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AMR
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remove clipboard functions

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dr. M.S. (Matthijs) Berends 2018-05-01 09:36:45 +02:00
parent 6fa93fc286
commit 19ccc51f40
5 changed files with 0 additions and 222 deletions
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6
NAMESPACE
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@ -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)

1
NEWS.md
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@ -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)

140
R/clipboard.R
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@ -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{<div style="text-align: left">}\figure{Excel_copy.png}\out{</div>}
#' \cr
#' And pasting in R: \cr \cr
#' \code{> data <- clipboard_import()} \cr
#' \code{> data} \cr
#' \out{<div style="text-align: left">}\figure{Excel_paste.png}\out{</div>}
#' }
#' @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).")
}
}
}

63
man/clipboard.Rd
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@ -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{<div style="text-align: left">}\figure{Excel_copy.png}\out{</div>}
\cr
And pasting in R: \cr \cr
\code{> data <- clipboard_import()} \cr
\code{> data} \cr
\out{<div style="text-align: left">}\figure{Excel_paste.png}\out{</div>}
}
}
\keyword{clipboard}
\keyword{clipboard_export}
\keyword{clipboard_import}
\keyword{export}
\keyword{import}

12
tests/testthat/test-clipboard.R
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@ -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)
}
})