diff --git a/NAMESPACE b/NAMESPACE
index 4388652b..b027ce30 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -25,8 +25,6 @@ export(anti_join_microorganisms)
export(as.mic)
export(as.rsi)
export(atc_property)
-export(clipboard_export)
-export(clipboard_import)
export(first_isolate)
export(freq)
export(frequency_tbl)
@@ -65,7 +63,6 @@ importFrom(dplyr,all_vars)
importFrom(dplyr,any_vars)
importFrom(dplyr,arrange)
importFrom(dplyr,arrange_at)
-importFrom(dplyr,as_tibble)
importFrom(dplyr,between)
importFrom(dplyr,desc)
importFrom(dplyr,filter)
@@ -99,8 +96,5 @@ importFrom(rvest,html_table)
importFrom(stats,fivenum)
importFrom(stats,quantile)
importFrom(stats,sd)
-importFrom(utils,object.size)
importFrom(utils,packageDescription)
-importFrom(utils,read.delim)
-importFrom(utils,write.table)
importFrom(xml2,read_html)
diff --git a/NEWS.md b/NEWS.md
index 4d6f62ef..ec2a0d5a 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,7 +4,6 @@
* Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)
* Function `guess_bactid` to **determine the ID** of a microorganism based on genus/species or known abbreviations like MRSA
* Function `guess_atc` to **determine the ATC** of an antibiotic based on name, trade name, or known abbreviations
-* Functions `clipboard_import` and `clipboard_export` as helper functions to **quickly copy and paste** from/to software like Excel and SPSS
* Function `freq` to create **frequency tables**, with additional info in a header
* Function `MDRO` to **determine Multi Drug Resistant Organisms (MDRO)** with support for country-specific guidelines.
* 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)
diff --git a/R/clipboard.R b/R/clipboard.R
deleted file mode 100644
index 70c56c60..00000000
--- a/R/clipboard.R
+++ /dev/null
@@ -1,140 +0,0 @@
-#' Import/export from clipboard
-#'
-#' 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.
-#' @rdname clipboard
-#' @name clipboard
-#' @inheritParams utils::read.table
-#' @inheritParams utils::write.table
-#' @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.
-#' @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.
-#' @param info print info about copying
-#' @keywords clipboard clipboard_import clipboard_export import export
-#' @importFrom dplyr %>% pull as_tibble
-#' @importFrom utils read.delim write.table object.size
-#' @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.
-#'
-#' \if{html}{
-#' Example for copying from Excel:
-#' \out{}\figure{Excel_copy.png}\out{
}
-#' \cr
-#' And pasting in R: \cr \cr
-#' \code{> data <- clipboard_import()} \cr
-#' \code{> data} \cr
-#' \out{}\figure{Excel_paste.png}\out{
}
-#' }
-#' @export
-#' @return data.frame
-clipboard_import <- function(sep = '\t',
- header = TRUE,
- dec = ".",
- na = c("", "NA", "NULL"),
- startrow = 1,
- as_vector = TRUE) {
-
- if (is_Windows() == TRUE) {
- file <- 'clipboard'
- } else {
- # use xclip package
- check_xclip()
- file <- pipe("xclip -o", "r")
- on.exit(close(file))
- }
-
- import_tbl <- tryCatch(read.delim(file = file,
- sep = sep,
- header = header,
- strip.white = TRUE,
- dec = dec,
- na.strings = na,
- fileEncoding = 'UTF-8',
- encoding = 'UTF-8',
- stringsAsFactors = FALSE),
- error = function(e) {
- FALSE
- })
-
- if (all(import_tbl == FALSE)) {
- cat("No clipboard content found.")
- if (Sys.info()['sysname'] %like% "Linux") {
- cat(" These functions do not work without X11 installed.")
- }
- cat("\n")
- return(invisible())
- }
-
- # use tibble, so column types will be translated correctly
- import_tbl <- as_tibble(import_tbl)
-
- if (startrow > 1) {
- # would else lose column headers
- import_tbl <- import_tbl[startrow:nrow(import_tbl),]
- }
-
- colnames(import_tbl) <- gsub('[.]+', '_', colnames(import_tbl))
-
- if (NCOL(import_tbl) == 1 & as_vector == TRUE) {
- import_tbl %>% pull(1)
- } else {
- import_tbl
- }
-}
-
-#' @rdname clipboard
-#' @importFrom dplyr %>% pull as_tibble
-#' @export
-clipboard_export <- function(x,
- sep = '\t',
- dec = ".",
- na = "",
- header = TRUE,
- info = TRUE) {
-
- x <- deparse(substitute(x))
- size <- x %>%
- get() %>%
- object.size() %>%
- formatC(format = 'd') %>%
- as.integer()
-
- x <- get(x)
-
- if (is_Windows() == TRUE) {
- # set size of clipboard to 125% of the object size of x
- file <- paste0("clipboard-", size * 1.25)
- } else {
- # use xclip package
- check_xclip()
- file <- pipe("xclip -i", "w")
- on.exit(close(file))
- }
-
- tryCatch(write.table(x = x,
- file = file,
- sep = sep,
- na = na,
- row.names = FALSE,
- col.names = header,
- dec = dec,
- quote = FALSE),
- error = function(e) {
- FALSE
- })
-
- if (info == TRUE) {
- cat("Successfully exported to clipboard:", NROW(x), "obs. of", NCOL(x), "variables.\n")
- }
-
-}
-
-is_Windows <- function() {
- Sys.info()['sysname'] %like% "Windows"
-}
-check_xclip <- function() {
- if (!isTRUE(file.exists(Sys.which("xclip")[1L]))) {
- if (Sys.info()['sysname'] %like% "Linux") {
- stop("Please install Linux package xclip first.")
- } else {
- stop("Please install package xclip first (use `brew install xclip` on macOS).")
- }
- }
-}
diff --git a/man/clipboard.Rd b/man/clipboard.Rd
deleted file mode 100644
index 09607b58..00000000
--- a/man/clipboard.Rd
+++ /dev/null
@@ -1,63 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/clipboard.R
-\name{clipboard}
-\alias{clipboard}
-\alias{clipboard_import}
-\alias{clipboard_export}
-\title{Import/export from clipboard}
-\usage{
-clipboard_import(sep = "\\t", header = TRUE, dec = ".", na = c("", "NA",
- "NULL"), startrow = 1, as_vector = TRUE)
-
-clipboard_export(x, sep = "\\t", dec = ".", na = "", header = TRUE,
- info = TRUE)
-}
-\arguments{
-\item{sep}{the field separator character. Values on each line of the
- file are separated by this character. If \code{sep = ""} (the
- default for \code{read.table}) the separator is \sQuote{white space},
- that is one or more spaces, tabs, newlines or carriage returns.}
-
-\item{header}{a logical value indicating whether the file contains the
- names of the variables as its first line. If missing, the value is
- determined from the file format: \code{header} is set to \code{TRUE}
- if and only if the first row contains one fewer field than the
- number of columns.}
-
-\item{dec}{the character used in the file for decimal points.}
-
-\item{na}{the string to use for missing values in the data.}
-
-\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.}
-
-\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.}
-
-\item{x}{the object to be written, preferably a matrix or data frame.
- If not, it is attempted to coerce \code{x} to a data frame.}
-
-\item{info}{print info about copying}
-}
-\value{
-data.frame
-}
-\description{
-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.
-}
-\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.
-
- \if{html}{
- Example for copying from Excel:
- \out{}\figure{Excel_copy.png}\out{
}
- \cr
- And pasting in R: \cr \cr
- \code{> data <- clipboard_import()} \cr
- \code{> data} \cr
- \out{}\figure{Excel_paste.png}\out{
}
- }
-}
-\keyword{clipboard}
-\keyword{clipboard_export}
-\keyword{clipboard_import}
-\keyword{export}
-\keyword{import}
diff --git a/tests/testthat/test-clipboard.R b/tests/testthat/test-clipboard.R
deleted file mode 100644
index 9d30bba5..00000000
--- a/tests/testthat/test-clipboard.R
+++ /dev/null
@@ -1,12 +0,0 @@
-context("clipboard.R")
-
-test_that("clipboard works", {
- if (grepl(Sys.info()['sysname'], "windows", ignore.case = TRUE)) {
- t1 <<- AMR::antibiotics # why is the <<- needed? Won't work without it...
- clipboard_export(t1, info = FALSE)
- t2 <- clipboard_import()
- expect_equal(t1, t2)
- } else {
- expect_equal(TRUE, TRUE)
- }
-})