.names)
|
||||
`%in%` <- function(x, table) {
|
||||
if (isTRUE(AMR_env$has_data.table) && is.character(x) && is.character(table)) {
|
||||
# data.table::`%chin%`() is 20-50% faster than base::`%in%`() for character
|
||||
getExportedValue(name = "%chin%", ns = asNamespace("data.table"))(x, table)
|
||||
} else {
|
||||
base::`%in%`(x, table)
|
||||
}
|
||||
}
|
||||
|
||||
if (getRversion() < "3.1") {
|
||||
# nolint start
|
||||
|
||||
# Register S3 methods ----
|
||||
# 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()
|
||||
}
|
||||
|
||||
|
||||
# Support old R versions ----
|
||||
# these functions were not available in previous versions of R
|
||||
# see here for the full list: https://github.com/r-lib/backports
|
||||
if (getRversion() < "3.1.0") {
|
||||
# R-3.0 does not contain these functions, set them here to prevent installation failure
|
||||
# (required for extension of the <mic> class)
|
||||
cospi <- function(...) 1
|
||||
sinpi <- function(...) 1
|
||||
tanpi <- function(...) 1
|
||||
}
|
||||
dir.exists <- function(paths) {
|
||||
x <- base::file.info(paths)$isdir
|
||||
!is.na(x) & x
|
||||
|
||||
if (getRversion() < "3.2.0") {
|
||||
anyNA <- function(x, recursive = FALSE) {
|
||||
if (isTRUE(recursive) && (is.list(x) || is.pairlist(x))) {
|
||||
return(any(rapply(x, anyNA, how = "unlist", recursive = FALSE)))
|
||||
}
|
||||
any(is.na(x))
|
||||
}
|
||||
dir.exists <- function(paths) {
|
||||
x <- base::file.info(paths)$isdir
|
||||
!is.na(x) & x
|
||||
}
|
||||
file.size <- function(...) {
|
||||
file.info(...)$size
|
||||
}
|
||||
file.mtime <- function(...) {
|
||||
file.info(...)$mtime
|
||||
}
|
||||
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() < "3.3.0") {
|
||||
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)
|
||||
}
|
||||
}
|
||||
|
||||
if (getRversion() < "3.5.0") {
|
||||
isFALSE <- function(x) {
|
||||
is.logical(x) && length(x) == 1L && !is.na(x) && !x
|
||||
}
|
||||
}
|
||||
|
||||
if (getRversion() < "3.6.0") {
|
||||
str2lang <- function(s) {
|
||||
stopifnot(length(s) == 1L)
|
||||
ex <- parse(text = s, keep.source = FALSE)
|
||||
stopifnot(length(ex) == 1L)
|
||||
ex[[1L]]
|
||||
}
|
||||
# trims() was introduced in 3.3.0, but its argument `whitespace` only in 3.6.0
|
||||
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))
|
||||
)
|
||||
}
|
||||
}
|
||||
|
||||
if (getRversion() < "4.0.0") {
|
||||
deparse1 <- function(expr, collapse = " ", width.cutoff = 500L, ...) {
|
||||
paste(deparse(expr, width.cutoff, ...), collapse = collapse)
|
||||
}
|
||||
}
|
||||
|
||||
# nolint end
|
||||
|
||||
Reference in New Issue
Block a user