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(v1.7.1.9005) ab class selectors for R-3.0 and R-3.1
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@ -170,65 +170,73 @@ search_type_in_df <- function(x, type, info = TRUE) {
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# remove attributes from other packages
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x <- as.data.frame(x, stringsAsFactors = FALSE)
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colnames(x) <- trimws(colnames(x))
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colnames_formatted <- tolower(generalise_antibiotic_name(colnames(x)))
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# -- mo
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if (type == "mo") {
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if (any(vapply(FUN.VALUE = logical(1), x, is.mo))) {
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found <- sort(colnames(x)[vapply(FUN.VALUE = logical(1), x, is.mo)])[1]
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} else if ("mo" %in% colnames(x) &
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suppressWarnings(
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all(x$mo %in% c(NA, microorganisms$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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found <- "mo"
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} else if (any(colnames(x) %like% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$")) {
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found <- sort(colnames(x)[colnames(x) %like% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$"])[1]
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} else if (any(colnames(x) %like% "^(microorganism|organism|bacteria|ba[ck]terie)")) {
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found <- sort(colnames(x)[colnames(x) %like% "^(microorganism|organism|bacteria|ba[ck]terie)"])[1]
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} else if (any(colnames(x) %like% "species")) {
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found <- sort(colnames(x)[colnames(x) %like% "species"])[1]
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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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} else if (any(colnames_formatted %like_case% "^(microorganism|organism|bacteria|ba[ck]terie)")) {
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found <- sort(colnames(x)[colnames_formatted %like_case% "^(microorganism|organism|bacteria|ba[ck]terie)"])
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} else if (any(colnames_formatted %like_case% "species")) {
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found <- sort(colnames(x)[colnames_formatted %like_case% "species"])
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}
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}
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# -- key antibiotics
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if (type %in% c("keyantibiotics", "keyantimicrobials")) {
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if (any(colnames(x) %like% "^key.*(ab|antibiotics|antimicrobials)")) {
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found <- sort(colnames(x)[colnames(x) %like% "^key.*(ab|antibiotics|antimicrobials)"])[1]
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if (any(colnames_formatted %like_case% "^key.*(ab|antibiotics|antimicrobials)")) {
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found <- sort(colnames(x)[colnames_formatted %like_case% "^key.*(ab|antibiotics|antimicrobials)"])
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}
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}
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# -- date
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if (type == "date") {
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if (any(colnames(x) %like% "^(specimen date|specimen_date|spec_date)")) {
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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(x) %like% "^(specimen date|specimen_date|spec_date)"])[1]
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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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stop(font_red(paste0("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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call. = FALSE)
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}
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} else if (any(vapply(FUN.VALUE = logical(1), x, function(x) inherits(x, c("Date", "POSIXct"))))) {
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found <- sort(colnames(x)[vapply(FUN.VALUE = logical(1), x, function(x) inherits(x, c("Date", "POSIXct")))])[1]
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# take first <Date> column
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found <- colnames(x)[vapply(FUN.VALUE = logical(1), x, function(x) inherits(x, c("Date", "POSIXct")))]
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}
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}
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# -- patient id
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if (type == "patient_id") {
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if (any(colnames(x) %like% "^(identification |patient|patid)")) {
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found <- sort(colnames(x)[colnames(x) %like% "^(identification |patient|patid)"])[1]
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crit1 <- colnames_formatted %like_case% "^(patient|patid)"
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if (any(crit1)) {
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found <- colnames(x)[crit1]
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} else {
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crit2 <- colnames_formatted %like_case% "(identification |patient|pat.*id)"
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if (any(crit2)) {
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found <- colnames(x)[crit2]
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}
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}
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}
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# -- specimen
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if (type == "specimen") {
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if (any(colnames(x) %like% "(specimen type|spec_type)")) {
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found <- sort(colnames(x)[colnames(x) %like% "(specimen type|spec_type)"])[1]
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} else if (any(colnames(x) %like% "^(specimen)")) {
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found <- sort(colnames(x)[colnames(x) %like% "^(specimen)"])[1]
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if (any(colnames_formatted %like_case% "(specimen type|spec_type)")) {
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found <- sort(colnames(x)[colnames_formatted %like_case% "(specimen type|spec_type)"])
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} else if (any(colnames_formatted %like_case% "^(specimen)")) {
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found <- sort(colnames(x)[colnames_formatted %like_case% "^(specimen)"])
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}
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}
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# -- UTI (urinary tract infection)
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if (type == "uti") {
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if (any(colnames(x) == "uti")) {
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found <- colnames(x)[colnames(x) == "uti"][1]
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} else if (any(colnames(x) %like% "(urine|urinary)")) {
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found <- sort(colnames(x)[colnames(x) %like% "(urine|urinary)"])[1]
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if (any(colnames_formatted == "uti")) {
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found <- colnames(x)[colnames_formatted == "uti"]
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} else if (any(colnames_formatted %like_case% "(urine|urinary)")) {
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found <- sort(colnames(x)[colnames_formatted %like_case% "(urine|urinary)"])
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}
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if (!is.null(found)) {
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# this column should contain logicals
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@ -241,10 +249,12 @@ search_type_in_df <- function(x, type, info = TRUE) {
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}
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}
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found <- found[1]
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if (!is.null(found) & info == TRUE) {
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if (message_not_thrown_before(fn = paste0("search_", 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", "specimen")) {
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if (type %in% c("keyantibiotics", "keyantimicrobials", "specimen")) {
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msg <- paste(msg, "Use", font_bold(paste0("col_", type), "= FALSE"), "to prevent this.")
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}
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message_(msg)
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@ -696,7 +706,7 @@ meet_criteria <- function(object,
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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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" (i.e., not be infinite)",
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" (i.e. not be infinite)",
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call = call_depth)
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}
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if (!is.null(contains_column_class)) {
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@ -713,13 +723,7 @@ meet_criteria <- function(object,
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return(invisible())
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}
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get_current_data <- function(arg_name, call, reuse_from_1st_call = TRUE) {
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# check if retrieved before, then get it from package environment to improve speed
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if (reuse_from_1st_call == TRUE &&
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identical(unique_call_id(entire_session = FALSE), pkg_env$get_current_data.call)) {
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return(pkg_env$get_current_data.out)
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}
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get_current_data <- function(arg_name, call) {
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# try dplyr::cur_data_all() first to support dplyr groups
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# only useful for e.g. dplyr::filter(), dplyr::mutate() and dplyr::summarise()
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# not useful (throws error) with e.g. dplyr::select() - but that will be caught later in this function
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@ -727,73 +731,32 @@ get_current_data <- function(arg_name, call, reuse_from_1st_call = TRUE) {
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if (!is.null(cur_data_all)) {
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out <- tryCatch(cur_data_all(), error = function(e) NULL)
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if (is.data.frame(out)) {
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out <- structure(out, type = "dplyr_cur_data_all")
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pkg_env$get_current_data.call <- unique_call_id(entire_session = FALSE)
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pkg_env$get_current_data.out <- out
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return(out)
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}
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}
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if (getRversion() < "3.2") {
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# R-3.0 and R-3.1 do not have an `x` element in the call stack, rendering this function useless
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# R-3.2 was released in April 2015
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if (is.na(arg_name)) {
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# such as for carbapenems() etc.
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warning_("this function requires R version 3.2 or later - you have ", R.version.string, call = call)
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return(data.frame())
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} else {
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# mimic a default R error, e.g. for example_isolates[which(mo_name() %like% "^ent"), ]
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stop_("argument `", arg_name, "` is missing with no default", call = call)
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return(structure(out, type = "dplyr_cur_data_all"))
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}
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}
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# try a (base R) method, by going over the complete system call stack with sys.frames()
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not_set <- TRUE
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source <- "base_R"
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frms <- lapply(sys.frames(), function(el) {
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if (not_set == TRUE && ".Generic" %in% names(el)) {
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if (tryCatch(".data" %in% names(el) && is.data.frame(el$`.data`), error = function(e) FALSE)) {
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# - - - -
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# dplyr
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# - - - -
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# an element `.data` will be in the system call stack when using dplyr::select()
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# [but not when using dplyr::filter(), dplyr::mutate() or dplyr::summarise()]
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not_set <<- FALSE
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source <<- "dplyr_selector"
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el$`.data`
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} else if (tryCatch(any(c("x", "xx") %in% names(el)), error = function(e) FALSE)) {
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# - - - -
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# base R
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# - - - -
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# an element `x` will be in this environment for only cols, e.g. `example_isolates[, carbapenems()]`
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# an element `xx` will be in this environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
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if (tryCatch(is.data.frame(el$xx), error = function(e) FALSE)) {
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not_set <<- FALSE
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el$xx
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} else if (tryCatch(is.data.frame(el$x))) {
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not_set <<- FALSE
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el$x
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} else {
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NULL
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}
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} else {
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NULL
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# try a manual (base R) method, by going over all underlying environments with sys.frames()
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for (el in sys.frames()) {
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if (!is.null(el$`.Generic`)) {
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# don't check `".Generic" %in% names(el)`, because in R < 3.2, `names(el)` is always NULL
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if (!is.null(el$`.data`) && is.data.frame(el$`.data`)) {
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# an element `.data` will be in the environment when using `dplyr::select()`
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# (but not when using `dplyr::filter()`, `dplyr::mutate()` or `dplyr::summarise()`)
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return(structure(el$`.data`, type = "dplyr_selector"))
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} else if (!is.null(el$xx) && is.data.frame(el$xx)) {
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# an element `xx` will be in the environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
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return(structure(el$xx, type = "base_R"))
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} else if (!is.null(el$x) && is.data.frame(el$x)) {
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# an element `x` will be in the environment for only cols, e.g. `example_isolates[, carbapenems()]`
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return(structure(el$x, type = "base_R"))
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}
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} else {
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NULL
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}
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})
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# lookup the matched frame and return its value: a data.frame
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vars_df <- tryCatch(frms[[which(!vapply(FUN.VALUE = logical(1), frms, is.null))]], error = function(e) NULL)
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if (is.data.frame(vars_df)) {
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out <- structure(vars_df, type = source)
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pkg_env$get_current_data.call <- unique_call_id(entire_session = FALSE)
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pkg_env$get_current_data.out <- out
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return(out)
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}
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# nothing worked, so:
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# no data.frame found, so an error must be returned:
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if (is.na(arg_name)) {
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if (isTRUE(is.numeric(call))) {
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fn <- as.character(sys.call(call + 1)[1])
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@ -982,8 +945,8 @@ font_grey_bg <- function(..., collapse = " ") {
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# similar to HTML #444444
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try_colour(..., before = "\033[48;5;238m", after = "\033[49m", collapse = collapse)
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} else {
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# similar to HTML #eeeeee
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try_colour(..., before = "\033[48;5;254m", after = "\033[49m", collapse = collapse)
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# similar to HTML #f0f0f0
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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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