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move tbl_parse_guess
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 0.2.0.9006
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Date: 2018-06-28
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Date: 2018-06-29
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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@ -4,7 +4,7 @@
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#'
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#' The data will be read and written as tab-separated by default, which makes it possible to copy and paste from other software like Excel and SPSS without further transformation.
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#'
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#' Supports automatic column type transformation and supports new classes \code{\link{as.rsi}} and \code{\link{as.mic}}.
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#' This also supports automatic column type transformation, with AMR classes \code{\link{as.rsi}} and \code{\link{as.mic}}.
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#' @rdname clipboard
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#' @name clipboard
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#' @inheritParams utils::read.table
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@ -12,16 +12,14 @@
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#' @inheritParams readr::locale
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#' @param startrow \emph{n}th row to start importing from. When \code{header = TRUE}, the import will start on row \code{startrow} \emph{below} the header.
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#' @param as_vector a logical value indicating whether data consisting of only one column should be imported as vector using \code{\link[dplyr]{pull}}. This will strip off the header.
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#' @param guess_col_types a logical value indicating whether column types should be guessed with the \code{readr} package.
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#' @param info print info about copying
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#' @param guess_col_types a logical value indicating whether column types should be guessed and transformed automatically with \code{\link[readr]{parse_guess}} from the \code{readr} package. Besides, the antimicrobial classes in this AMR package (\code{\link{as.rsi}} and \code{\link{as.mic}}) are also supported.
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#' @param info print info to console
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#' @keywords clipboard clipboard_import clipboard_export import export
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#' @importFrom dplyr %>% pull as_tibble
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#' @importFrom clipr read_clip_tbl write_clip
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#' @importFrom utils read.delim write.table object.size
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#' @importFrom readr parse_guess locale
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#' @details
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#' When using \code{guess_col_types = TRUE}, all column types will be determined automatically with \code{\link[readr]{parse_guess}} from the \code{readr} package. Besides, the antimicrobial classes in this AMR package (\code{\link{as.rsi}} and \code{\link{as.mic}}) are also supported.
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#'
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#' \if{html}{
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#' \strong{Example for copying from Excel:}
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#' \out{<div style="text-align: left">}\figure{clipboard_copy.png}\out{</div>}
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@ -50,11 +48,7 @@ clipboard_import <- function(sep = '\t',
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time_format = '%H:%M',
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tz = Sys.timezone(),
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encoding = "UTF-8",
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info = FALSE) {
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if (clipr::clipr_available() & info == TRUE) {
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cat('Importing from clipboard...')
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}
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info = TRUE) {
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# this will fail when clipr is not available
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import_tbl <- clipr::read_clip_tbl(file = file,
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@ -66,25 +60,21 @@ clipboard_import <- function(sep = '\t',
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encoding = 'UTF-8',
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stringsAsFactors = FALSE)
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if (info == TRUE) {
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cat('OK\n')
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}
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# use tibble, so column types will be translated correctly
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import_tbl <- as_tibble(import_tbl)
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if (startrow > 1) {
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# would else lose column headers
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import_tbl <- import_tbl[startrow:nrow(import_tbl),]
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import_tbl <- import_tbl[startrow:NROW(import_tbl),]
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}
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colnames(import_tbl) <- gsub('[.]+', '_', colnames(import_tbl))
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if (guess_col_types == TRUE) {
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if (info == TRUE) {
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cat('Transforming columns with readr::parse_guess...')
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cat('Transforming data by guessing column types...')
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}
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import_tbl <- clipboard_format(tbl = import_tbl,
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import_tbl <- tbl_parse_guess(tbl = import_tbl,
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date_names = date_names,
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date_format = date_format,
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time_format = time_format,
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@ -133,46 +123,3 @@ clipboard_export <- function(x,
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}
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clipboard_format <- function(tbl,
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date_names = 'en',
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date_format = '%Y-%m-%d',
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time_format = '%H:%M',
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decimal_mark = '.',
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tz = Sys.timezone(),
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encoding = "UTF-8",
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na = c("", "NA", "NULL")) {
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date_format <- date_generic(date_format)
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time_format <- date_generic(time_format)
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# set col types with readr
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for (i in 1:ncol(tbl)) {
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if (!all(tbl %>% pull(i) %>% class() %in% c('list', 'matrix'))) {
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tbl[, i] <- readr::parse_guess(x = tbl %>% pull(i) %>% as.character(),
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na = na,
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locale = readr::locale(date_names = date_names,
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date_format = date_format,
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time_format = time_format,
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decimal_mark = decimal_mark,
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encoding = encoding,
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tz = tz,
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asciify = FALSE))
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}
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if (any(tbl %>% pull(i) %>% class() %in% c('factor', 'character'))) {
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# get values
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distinct_val <- tbl %>% pull(i) %>% unique() %>% sort()
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# remove ASCII escape character: https://en.wikipedia.org/wiki/Escape_character#ASCII_escape_character
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tbl[, i] <- tbl %>% pull(i) %>% gsub('\033', ' ', ., fixed = TRUE)
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# look for RSI, shouldn't all be "" and must be valid antibiotic interpretations
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if (!all(distinct_val[!is.na(distinct_val)] == '')
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& all(distinct_val[!is.na(distinct_val)] %in% c('', 'I', 'I;I', 'R', 'R;R', 'S', 'S;S'))) {
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tbl[, i] <- tbl %>% pull(i) %>% as.rsi()
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}
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}
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# convert to MIC class
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if (colnames(tbl)[i] %like% '_mic$') {
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tbl[, i] <- tbl %>% pull(i) %>% as.mic()
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}
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}
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tbl
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}
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44
R/misc.R
44
R/misc.R
@ -115,6 +115,50 @@ size_humanreadable <- function(bytes, decimals = 1) {
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out
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}
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# based on readr::parse_guess
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tbl_parse_guess <- function(tbl,
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date_names = 'en',
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date_format = '%Y-%m-%d',
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time_format = '%H:%M',
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decimal_mark = '.',
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tz = Sys.timezone(),
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encoding = "UTF-8",
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na = c("", "NA", "NULL")) {
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date_format <- date_generic(date_format)
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time_format <- date_generic(time_format)
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# set col types with readr
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for (i in 1:ncol(tbl)) {
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if (!all(tbl %>% pull(i) %>% class() %in% c('list', 'matrix'))) {
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tbl[, i] <- readr::parse_guess(x = tbl %>% pull(i) %>% as.character(),
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na = na,
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locale = readr::locale(date_names = date_names,
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date_format = date_format,
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time_format = time_format,
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decimal_mark = decimal_mark,
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encoding = encoding,
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tz = tz,
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asciify = FALSE))
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}
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if (any(tbl %>% pull(i) %>% class() %in% c('factor', 'character'))) {
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# get values
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distinct_val <- tbl %>% pull(i) %>% unique() %>% sort()
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# remove ASCII escape character: https://en.wikipedia.org/wiki/Escape_character#ASCII_escape_character
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tbl[, i] <- tbl %>% pull(i) %>% gsub('\033', ' ', ., fixed = TRUE)
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# look for RSI, shouldn't all be "" and must be valid antibiotic interpretations
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if (!all(distinct_val[!is.na(distinct_val)] == '')
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& all(distinct_val[!is.na(distinct_val)] %in% c('', 'I', 'I;I', 'R', 'R;R', 'S', 'S;S'))) {
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tbl[, i] <- tbl %>% pull(i) %>% as.rsi()
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}
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}
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# convert to MIC class
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if (colnames(tbl)[i] %like% '_mic$') {
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tbl[, i] <- tbl %>% pull(i) %>% as.mic()
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}
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}
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tbl
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}
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# transforms date format like "dddd d mmmm yyyy" to "%A %e %B %Y"
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date_generic <- function(format) {
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if (!grepl('%', format, fixed = TRUE)) {
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@ -5,5 +5,9 @@ test_that("clipboard works", {
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clipboard_export(antibiotics)
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expect_identical(antibiotics,
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clipboard_import())
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clipboard_import(date_format = "yyyy-mm-dd"))
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clipboard_export(septic_patients[1:100,])
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expect_identical(tbl_parse_guess(septic_patients[1:100,]),
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clipboard_import(guess_col_types = TRUE))
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})
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