mirror of https://github.com/msberends/AMR.git
freq - decimals
This commit is contained in:
parent
8e8a9cd190
commit
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@ -5,6 +5,7 @@
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# how the Docker+R images work: https://hub.docker.com/r/rocker/r-ver/
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R 3:
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image: rocker/r-ver:3 # test on R v3.*.*
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allow_failure: true
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script:
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- apt-get update
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# install dependencies for package
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@ -14,13 +15,15 @@ R 3:
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# remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
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- rm -rf vignettes
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- Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
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# set environmental variable
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- Rscript -e 'Sys.setenv(NOT_CRAN = "true")'
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# build package
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- R CMD build . --no-build-vignettes --no-manual
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- PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
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- R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran
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# code coverage
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- apt-get install --yes git
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- Rscript -e "cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = '50ffa0aa-fee0-4f8b-a11d-8c7edc6d32ca'); cat('Code coverage:', covr::percent_coverage(cc))"
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- Rscript -e 'cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = "50ffa0aa-fee0-4f8b-a11d-8c7edc6d32ca"); cat("Code coverage:", covr::percent_coverage(cc))'
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coverage: '/Code coverage: \d+\.\d+/'
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artifacts:
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paths:
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 0.5.0.9002
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Date: 2018-12-07
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Version: 0.5.0.9003
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Date: 2018-12-10
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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10
NEWS.md
10
NEWS.md
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@ -9,13 +9,17 @@
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* Finds better results when input is in other languages
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* Better handling for subspecies
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* Better handling for *Salmonellae*
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* There will be looked for uncertain results at default - these results will be returned with a informative warning
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* Extended manual text about algorithms
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* There will be looked for uncertain results at default - these results will be returned with an informative warning
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* Manual now contains more info about the algorithms
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* Progress bar will be shown when it takes more than 3 seconds to get results
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* Function `first_isolate` will now use a column named like "patid" for the patient ID, when this parameter was left blank
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* Reduce false positives for `is.rsi.eligible`
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* Summaries of class `mo` will now return the top 3 and the unique count, e.g. using `summary(mo)`
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* Small text updates to summaries of class `rsi` and `mic`
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* Function `as.mo` now prints a progress bar when it takes more than 3 seconds the get results
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* Frequency tables (`freq` function):
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* Added header info for class `mo` to show unique count of families, genera and species
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* Now honours the `decimal.mark` setting, which just like `format` defaults to `getOption("OutDec")`
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* The new `big.mark` parameter will at default be `","` when `decimal.mark = "."` and `"."` otherwise
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# 0.5.0 (latest stable release)
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77
R/freq.R
77
R/freq.R
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@ -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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#' @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
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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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@ -16,10 +16,11 @@ cache:
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# Adapt as necessary starting from here
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environment:
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global:
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R_ARCH: x64
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GCC_PATH: mingw_64
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WARNINGS_ARE_ERRORS: 1
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R_ARCH: x64
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GCC_PATH: mingw_64
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WARNINGS_ARE_ERRORS: 1
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PKGTYPE: win.binary
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# USE_RTOOLS: true
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matrix:
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- R_VERSION: release
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19
man/freq.Rd
19
man/freq.Rd
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@ -10,17 +10,22 @@
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frequency_tbl(x, ..., sort.count = TRUE,
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nmax = getOption("max.print.freq"), na.rm = TRUE, row.names = TRUE,
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markdown = !interactive(), digits = 2, quote = FALSE,
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header = !markdown, title = NULL, na = "<NA>", sep = " ")
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header = !markdown, title = NULL, na = "<NA>", sep = " ",
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decimal.mark = getOption("OutDec"), big.mark = ifelse(decimal.mark !=
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",", ",", "."))
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freq(x, ..., sort.count = TRUE, nmax = getOption("max.print.freq"),
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na.rm = TRUE, row.names = TRUE, markdown = !interactive(),
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digits = 2, quote = FALSE, header = !markdown, title = NULL,
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na = "<NA>", sep = " ")
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na = "<NA>", sep = " ", decimal.mark = getOption("OutDec"),
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big.mark = ifelse(decimal.mark != ",", ",", "."))
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top_freq(f, n)
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\method{print}{frequency_tbl}(x, nmax = getOption("max.print.freq",
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default = 15), markdown = !interactive(), header = !markdown, ...)
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default = 15), markdown = !interactive(), header = !markdown,
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decimal.mark = getOption("OutDec"), big.mark = ifelse(decimal.mark !=
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",", ",", "."), ...)
|
||||
}
|
||||
\arguments{
|
||||
\item{x}{vector of any class or a \code{\link{data.frame}}, \code{\link{tibble}} (may contain a grouping variable) or \code{\link{table}}}
|
||||
|
|
@ -49,6 +54,14 @@ top_freq(f, n)
|
|||
|
||||
\item{sep}{a character string to separate the terms when selecting multiple columns}
|
||||
|
||||
\item{decimal.mark}{%
|
||||
used for prettying (longish) numerical and complex sequences.
|
||||
Passed to \code{\link{prettyNum}}: that help page explains the details.}
|
||||
|
||||
\item{big.mark}{%
|
||||
used for prettying (longish) numerical and complex sequences.
|
||||
Passed to \code{\link{prettyNum}}: that help page explains the details.}
|
||||
|
||||
\item{f}{a frequency table}
|
||||
|
||||
\item{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.}
|
||||
|
|
|
|||
|
|
@ -26,8 +26,9 @@ test_that("frequency table works", {
|
|||
expect_output(print(freq(septic_patients$age, markdown = TRUE, title = "TITLE")))
|
||||
|
||||
# character
|
||||
expect_output(print(freq(septic_patients$mo)))
|
||||
expect_output(suppressWarnings(print(freq(microorganisms$fullname))))
|
||||
# mo
|
||||
expect_output(print(freq(septic_patients$mo)))
|
||||
# integer
|
||||
expect_output(print(freq(septic_patients$age)))
|
||||
# date
|
||||
|
|
|
|||
Loading…
Reference in New Issue