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freq - decimals
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77
R/freq.R
77
R/freq.R
@ -32,6 +32,7 @@
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#' @param title text to show above frequency table, at default to tries to coerce from the variables passed to \code{x}
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#' @param na a character string to should be used to show empty (\code{NA}) values (only useful when \code{na.rm = FALSE})
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#' @param sep a character string to separate the terms when selecting multiple columns
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#' @inheritParams base::format
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#' @param f a frequency table
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#' @param n number of top \emph{n} items to return, use -n for the bottom \emph{n} items. It will include more than \code{n} rows if there are ties.
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#' @details Frequency tables (or frequency distributions) are summaries of the distribution of values in a sample. With the `freq` function, you can create univariate frequency tables. Multiple variables will be pasted into one variable, so it forces a univariate distribution. This package also has a vignette available to explain the use of this function further, run \code{browseVignettes("AMR")} to read it.
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@ -182,7 +183,9 @@ frequency_tbl <- function(x,
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header = !markdown,
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title = NULL,
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na = "<NA>",
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sep = " ") {
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sep = " ",
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decimal.mark = getOption("OutDec"),
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big.mark = ifelse(decimal.mark != ",", ",", ".")) {
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mult.columns <- 0
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x.group = character(0)
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@ -314,8 +317,8 @@ frequency_tbl <- function(x,
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}
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if (NROW(x) > 0) {
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na_txt <- paste0(NAs %>% length() %>% format(), ' = ',
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(NAs %>% length() / (NAs %>% length() + x %>% length())) %>% percent(force_zero = TRUE, round = digits) %>%
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na_txt <- paste0(NAs %>% length() %>% format(decimal.mark = decimal.mark, big.mark = big.mark), ' = ',
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(NAs %>% length() / (NAs %>% length() + x %>% length())) %>% percent(force_zero = TRUE, round = digits, decimal.mark = decimal.mark) %>%
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sub('NaN', '0', ., fixed = TRUE))
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if (!na_txt %like% "^0 =") {
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na_txt <- red(na_txt)
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@ -327,14 +330,21 @@ frequency_tbl <- function(x,
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na_txt <- ""
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}
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header_txt <- header_txt %>% paste0(markdown_line, '\nLength: ', (NAs %>% length() + x %>% length()) %>% format(),
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header_txt <- header_txt %>% paste0(markdown_line, '\nLength: ', (NAs %>% length() + x %>% length()) %>% format(decimal.mark = decimal.mark, big.mark = big.mark),
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' ', na_txt)
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header_txt <- header_txt %>% paste0(markdown_line, '\nUnique: ', x %>% n_distinct() %>% format())
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header_txt <- header_txt %>% paste0(markdown_line, '\nUnique: ', x %>% n_distinct() %>% format(decimal.mark = decimal.mark, big.mark = big.mark))
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if (NROW(x) > 0 & any(class(x) == "character")) {
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header_txt <- header_txt %>% paste0('\n')
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header_txt <- header_txt %>% paste0(markdown_line, '\nShortest: ', x %>% base::nchar() %>% base::min(na.rm = TRUE))
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header_txt <- header_txt %>% paste0(markdown_line, '\nLongest: ', x %>% base::nchar() %>% base::max(na.rm = TRUE))
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header_txt <- header_txt %>% paste0(markdown_line, '\nShortest: ', x %>% base::nchar() %>% base::min(na.rm = TRUE) %>% format(decimal.mark = decimal.mark, big.mark = big.mark))
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header_txt <- header_txt %>% paste0(markdown_line, '\nLongest: ', x %>% base::nchar() %>% base::max(na.rm = TRUE) %>% format(decimal.mark = decimal.mark, big.mark = big.mark))
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}
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if (NROW(x) > 0 & any(class(x) == "mo")) {
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header_txt <- header_txt %>% paste0('\n')
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header_txt <- header_txt %>% paste0(markdown_line, '\nFamilies: ', x %>% mo_family() %>% n_distinct() %>% format(decimal.mark = decimal.mark, big.mark = big.mark))
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header_txt <- header_txt %>% paste0(markdown_line, '\nGenera: ', x %>% mo_genus() %>% n_distinct() %>% format(decimal.mark = decimal.mark, big.mark = big.mark))
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header_txt <- header_txt %>% paste0(markdown_line, '\nSpecies: ', x %>% mo_species() %>% n_distinct() %>% format(decimal.mark = decimal.mark, big.mark = big.mark))
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}
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if (NROW(x) > 0 & any(class(x) == "difftime") & !is.hms(x)) {
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@ -349,13 +359,13 @@ frequency_tbl <- function(x,
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Tukey_five <- stats::fivenum(x, na.rm = TRUE)
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x_align <- 'r'
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header_txt <- header_txt %>% paste0('\n')
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header_txt <- header_txt %>% paste(markdown_line, '\nMean: ', x %>% base::mean(na.rm = TRUE) %>% format(digits = digits))
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header_txt <- header_txt %>% paste0(markdown_line, '\nStd. dev.: ', x %>% stats::sd(na.rm = TRUE) %>% format(digits = digits),
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' (CV: ', x %>% cv(na.rm = TRUE) %>% format(digits = digits),
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', MAD: ', x %>% stats::mad(na.rm = TRUE) %>% format(digits = digits), ')')
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header_txt <- header_txt %>% paste0(markdown_line, '\nFive-Num: ', Tukey_five %>% format(digits = digits) %>% trimws() %>% paste(collapse = ' | '),
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' (IQR: ', (Tukey_five[4] - Tukey_five[2]) %>% format(digits = digits),
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', CQV: ', x %>% cqv(na.rm = TRUE) %>% format(digits = digits), ')')
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header_txt <- header_txt %>% paste(markdown_line, '\nMean: ', x %>% base::mean(na.rm = TRUE) %>% format(digits = digits, decimal.mark = decimal.mark, big.mark = big.mark))
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header_txt <- header_txt %>% paste0(markdown_line, '\nStd. dev.: ', x %>% stats::sd(na.rm = TRUE) %>% format(digits = digits, decimal.mark = decimal.mark, big.mark = big.mark),
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' (CV: ', x %>% cv(na.rm = TRUE) %>% format(digits = digits, decimal.mark = decimal.mark, big.mark = big.mark),
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', MAD: ', x %>% stats::mad(na.rm = TRUE) %>% format(digits = digits, decimal.mark = decimal.mark, big.mark = big.mark), ')')
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header_txt <- header_txt %>% paste0(markdown_line, '\nFive-Num: ', Tukey_five %>% format(digits = digits, decimal.mark = decimal.mark, big.mark = big.mark) %>% trimws() %>% paste(collapse = ' | '),
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' (IQR: ', (Tukey_five[4] - Tukey_five[2]) %>% format(digits = digits, decimal.mark = decimal.mark, big.mark = big.mark),
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', CQV: ', x %>% cqv(na.rm = TRUE) %>% format(digits = digits, decimal.mark = decimal.mark, big.mark = big.mark), ')')
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outlier_length <- length(boxplot.stats(x)$out)
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header_txt <- header_txt %>% paste0(markdown_line, '\nOutliers: ', outlier_length)
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if (outlier_length > 0) {
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@ -367,8 +377,8 @@ frequency_tbl <- function(x,
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cnt_S <- sum(x == "S", na.rm = TRUE)
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cnt_IR <- sum(x %in% c("I", "R"), na.rm = TRUE)
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header_txt <- header_txt %>% paste(markdown_line, '\n%IR: ',
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(cnt_IR / sum(!is.na(x), na.rm = TRUE)) %>% percent(force_zero = TRUE, round = digits),
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paste0('(ratio S : IR = 1.0 : ', (cnt_IR / cnt_S) %>% format(digits = 1, nsmall = 1), ")"))
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(cnt_IR / sum(!is.na(x), na.rm = TRUE)) %>% percent(force_zero = TRUE, round = digits, decimal.mark = decimal.mark),
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paste0('(ratio S : IR = 1.0 : ', (cnt_IR / cnt_S) %>% format(digits = 1, nsmall = 1, decimal.mark = decimal.mark, big.mark = big.mark), ")"))
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if (NROW(x) < 30) {
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header_txt <- header_txt %>% paste(markdown_line, red('\nToo few isolates for reliable resistance interpretation.'))
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}
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@ -391,15 +401,15 @@ frequency_tbl <- function(x,
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# hms
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header_txt <- header_txt %>% paste0(markdown_line, '\nEarliest: ', mindate %>% format(formatdates) %>% trimws())
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header_txt <- header_txt %>% paste0(markdown_line, '\nLatest: ', maxdate %>% format(formatdates) %>% trimws(),
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' (+', difftime(maxdate, mindate, units = 'mins') %>% as.double() %>% format(digits = digits), ' min.)')
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' (+', difftime(maxdate, mindate, units = 'mins') %>% as.double() %>% format(digits = digits, decimal.mark = decimal.mark, big.mark = big.mark), ' min.)')
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} else {
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# other date formats
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header_txt <- header_txt %>% paste0(markdown_line, '\nOldest: ', mindate %>% format(formatdates) %>% trimws())
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header_txt <- header_txt %>% paste0(markdown_line, '\nNewest: ', maxdate %>% format(formatdates) %>% trimws(),
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' (+', difftime(maxdate, mindate, units = 'auto') %>% as.double() %>% format(digits = digits), ')')
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' (+', difftime(maxdate, mindate, units = 'auto') %>% as.double() %>% format(digits = digits, decimal.mark = decimal.mark, big.mark = big.mark), ')')
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}
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header_txt <- header_txt %>% paste0(markdown_line, '\nMedian: ', mediandate %>% format(formatdates) %>% trimws(),
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' (~', percent(median_days / maxdate_days, round = 0), ')')
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' (~', percent(median_days / maxdate_days, round = 0, decimal.mark = decimal.mark), ')')
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}
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if (any(class(x) == 'POSIXlt')) {
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x <- x %>% format(formatdates)
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@ -485,6 +495,8 @@ frequency_tbl <- function(x,
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row_names = row.names,
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column_names = column_names,
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column_align = column_align,
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decimal.mark = decimal.mark,
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big.mark = big.mark,
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tbl_format = tbl_format,
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na = na,
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nmax = nmax,
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@ -573,7 +585,10 @@ diff.frequency_tbl <- function(x, y, ...) {
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#' @importFrom crayon bold silver
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#' @export
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print.frequency_tbl <- function(x, nmax = getOption("max.print.freq", default = 15),
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markdown = !interactive(), header = !markdown, ...) {
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markdown = !interactive(), header = !markdown,
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decimal.mark = getOption("OutDec"),
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big.mark = ifelse(decimal.mark != ",", ",", "."),
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...) {
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opt <- attr(x, 'opt')
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@ -612,6 +627,12 @@ print.frequency_tbl <- function(x, nmax = getOption("max.print.freq", default =
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opt$nmax <- nmax
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opt$nmax.set <- TRUE
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}
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if (!missing(decimal.mark)) {
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opt$decimal.mark <- decimal.mark
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}
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if (!missing(big.mark)) {
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opt$big.mark <- big.mark
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}
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dots <- list(...)
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if ("markdown" %in% names(dots)) {
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if (dots$markdown == TRUE) {
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@ -677,11 +698,11 @@ print.frequency_tbl <- function(x, nmax = getOption("max.print.freq", default =
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}
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footer <- paste(footer,
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' -- omitted ',
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format(x.rows - opt$nmax),
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format(x.rows - opt$nmax, big.mark = opt$big.mark),
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' entries, n = ',
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format(x.unprinted),
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format(x.unprinted, big.mark = opt$big.mark),
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' (',
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(x.unprinted / (x.unprinted + x.printed)) %>% percent(force_zero = TRUE),
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(x.unprinted / (x.unprinted + x.printed)) %>% percent(force_zero = TRUE, decimal.mark = opt$decimal.mark),
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') ]\n', sep = '')
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if (opt$tbl_format == "pandoc") {
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footer <- silver(footer) # only silver in regular printing
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@ -692,7 +713,7 @@ print.frequency_tbl <- function(x, nmax = getOption("max.print.freq", default =
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if ("item" %in% colnames(x)) {
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if (any(class(x$item) %in% c('double', 'integer', 'numeric', 'raw', 'single'))) {
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x$item <- format(x$item)
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x$item <- format(x$item, decimal.mark = opt$decimal.mark, big.mark = opt$big.mark)
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}
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} else {
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opt$column_names <- opt$column_names[!opt$column_names == "Item"]
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@ -701,22 +722,22 @@ print.frequency_tbl <- function(x, nmax = getOption("max.print.freq", default =
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if (all(x$count == 1)) {
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warning('All observations are unique.', call. = FALSE)
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}
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x$count <- format(x$count)
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x$count <- format(x$count, decimal.mark = opt$decimal.mark, big.mark = opt$big.mark)
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} else {
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opt$column_names <- opt$column_names[!opt$column_names == "Count"]
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}
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if ("percent" %in% colnames(x)) {
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x$percent <- percent(x$percent, force_zero = TRUE)
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x$percent <- percent(x$percent, force_zero = TRUE, decimal.mark = opt$decimal.mark)
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} else {
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opt$column_names <- opt$column_names[!opt$column_names == "Percent"]
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}
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if ("cum_count" %in% colnames(x)) {
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x$cum_count <- format(x$cum_count)
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x$cum_count <- format(x$cum_count, decimal.mark = opt$decimal.mark, big.mark = opt$big.mark)
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} else {
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opt$column_names <- opt$column_names[!opt$column_names == "Cum. Count"]
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}
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if ("cum_percent" %in% colnames(x)) {
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x$cum_percent <- percent(x$cum_percent, force_zero = TRUE)
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x$cum_percent <- percent(x$cum_percent, force_zero = TRUE, decimal.mark = opt$decimal.mark)
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} else {
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opt$column_names <- opt$column_names[!opt$column_names == "Cum. Percent"]
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}
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9
R/misc.R
9
R/misc.R
@ -27,7 +27,10 @@ addin_insert_like <- function() {
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}
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# No export, no Rd
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percent <- function(x, round = 1, force_zero = FALSE, ...) {
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percent <- function(x, round = 1, force_zero = FALSE, decimal.mark = getOption("OutDec"), ...) {
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decimal.mark.options <- getOption("OutDec")
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options(OutDec = ".")
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# https://stackoverflow.com/a/12688836/4575331
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round2 <- function(x, n) (trunc((abs(x) * 10 ^ n) + 0.5) / 10 ^ n) * sign(x)
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@ -46,6 +49,10 @@ percent <- function(x, round = 1, force_zero = FALSE, ...) {
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}
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pct <- base::paste0(val, "%")
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pct[pct %in% c("NA%", "NaN%")] <- NA_character_
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if (decimal.mark != ".") {
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pct <- gsub(".", decimal.mark, pct, fixed = TRUE)
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}
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options(OutDec = decimal.mark.options)
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pct
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}
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