mirror of
https://github.com/msberends/AMR.git
synced 2025-01-12 22:11:38 +01:00
remove clipboard functions
This commit is contained in:
parent
6fa93fc286
commit
19ccc51f40
@ -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
1
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)
|
||||
|
||||
140
R/clipboard.R
140
R/clipboard.R
@ -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).")
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -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}
|
||||
@ -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)
|
||||
}
|
||||
})
|
||||
Loading…
Reference in New Issue
Block a user