From 649a8025aabfc2b41f99951757b4317d635f341b Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Wed, 27 Jun 2018 15:54:56 +0200
Subject: [PATCH] add clipboard functions again

---
 DESCRIPTION                     |   6 +-
 NAMESPACE                       |   9 ++
 NEWS.md                         |   1 +
 R/clipboard.R                   | 178 ++++++++++++++++++++++++++++++++
 R/misc.R                        |  52 ++++++++++
 man/clipboard.Rd                | 105 +++++++++++++++++++
 man/figures/clipboard_copy.png  | Bin 0 -> 2283 bytes
 man/figures/clipboard_paste.png | Bin 0 -> 4620 bytes
 man/figures/clipboard_rsi.png   | Bin 0 -> 3505 bytes
 tests/testthat/test-clipboard.R |   9 ++
 10 files changed, 358 insertions(+), 2 deletions(-)
 create mode 100644 R/clipboard.R
 create mode 100644 man/clipboard.Rd
 create mode 100644 man/figures/clipboard_copy.png
 create mode 100644 man/figures/clipboard_paste.png
 create mode 100644 man/figures/clipboard_rsi.png
 create mode 100644 tests/testthat/test-clipboard.R

diff --git a/DESCRIPTION b/DESCRIPTION
index ca6ad891..32838e50 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.2.0.9005
-Date: 2018-06-20
+Version: 0.2.0.9006
+Date: 2018-06-28
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(
@@ -28,12 +28,14 @@ Depends:
     R (>= 3.0.0)
 Imports:
     backports,
+    clipr,
     curl,
     dplyr (>= 0.7.0),
     data.table (>= 1.10.0),
     reshape2 (>= 1.4.0),
     xml2 (>= 1.0.0),
     knitr (>= 1.0.0),
+    readr,
     rvest (>= 0.3.2),
     tibble
 Suggests:
diff --git a/NAMESPACE b/NAMESPACE
index d9fe12d7..e739d96c 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -28,6 +28,8 @@ export(as.rsi)
 export(atc_ddd)
 export(atc_groups)
 export(atc_property)
+export(clipboard_export)
+export(clipboard_import)
 export(first_isolate)
 export(freq)
 export(frequency_tbl)
@@ -63,6 +65,8 @@ exportMethods(print.tbl)
 exportMethods(print.tbl_df)
 exportMethods(summary.mic)
 exportMethods(summary.rsi)
+importFrom(clipr,read_clip_tbl)
+importFrom(clipr,write_clip)
 importFrom(curl,nslookup)
 importFrom(data.table,data.table)
 importFrom(dplyr,"%>%")
@@ -70,6 +74,7 @@ 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)
@@ -98,6 +103,8 @@ importFrom(graphics,axis)
 importFrom(graphics,barplot)
 importFrom(graphics,plot)
 importFrom(graphics,text)
+importFrom(readr,locale)
+importFrom(readr,parse_guess)
 importFrom(reshape2,dcast)
 importFrom(rvest,html_children)
 importFrom(rvest,html_node)
@@ -109,4 +116,6 @@ importFrom(stats,sd)
 importFrom(utils,browseVignettes)
 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 c41196fb..9e1c176e 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -3,6 +3,7 @@
 * Function `top_freq` function to get the top/below *n* items of frequency tables
 * Vignette about frequency tables
 * Possibility to globally set the default for the amount of items to print in frequency tables (`freq` function), with `options(max.print.freq = n)`
+* Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS
 
 #### Changed
 * Renamed `toConsole` parameter of `freq` function to `as.data.frame`
diff --git a/R/clipboard.R b/R/clipboard.R
new file mode 100644
index 00000000..dde0d70d
--- /dev/null
+++ b/R/clipboard.R
@@ -0,0 +1,178 @@
+#' Import/export from clipboard
+#'
+#' @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}}.
+#' @rdname clipboard
+#' @name clipboard
+#' @inheritParams utils::read.table
+#' @inheritParams utils::write.table
+#' @inheritParams readr::locale
+#' @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 guess_col_types a logical value indicating whether column types should be guessed with the \code{readr} package.
+#' @param info print info about copying
+#' @keywords clipboard clipboard_import clipboard_export import export
+#' @importFrom dplyr %>% pull as_tibble
+#' @importFrom clipr read_clip_tbl write_clip
+#' @importFrom utils read.delim write.table object.size
+#' @importFrom readr parse_guess locale
+#' @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>}
+#'   }
+#' @export
+clipboard_import <- function(sep = '\t',
+                             header = TRUE,
+                             dec = ".",
+                             na = c("", "NA", "NULL"),
+                             startrow = 1,
+                             as_vector = TRUE,
+                             guess_col_types = TRUE,
+                             date_names = 'en',
+                             date_format = '%Y-%m-%d',
+                             time_format = '%H:%M',
+                             tz = Sys.timezone(),
+                             encoding = "UTF-8",
+                             info = FALSE) {
+
+  if (clipr::clipr_available() & info == TRUE) {
+    cat('Importing from clipboard...')
+  }
+
+  # this will fail when clipr is not available
+  import_tbl <- clipr::read_clip_tbl(file = file,
+                                     sep = sep,
+                                     header = header,
+                                     strip.white = TRUE,
+                                     dec = dec,
+                                     na.strings = na,
+                                     encoding = 'UTF-8',
+                                     stringsAsFactors = FALSE)
+
+  if (info == TRUE) {
+    cat('OK\n')
+  }
+
+  # 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 (guess_col_types == TRUE) {
+    if (info == TRUE) {
+      cat('Transforming columns with readr::parse_guess...')
+    }
+    import_tbl <- clipboard_format(tbl = import_tbl,
+                                   date_names = date_names,
+                                   date_format = date_format,
+                                   time_format = time_format,
+                                   decimal_mark = dec,
+                                   tz = tz,
+                                   encoding = encoding,
+                                   na = na)
+    if (info == TRUE) {
+      cat('OK\n')
+    }
+  }
+
+  if (NCOL(import_tbl) == 1 & as_vector == TRUE) {
+    import_tbl <-  import_tbl %>% pull(1)
+  }
+
+  if (info == TRUE) {
+    cat("Successfully imported from clipboard:", NROW(import_tbl), "obs. of", NCOL(import_tbl), "variables.\n")
+  }
+
+  import_tbl
+
+}
+
+#' @rdname clipboard
+#' @importFrom dplyr %>% pull as_tibble
+#' @export
+clipboard_export <- function(x,
+                             sep = '\t',
+                             dec = ".",
+                             na = "",
+                             header = TRUE,
+                             info = TRUE) {
+
+  clipr::write_clip(content = x,
+                    na = na,
+                    sep = sep,
+                    row.names = FALSE,
+                    col.names = header,
+                    dec = dec,
+                    quote = FALSE)
+
+  if (info == TRUE) {
+    cat("Successfully exported to clipboard:", NROW(x), "obs. of", NCOL(x), "variables.\n")
+  }
+
+}
+
+clipboard_format <- function(tbl,
+                             date_names = 'en',
+                             date_format = '%Y-%m-%d',
+                             time_format = '%H:%M',
+                             decimal_mark = '.',
+                             tz = Sys.timezone(),
+                             encoding = "UTF-8",
+                             na = c("", "NA", "NULL")) {
+
+  date_format <- date_generic(date_format)
+  time_format <- date_generic(time_format)
+  # set col types with readr
+  for (i in 1:ncol(tbl)) {
+    if (!all(tbl %>% pull(i) %>% class() %in% c('list', 'matrix'))) {
+      tbl[, i] <- readr::parse_guess(x = tbl %>% pull(i) %>% as.character(),
+                                     na = na,
+                                     locale = readr::locale(date_names = date_names,
+                                                            date_format = date_format,
+                                                            time_format = time_format,
+                                                            decimal_mark = decimal_mark,
+                                                            encoding = encoding,
+                                                            tz = tz,
+                                                            asciify = FALSE))
+    }
+    if (any(tbl %>% pull(i) %>% class() %in% c('factor', 'character'))) {
+      # get values
+      distinct_val <- tbl %>% pull(i) %>% unique() %>% sort()
+      # remove ASCII escape character: https://en.wikipedia.org/wiki/Escape_character#ASCII_escape_character
+      tbl[, i] <- tbl %>% pull(i) %>% gsub('\033', ' ', ., fixed = TRUE)
+      # look for RSI, shouldn't all be "" and must be valid antibiotic interpretations
+      if (!all(distinct_val[!is.na(distinct_val)] == '')
+          & all(distinct_val[!is.na(distinct_val)] %in% c('', 'I', 'I;I', 'R', 'R;R', 'S', 'S;S'))) {
+        tbl[, i] <- tbl %>% pull(i) %>% as.rsi()
+      }
+    }
+    # convert to MIC class
+    if (colnames(tbl)[i] %like% '_mic$') {
+      tbl[, i] <- tbl %>% pull(i) %>% as.mic()
+    }
+  }
+  tbl
+}
+
diff --git a/R/misc.R b/R/misc.R
index fb6bf27a..3a2a58d9 100755
--- a/R/misc.R
+++ b/R/misc.R
@@ -114,3 +114,55 @@ size_humanreadable <- function(bytes, decimals = 1) {
   out <- paste(sprintf(paste0("%.", decimals, "f"), bytes / (1024 ^ factor)), size[factor + 1])
   out
 }
+
+# transforms date format like "dddd d mmmm yyyy" to "%A %e %B %Y"
+date_generic <- function(format) {
+  if (!grepl('%', format, fixed = TRUE)) {
+
+    # first months and minutes, after that everything is case INsensitive
+    format <- gsub('mmmm', '%B1', format, fixed = TRUE)
+    format <- gsub('mmm', '%b', format, fixed = TRUE)
+    format <- gsub('mm', '%m', format, fixed = TRUE)
+    format <- gsub('MM', '%M1', format, fixed = TRUE)
+    format <- format %>%
+      tolower() %>%
+      gsub('%b1', '%B', ., fixed = TRUE) %>%
+      gsub('%m1', '%M', ., fixed = TRUE)
+
+    # dates
+    format <- gsub('dddd', '%A', format, fixed = TRUE)
+    format <- gsub('ddd', '%a', format, fixed = TRUE)
+    format <- gsub('dd', '%!', format, fixed = TRUE)
+    format <- gsub('d', '%e', format, fixed = TRUE)
+    format <- gsub('%!', '%d', format, fixed = TRUE)
+
+    format <- gsub('ww', '%V', format, fixed = TRUE)
+    format <- gsub('w', '%V', format, fixed = TRUE)
+
+    format <- gsub('qq', 'Qq', format, fixed = TRUE) # so will be 'Q%%q' after this
+    format <- gsub('kk', 'Kq', format, fixed = TRUE)
+    format <- gsub('k', 'q', format, fixed = TRUE)
+    format <- gsub('q', '%%q', format, fixed = TRUE)
+
+    format <- gsub('yyyy_iso', '%G', format, fixed = TRUE)
+    format <- gsub('jjjj_iso', '%G', format, fixed = TRUE)
+    format <- gsub('yyyy', '%Y', format, fixed = TRUE)
+    format <- gsub('jjjj', '%Y', format, fixed = TRUE)
+    format <- gsub('yy_iso', '%g', format, fixed = TRUE)
+    format <- gsub('jj_iso', '%g', format, fixed = TRUE)
+    format <- gsub('yy', '%y', format, fixed = TRUE)
+    format <- gsub('jj', '%y', format, fixed = TRUE)
+
+    # time
+    format <- gsub('hh', '%H', format, fixed = TRUE)
+    format <- gsub('h', '%k', format, fixed = TRUE)
+    format <- gsub('ss', '%S', format, fixed = TRUE)
+
+    # seconds since the Epoch, 1970-01-01 00:00:00
+    format <- gsub('unix', '%s', format, fixed = TRUE)
+    # Equivalent to %Y-%m-%d (the ISO 8601 date format)
+    format <- gsub('iso', '%F', format, fixed = TRUE)
+
+  }
+  format
+}
diff --git a/man/clipboard.Rd b/man/clipboard.Rd
new file mode 100644
index 00000000..665fc4d2
--- /dev/null
+++ b/man/clipboard.Rd
@@ -0,0 +1,105 @@
+% 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, guess_col_types = TRUE,
+  date_names = "en", date_format = "\%Y-\%m-\%d", time_format = "\%H:\%M",
+  tz = Sys.timezone(), encoding = "UTF-8", info = FALSE)
+
+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{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}
diff --git a/man/figures/clipboard_copy.png b/man/figures/clipboard_copy.png
new file mode 100644
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diff --git a/tests/testthat/test-clipboard.R b/tests/testthat/test-clipboard.R
new file mode 100644
index 00000000..9429e96f
--- /dev/null
+++ b/tests/testthat/test-clipboard.R
@@ -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())
+})