mirror of
https://github.com/msberends/AMR.git
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add clipboard functions again
This commit is contained in:
parent
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commit
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@ -1,6 +1,6 @@
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Package: AMR
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Package: AMR
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Version: 0.2.0.9005
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Version: 0.2.0.9006
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Date: 2018-06-20
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Date: 2018-06-28
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Title: Antimicrobial Resistance Analysis
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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Authors@R: c(
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person(
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person(
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@ -28,12 +28,14 @@ Depends:
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R (>= 3.0.0)
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R (>= 3.0.0)
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Imports:
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Imports:
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backports,
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backports,
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clipr,
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curl,
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curl,
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dplyr (>= 0.7.0),
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dplyr (>= 0.7.0),
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data.table (>= 1.10.0),
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data.table (>= 1.10.0),
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reshape2 (>= 1.4.0),
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reshape2 (>= 1.4.0),
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xml2 (>= 1.0.0),
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xml2 (>= 1.0.0),
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knitr (>= 1.0.0),
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knitr (>= 1.0.0),
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readr,
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rvest (>= 0.3.2),
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rvest (>= 0.3.2),
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tibble
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tibble
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Suggests:
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Suggests:
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@ -28,6 +28,8 @@ export(as.rsi)
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export(atc_ddd)
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export(atc_ddd)
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export(atc_groups)
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export(atc_groups)
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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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@ -63,6 +65,8 @@ exportMethods(print.tbl)
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exportMethods(print.tbl_df)
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exportMethods(print.tbl_df)
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exportMethods(summary.mic)
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exportMethods(summary.mic)
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exportMethods(summary.rsi)
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exportMethods(summary.rsi)
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importFrom(clipr,read_clip_tbl)
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importFrom(clipr,write_clip)
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importFrom(curl,nslookup)
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importFrom(curl,nslookup)
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importFrom(data.table,data.table)
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importFrom(data.table,data.table)
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importFrom(dplyr,"%>%")
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importFrom(dplyr,"%>%")
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@ -70,6 +74,7 @@ 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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@ -98,6 +103,8 @@ importFrom(graphics,axis)
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importFrom(graphics,barplot)
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importFrom(graphics,barplot)
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importFrom(graphics,plot)
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importFrom(graphics,plot)
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importFrom(graphics,text)
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importFrom(graphics,text)
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importFrom(readr,locale)
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importFrom(readr,parse_guess)
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importFrom(reshape2,dcast)
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importFrom(reshape2,dcast)
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importFrom(rvest,html_children)
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importFrom(rvest,html_children)
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importFrom(rvest,html_node)
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importFrom(rvest,html_node)
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@ -109,4 +116,6 @@ importFrom(stats,sd)
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importFrom(utils,browseVignettes)
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importFrom(utils,browseVignettes)
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importFrom(utils,object.size)
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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
@ -3,6 +3,7 @@
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* Function `top_freq` function to get the top/below *n* items of frequency tables
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* Function `top_freq` function to get the top/below *n* items of frequency tables
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* Vignette about frequency tables
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* Vignette about frequency tables
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* Possibility to globally set the default for the amount of items to print in frequency tables (`freq` function), with `options(max.print.freq = n)`
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* Possibility to globally set the default for the amount of items to print in frequency tables (`freq` function), with `options(max.print.freq = n)`
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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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#### Changed
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#### Changed
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* Renamed `toConsole` parameter of `freq` function to `as.data.frame`
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* Renamed `toConsole` parameter of `freq` function to `as.data.frame`
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178
R/clipboard.R
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178
R/clipboard.R
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@ -0,0 +1,178 @@
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#' Import/export from clipboard
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#'
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#' @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.
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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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#' @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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#' @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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#' @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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#' \cr
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#' \strong{And pasting in R:} \cr
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#' \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{clipboard_paste.png}\out{</div>}
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#' \cr
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#' \strong{The resulting data contains the right RSI-classes:} \cr
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#' \cr
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#' \code{> data$amox} \cr
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#' \out{<div style="text-align: left">}\figure{clipboard_rsi.png}\out{</div>}
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#' }
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#' @export
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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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guess_col_types = TRUE,
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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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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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# this will fail when clipr is not available
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import_tbl <- clipr::read_clip_tbl(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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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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}
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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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}
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import_tbl <- clipboard_format(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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decimal_mark = dec,
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tz = tz,
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encoding = encoding,
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na = na)
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if (info == TRUE) {
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cat('OK\n')
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}
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}
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if (NCOL(import_tbl) == 1 & as_vector == TRUE) {
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import_tbl <- import_tbl %>% pull(1)
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}
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if (info == TRUE) {
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cat("Successfully imported from clipboard:", NROW(import_tbl), "obs. of", NCOL(import_tbl), "variables.\n")
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}
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import_tbl
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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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clipr::write_clip(content = x,
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na = na,
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sep = sep,
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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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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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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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52
R/misc.R
52
R/misc.R
@ -114,3 +114,55 @@ size_humanreadable <- function(bytes, decimals = 1) {
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out <- paste(sprintf(paste0("%.", decimals, "f"), bytes / (1024 ^ factor)), size[factor + 1])
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out <- paste(sprintf(paste0("%.", decimals, "f"), bytes / (1024 ^ factor)), size[factor + 1])
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out
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out
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}
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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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# first months and minutes, after that everything is case INsensitive
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format <- gsub('mmmm', '%B1', format, fixed = TRUE)
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format <- gsub('mmm', '%b', format, fixed = TRUE)
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format <- gsub('mm', '%m', format, fixed = TRUE)
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format <- gsub('MM', '%M1', format, fixed = TRUE)
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format <- format %>%
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tolower() %>%
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gsub('%b1', '%B', ., fixed = TRUE) %>%
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gsub('%m1', '%M', ., fixed = TRUE)
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# dates
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format <- gsub('dddd', '%A', format, fixed = TRUE)
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format <- gsub('ddd', '%a', format, fixed = TRUE)
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format <- gsub('dd', '%!', format, fixed = TRUE)
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format <- gsub('d', '%e', format, fixed = TRUE)
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format <- gsub('%!', '%d', format, fixed = TRUE)
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format <- gsub('ww', '%V', format, fixed = TRUE)
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format <- gsub('w', '%V', format, fixed = TRUE)
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format <- gsub('qq', 'Qq', format, fixed = TRUE) # so will be 'Q%%q' after this
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format <- gsub('kk', 'Kq', format, fixed = TRUE)
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format <- gsub('k', 'q', format, fixed = TRUE)
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format <- gsub('q', '%%q', format, fixed = TRUE)
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format <- gsub('yyyy_iso', '%G', format, fixed = TRUE)
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format <- gsub('jjjj_iso', '%G', format, fixed = TRUE)
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format <- gsub('yyyy', '%Y', format, fixed = TRUE)
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format <- gsub('jjjj', '%Y', format, fixed = TRUE)
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format <- gsub('yy_iso', '%g', format, fixed = TRUE)
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format <- gsub('jj_iso', '%g', format, fixed = TRUE)
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format <- gsub('yy', '%y', format, fixed = TRUE)
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format <- gsub('jj', '%y', format, fixed = TRUE)
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# time
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format <- gsub('hh', '%H', format, fixed = TRUE)
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format <- gsub('h', '%k', format, fixed = TRUE)
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format <- gsub('ss', '%S', format, fixed = TRUE)
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# seconds since the Epoch, 1970-01-01 00:00:00
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format <- gsub('unix', '%s', format, fixed = TRUE)
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# Equivalent to %Y-%m-%d (the ISO 8601 date format)
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format <- gsub('iso', '%F', format, fixed = TRUE)
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}
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format
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}
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105
man/clipboard.Rd
Normal file
105
man/clipboard.Rd
Normal file
@ -0,0 +1,105 @@
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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, guess_col_types = TRUE,
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date_names = "en", date_format = "\%Y-\%m-\%d", time_format = "\%H:\%M",
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tz = Sys.timezone(), encoding = "UTF-8", info = FALSE)
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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{
|
||||||
|
\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{guess_col_types}{a logical value indicating whether column types should be guessed with the \code{readr} package.}
|
||||||
|
|
||||||
|
\item{date_names}{Character representations of day and month names. Either
|
||||||
|
the language code as string (passed on to \code{\link[=date_names_lang]{date_names_lang()}})
|
||||||
|
or an object created by \code{\link[=date_names]{date_names()}}.}
|
||||||
|
|
||||||
|
\item{date_format}{Default date and time formats.}
|
||||||
|
|
||||||
|
\item{time_format}{Default date and time formats.}
|
||||||
|
|
||||||
|
\item{tz}{Default tz. This is used both for input (if the time zone isn't
|
||||||
|
present in individual strings), and for output (to control the default
|
||||||
|
display). The default is to use "UTC", a time zone that does not use
|
||||||
|
daylight savings time (DST) and hence is typically most useful for data.
|
||||||
|
The absence of time zones makes it approximately 50x faster to generate
|
||||||
|
UTC times than any other time zone.
|
||||||
|
|
||||||
|
Use \code{""} to use the system default time zone, but beware that this
|
||||||
|
will not be reproducible across systems.
|
||||||
|
|
||||||
|
For a complete list of possible time zones, see \code{\link{OlsonNames}()}.
|
||||||
|
Americans, note that "EST" is a Canadian time zone that does not have
|
||||||
|
DST. It is \emph{not} Eastern Standard Time. It's better to use
|
||||||
|
"US/Eastern", "US/Central" etc.}
|
||||||
|
|
||||||
|
\item{encoding}{encoding to be assumed for input strings. It is
|
||||||
|
used to mark character strings as known to be in
|
||||||
|
Latin-1 or UTF-8 (see \code{\link{Encoding}}): it is not used to
|
||||||
|
re-encode the input, but allows \R to handle encoded strings in
|
||||||
|
their native encoding (if one of those two). See \sQuote{Value}
|
||||||
|
and \sQuote{Note}.
|
||||||
|
}
|
||||||
|
|
||||||
|
\item{info}{print info about copying}
|
||||||
|
|
||||||
|
\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.}
|
||||||
|
}
|
||||||
|
\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.
|
||||||
|
|
||||||
|
Supports automatic column type transformation and supports new classes \code{\link{as.rsi}} and \code{\link{as.mic}}.
|
||||||
|
}
|
||||||
|
\details{
|
||||||
|
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.
|
||||||
|
|
||||||
|
\if{html}{
|
||||||
|
\strong{Example for copying from Excel:}
|
||||||
|
\out{<div style="text-align: left">}\figure{clipboard_copy.png}\out{</div>}
|
||||||
|
\cr
|
||||||
|
\strong{And pasting in R:} \cr
|
||||||
|
\cr
|
||||||
|
\code{> data <- clipboard_import()} \cr
|
||||||
|
\code{> data} \cr
|
||||||
|
\out{<div style="text-align: left">}\figure{clipboard_paste.png}\out{</div>}
|
||||||
|
\cr
|
||||||
|
\strong{The resulting data contains the right RSI-classes:} \cr
|
||||||
|
\cr
|
||||||
|
\code{> data$amox} \cr
|
||||||
|
\out{<div style="text-align: left">}\figure{clipboard_rsi.png}\out{</div>}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
\keyword{clipboard}
|
||||||
|
\keyword{clipboard_export}
|
||||||
|
\keyword{clipboard_import}
|
||||||
|
\keyword{export}
|
||||||
|
\keyword{import}
|
BIN
man/figures/clipboard_copy.png
Normal file
BIN
man/figures/clipboard_copy.png
Normal file
Binary file not shown.
After Width: | Height: | Size: 2.2 KiB |
BIN
man/figures/clipboard_paste.png
Normal file
BIN
man/figures/clipboard_paste.png
Normal file
Binary file not shown.
After Width: | Height: | Size: 4.5 KiB |
BIN
man/figures/clipboard_rsi.png
Normal file
BIN
man/figures/clipboard_rsi.png
Normal file
Binary file not shown.
After Width: | Height: | Size: 3.4 KiB |
9
tests/testthat/test-clipboard.R
Normal file
9
tests/testthat/test-clipboard.R
Normal file
@ -0,0 +1,9 @@
|
|||||||
|
context("clipboard.R")
|
||||||
|
|
||||||
|
test_that("clipboard works", {
|
||||||
|
skip_if_not(clipr::clipr_available())
|
||||||
|
|
||||||
|
clipboard_export(antibiotics)
|
||||||
|
expect_identical(antibiotics,
|
||||||
|
clipboard_import())
|
||||||
|
})
|
Loading…
Reference in New Issue
Block a user