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https://github.com/msberends/AMR.git
synced 2025-01-13 04:11:40 +01:00
remove clipboard functions
This commit is contained in:
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6fa93fc286
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@ -25,8 +25,6 @@ export(anti_join_microorganisms)
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export(as.mic)
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export(as.mic)
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export(as.rsi)
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export(as.rsi)
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export(atc_property)
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export(atc_property)
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export(clipboard_export)
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export(clipboard_import)
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export(first_isolate)
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export(first_isolate)
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export(freq)
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export(freq)
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export(frequency_tbl)
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export(frequency_tbl)
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@ -65,7 +63,6 @@ importFrom(dplyr,all_vars)
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importFrom(dplyr,any_vars)
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importFrom(dplyr,any_vars)
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importFrom(dplyr,arrange)
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importFrom(dplyr,arrange)
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importFrom(dplyr,arrange_at)
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importFrom(dplyr,arrange_at)
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importFrom(dplyr,as_tibble)
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importFrom(dplyr,between)
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importFrom(dplyr,between)
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importFrom(dplyr,desc)
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importFrom(dplyr,desc)
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importFrom(dplyr,filter)
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importFrom(dplyr,filter)
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@ -99,8 +96,5 @@ importFrom(rvest,html_table)
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importFrom(stats,fivenum)
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importFrom(stats,fivenum)
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importFrom(stats,quantile)
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importFrom(stats,quantile)
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importFrom(stats,sd)
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importFrom(stats,sd)
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importFrom(utils,object.size)
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importFrom(utils,packageDescription)
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importFrom(utils,packageDescription)
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importFrom(utils,read.delim)
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importFrom(utils,write.table)
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importFrom(xml2,read_html)
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importFrom(xml2,read_html)
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1
NEWS.md
1
NEWS.md
@ -4,7 +4,6 @@
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* Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)
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* Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)
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* Function `guess_bactid` to **determine the ID** of a microorganism based on genus/species or known abbreviations like MRSA
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* Function `guess_bactid` to **determine the ID** of a microorganism based on genus/species or known abbreviations like MRSA
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* Function `guess_atc` to **determine the ATC** of an antibiotic based on name, trade name, or known abbreviations
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* Function `guess_atc` to **determine the ATC** of an antibiotic based on name, trade name, or known abbreviations
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* Functions `clipboard_import` and `clipboard_export` as helper functions to **quickly copy and paste** from/to software like Excel and SPSS
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* Function `freq` to create **frequency tables**, with additional info in a header
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* Function `freq` to create **frequency tables**, with additional info in a header
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* Function `MDRO` to **determine Multi Drug Resistant Organisms (MDRO)** with support for country-specific guidelines.
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* Function `MDRO` to **determine Multi Drug Resistant Organisms (MDRO)** with support for country-specific guidelines.
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* Suggest your own via [https://github.com/msberends/AMR/issues/new](https://github.com/msberends/AMR/issues/new?title=New%20guideline%20for%20MDRO&body=%3C--%20Please%20add%20your%20country%20code,%20guideline%20name,%20version%20and%20source%20below%20and%20remove%20this%20line--%3E)
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* Suggest your own via [https://github.com/msberends/AMR/issues/new](https://github.com/msberends/AMR/issues/new?title=New%20guideline%20for%20MDRO&body=%3C--%20Please%20add%20your%20country%20code,%20guideline%20name,%20version%20and%20source%20below%20and%20remove%20this%20line--%3E)
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140
R/clipboard.R
140
R/clipboard.R
@ -1,140 +0,0 @@
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#' Import/export from clipboard
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#'
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#' These are helper functions around \code{\link{read.table}} and \code{\link{write.table}} to import from and export to clipboard with support for Windows, Linux and macOS. 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. See Details for an example.
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#' @rdname clipboard
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#' @name clipboard
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#' @inheritParams utils::read.table
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#' @inheritParams utils::write.table
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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 info print info about copying
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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 utils read.delim write.table object.size
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#' @details For \code{clipboard_export()}, the reserved clipboard size for exporting will be set to 125\% of the object size of \code{x}. This way, it is possible to export data with thousands of rows as the only limit will be your systems RAM.
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#'
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#' \if{html}{
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#' Example for copying from Excel:
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#' \out{<div style="text-align: left">}\figure{Excel_copy.png}\out{</div>}
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#' \cr
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#' And pasting in R: \cr \cr
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#' \code{> data <- clipboard_import()} \cr
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#' \code{> data} \cr
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#' \out{<div style="text-align: left">}\figure{Excel_paste.png}\out{</div>}
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#' }
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#' @export
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#' @return data.frame
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clipboard_import <- function(sep = '\t',
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header = TRUE,
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dec = ".",
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na = c("", "NA", "NULL"),
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startrow = 1,
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as_vector = TRUE) {
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if (is_Windows() == TRUE) {
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file <- 'clipboard'
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} else {
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# use xclip package
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check_xclip()
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file <- pipe("xclip -o", "r")
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on.exit(close(file))
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}
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import_tbl <- tryCatch(read.delim(file = file,
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sep = sep,
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header = header,
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strip.white = TRUE,
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dec = dec,
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na.strings = na,
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fileEncoding = 'UTF-8',
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encoding = 'UTF-8',
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stringsAsFactors = FALSE),
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error = function(e) {
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FALSE
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})
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if (all(import_tbl == FALSE)) {
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cat("No clipboard content found.")
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if (Sys.info()['sysname'] %like% "Linux") {
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cat(" These functions do not work without X11 installed.")
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}
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cat("\n")
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return(invisible())
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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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}
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colnames(import_tbl) <- gsub('[.]+', '_', colnames(import_tbl))
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if (NCOL(import_tbl) == 1 & as_vector == TRUE) {
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import_tbl %>% pull(1)
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} else {
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import_tbl
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}
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}
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#' @rdname clipboard
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#' @importFrom dplyr %>% pull as_tibble
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#' @export
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clipboard_export <- function(x,
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sep = '\t',
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dec = ".",
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na = "",
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header = TRUE,
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info = TRUE) {
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x <- deparse(substitute(x))
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size <- x %>%
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get() %>%
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object.size() %>%
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formatC(format = 'd') %>%
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as.integer()
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x <- get(x)
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if (is_Windows() == TRUE) {
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# set size of clipboard to 125% of the object size of x
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file <- paste0("clipboard-", size * 1.25)
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} else {
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# use xclip package
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check_xclip()
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file <- pipe("xclip -i", "w")
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on.exit(close(file))
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}
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tryCatch(write.table(x = x,
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file = file,
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sep = sep,
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na = na,
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row.names = FALSE,
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col.names = header,
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dec = dec,
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quote = FALSE),
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error = function(e) {
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FALSE
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})
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if (info == TRUE) {
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cat("Successfully exported to clipboard:", NROW(x), "obs. of", NCOL(x), "variables.\n")
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}
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}
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is_Windows <- function() {
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Sys.info()['sysname'] %like% "Windows"
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}
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check_xclip <- function() {
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if (!isTRUE(file.exists(Sys.which("xclip")[1L]))) {
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if (Sys.info()['sysname'] %like% "Linux") {
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stop("Please install Linux package xclip first.")
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} else {
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stop("Please install package xclip first (use `brew install xclip` on macOS).")
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}
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}
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}
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@ -1,63 +0,0 @@
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/clipboard.R
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\name{clipboard}
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\alias{clipboard}
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\alias{clipboard_import}
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\alias{clipboard_export}
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\title{Import/export from clipboard}
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\usage{
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clipboard_import(sep = "\\t", header = TRUE, dec = ".", na = c("", "NA",
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"NULL"), startrow = 1, as_vector = TRUE)
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clipboard_export(x, sep = "\\t", dec = ".", na = "", header = TRUE,
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info = TRUE)
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}
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\arguments{
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\item{sep}{the field separator character. Values on each line of the
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file are separated by this character. If \code{sep = ""} (the
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default for \code{read.table}) the separator is \sQuote{white space},
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that is one or more spaces, tabs, newlines or carriage returns.}
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\item{header}{a logical value indicating whether the file contains the
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names of the variables as its first line. If missing, the value is
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determined from the file format: \code{header} is set to \code{TRUE}
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if and only if the first row contains one fewer field than the
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number of columns.}
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\item{dec}{the character used in the file for decimal points.}
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\item{na}{the string to use for missing values in the data.}
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\item{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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\item{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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\item{x}{the object to be written, preferably a matrix or data frame.
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If not, it is attempted to coerce \code{x} to a data frame.}
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\item{info}{print info about copying}
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}
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\value{
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data.frame
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}
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\description{
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These are helper functions around \code{\link{read.table}} and \code{\link{write.table}} to import from and export to clipboard with support for Windows, Linux and macOS. 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. See Details for an example.
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}
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\details{
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For \code{clipboard_export()}, the reserved clipboard size for exporting will be set to 125\% of the object size of \code{x}. This way, it is possible to export data with thousands of rows as the only limit will be your systems RAM.
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\if{html}{
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Example for copying from Excel:
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\out{<div style="text-align: left">}\figure{Excel_copy.png}\out{</div>}
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\cr
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And pasting in R: \cr \cr
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\code{> data <- clipboard_import()} \cr
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\code{> data} \cr
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\out{<div style="text-align: left">}\figure{Excel_paste.png}\out{</div>}
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}
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}
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\keyword{clipboard}
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\keyword{clipboard_export}
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\keyword{clipboard_import}
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\keyword{export}
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\keyword{import}
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@ -1,12 +0,0 @@
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context("clipboard.R")
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test_that("clipboard works", {
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if (grepl(Sys.info()['sysname'], "windows", ignore.case = TRUE)) {
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t1 <<- AMR::antibiotics # why is the <<- needed? Won't work without it...
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clipboard_export(t1, info = FALSE)
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t2 <- clipboard_import()
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expect_equal(t1, t2)
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} else {
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expect_equal(TRUE, TRUE)
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}
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})
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