removed clipboard functions as it violated CRAN policies

.travis.yml

@@ -35,12 +35,6 @@ matrix:
 r_packages: covr
 cache: packages
 cran: https://cran.rstudio.com
-before_install:
-  # needed for clipboard function:
-  # - if [ $TRAVIS_OS_NAME = linux ]; then sudo apt-get -qq update; fi
-  # - if [ $TRAVIS_OS_NAME = linux ]; then sudo apt-get install -y xclip; fi
-  - if [ $TRAVIS_OS_NAME = osx ]; then brew install xclip; fi
-  - if [ $TRAVIS_OS_NAME = osx ]; then brew install libgit2; fi
 
 install:
   - Rscript -e "install.packages(c('devtools', 'backports', 'clipr', 'curl', 'data.table', 'dplyr', 'hms', 'knitr', 'readr', 'rlang', 'rvest', 'xml2', 'covr', 'ggplot2', 'rmarkdown', 'testthat', 'tidyr'))"
@@ -48,8 +42,7 @@ install:
 
 # postrun
 after_success:
-  # only run codecov on osx, so clipboard functions can be checked
+  - Rscript -e 'covr::codecov()'
-  - if [ $TRAVIS_OS_NAME = osx ]; then Rscript -e 'covr::codecov()'; fi
 notifications:
   email:
     recipients:

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 0.3.0.9009
+Version: 0.3.0.9010
 Date: 2018-09-27
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
@@ -46,13 +46,11 @@ Depends:
     R (>= 3.1.0)
 Imports:
     backports,
-    clipr,
     curl,
     data.table (>= 1.9.0),
     dplyr (>= 0.7.0),
     hms,
     knitr (>= 1.0.0),
-    readr,
     rlang (>= 0.2.0),
     rvest (>= 0.3.2),
     xml2 (>= 1.0.0)

NAMESPACE

@@ -57,8 +57,6 @@ export(as.rsi)
 export(atc_ddd)
 export(atc_groups)
 export(atc_property)
-export(clipboard_export)
-export(clipboard_import)
 export(count_I)
 export(count_IR)
 export(count_R)
@@ -159,8 +157,6 @@ exportMethods(skewness.default)
 exportMethods(skewness.matrix)
 exportMethods(summary.mic)
 exportMethods(summary.rsi)
-importFrom(clipr,read_clip_tbl)
-importFrom(clipr,write_clip)
 importFrom(curl,nslookup)
 importFrom(data.table,as.data.table)
 importFrom(data.table,data.table)
@@ -200,8 +196,6 @@ importFrom(graphics,hist)
 importFrom(graphics,plot)
 importFrom(graphics,text)
 importFrom(knitr,kable)
-importFrom(readr,locale)
-importFrom(readr,parse_guess)
 importFrom(rvest,html_children)
 importFrom(rvest,html_node)
 importFrom(rvest,html_nodes)
@@ -217,7 +211,4 @@ importFrom(stats,sd)
 importFrom(utils,View)
 importFrom(utils,browseVignettes)
 importFrom(utils,installed.packages)
-importFrom(utils,object.size)
-importFrom(utils,read.delim)
-importFrom(utils,write.table)
 importFrom(xml2,read_html)

NEWS.md

@@ -54,9 +54,9 @@
 
 * Function `ab_property` and its aliases: `ab_name`, `ab_tradenames`, `ab_certe`, `ab_umcg` and `ab_trivial_nl`
 * Introduction to AMR as a vignette
+* Removed clipbaord functions as it violated the CRAN policy
 
 #### Changed
-* Added almost 200 microorganisms to the `microorganisms` data set and removed the few viruses it contained
 * Added three antimicrobial agents to the `antibiotics` data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)
 * Added 163 trade names to the `antibiotics` data set, it now contains 298 different trade names in total, e.g.:
   ```r

R/clipboard.R

@@ -1,165 +0,0 @@
-#' 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.
-#'
-#' This also supports automatic column type transformation, with AMR classes \code{\link{as.rsi}} and \code{\link{as.mic}}.
-#' @rdname clipboard
-#' @name clipboard
-#' @inheritParams base::data.frame
-#' @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 and transformed 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.
-#' @param remove_ASCII_escape_char remove ASCII escape character
-#' @param info print info to console
-#' @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
-#' The parameter \code{stringsAsFactors} defaults to \code{FALSE}, as opposed to most base \R methods.
-#'
-#' The parameters \code{date_format} and \code{time_format} also support generic date and time formats like \code{"dd-mm-yyyy"} like Excel.
-#'
-#'   \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
-#' @examples
-#' \dontrun{
-#'
-#' df1 <- data.frame(a = letters[1:12],
-#'                   b = runif(n = 12, min = 1000, max = 2000),
-#'                   stringsAsFactors = FALSE)
-#' clipboard_export(df1)
-#' df2 <- clipboard_import()
-#' identical(df1, df2)
-#'
-#' # send frequency table to clipboard (e.g. for pasting in Excel)
-#' septic_patients %>%
-#'   freq(age) %>%
-#'   format() %>%       # this will format the percentages
-#'   clipboard_export()
-#' }
-clipboard_import <- function(sep = '\t',
-                             quote = "",
-                             header = TRUE,
-                             dec = ".",
-                             na = c("", "NA", "NULL"),
-                             stringsAsFactors = FALSE,
-                             startrow = 1,
-                             as_vector = TRUE,
-                             guess_col_types = TRUE,
-                             date_names = 'en',
-                             date_format = '%Y-%m-%d',
-                             time_format = '%H:%M',
-                             remove_ASCII_escape_char = FALSE,
-                             tz = "UTC",
-                             encoding = "UTF-8",
-                             info = TRUE) {
-
-  if (!clipr::clipr_available() & Sys.info()['sysname'] == "Linux") {
-    # try to support on X11, by setting the R variable DISPLAY
-    Sys.setenv(DISPLAY = "localhost:10.0")
-  }
-
-  # this will fail when clipr is (still) not available
-  import_tbl <- clipr::read_clip_tbl(file = file,
-                                     sep = sep,
-                                     quote = quote,
-                                     header = header,
-                                     strip.white = TRUE,
-                                     dec = dec,
-                                     na.strings = na,
-                                     encoding = 'UTF-8',
-                                     stringsAsFactors = stringsAsFactors)
-
-  # 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 data by guessing column types...')
-    }
-    import_tbl <- tbl_parse_guess(tbl = import_tbl,
-                                  date_names = date_names,
-                                  date_format = date_format,
-                                  time_format = time_format,
-                                  decimal_mark = dec,
-                                  tz = tz,
-                                  encoding = encoding,
-                                  remove_ASCII_escape_char = remove_ASCII_escape_char,
-                                  na = na)
-    if (info == TRUE) {
-      cat('OK\n')
-    }
-  }
-
-  if (NCOL(import_tbl) == 1 & as_vector == TRUE) {
-    import_tbl <-  import_tbl %>% pull(1)
-  }
-
-  # and transform back to data.frame
-  import_tbl <- as.data.frame(import_tbl, stringsAsFactors = stringsAsFactors)
-
-  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) {
-
-  if (!clipr::clipr_available() & Sys.info()['sysname'] == "Linux") {
-    # try to support on X11, by setting the R variable DISPLAY
-    Sys.setenv(DISPLAY = "localhost:10.0")
-  }
-
-  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")
-  }
-
-}
-

R/misc.R

@@ -110,99 +110,3 @@ size_humanreadable <- function(bytes, decimals = 1) {
   out <- paste(sprintf(paste0("%.", decimals, "f"), bytes / (1024 ^ factor)), size[factor + 1])
   out
 }
-
-# based on readr::parse_guess
-tbl_parse_guess <- function(tbl,
-                            date_names = 'en',
-                            date_format = '%Y-%m-%d',
-                            time_format = '%H:%M',
-                            decimal_mark = '.',
-                            tz = "UTC",
-                            encoding = "UTF-8",
-                            remove_ASCII_escape_char = FALSE,
-                            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'))) {
-      if (remove_ASCII_escape_char == TRUE) {
-        # remove ASCII escape character: https://en.wikipedia.org/wiki/Escape_character#ASCII_escape_character
-        tbl[, i] <- tbl %>% pull(i) %>% gsub('\033', ' ', ., fixed = TRUE)
-      }
-      if (tbl %>% pull(i) %>% is.rsi.eligible()) {
-        # look for RSI
-        tbl[, i] <- as.rsi(tbl[, i])
-      }
-    }
-    # convert to MIC class when ends on `_mic`
-    if (colnames(tbl)[i] %like% '_mic$') {
-      tbl[, i] <- as.mic(tbl[, i])
-    }
-  }
-  tbl
-}
-
-# 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
-}

README.md

@@ -1,4 +1,4 @@
-# `AMR`
+# `AMR` <img src="man/figures/logo_amr.png" align="right" height="120px" />
 ### An [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and work with antibiotic properties by using evidence-based methods.
 
 This R package was created for academic research by PhD students of the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl) and the Medical Microbiology & Infection Prevention (MMBI) department of the [University Medical Center Groningen (UMCG)](https://www.umcg.nl).

man/clipboard.Rd

@@ -1,139 +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", quote = "", header = TRUE, dec = ".",
-  na = c("", "NA", "NULL"), stringsAsFactors = FALSE, startrow = 1,
-  as_vector = TRUE, guess_col_types = TRUE, date_names = "en",
-  date_format = "\%Y-\%m-\%d", time_format = "\%H:\%M",
-  remove_ASCII_escape_char = FALSE, tz = "UTC", encoding = "UTF-8",
-  info = 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{quote}{the set of quoting characters. To disable quoting
-    altogether, use \code{quote = ""}.  See \code{\link{scan}} for the
-    behaviour on quotes embedded in quotes.  Quoting is only considered
-    for columns read as character, which is all of them unless
-    \code{colClasses} is specified.}
-
-\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{stringsAsFactors}{logical: should character vectors be converted
-    to factors?  The \sQuote{factory-fresh} default is \code{TRUE}, but
-    this can be changed by setting \code{\link{options}(stringsAsFactors
-      = FALSE)}.}
-
-\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 and transformed 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.}
-
-\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{remove_ASCII_escape_char}{remove ASCII escape character}
-
-\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 to console}
-
-\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.
-
-This also supports automatic column type transformation, with AMR classes \code{\link{as.rsi}} and \code{\link{as.mic}}.
-}
-\details{
-The parameter \code{stringsAsFactors} defaults to \code{FALSE}, as opposed to most base \R methods.
-
-The parameters \code{date_format} and \code{time_format} also support generic date and time formats like \code{"dd-mm-yyyy"} like Excel.
-
-  \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>}
-  }
-}
-\examples{
-\dontrun{
-
-df1 <- data.frame(a = letters[1:12],
-                  b = runif(n = 12, min = 1000, max = 2000),
-                  stringsAsFactors = FALSE)
-clipboard_export(df1)
-df2 <- clipboard_import()
-identical(df1, df2)
-
-# send frequency table to clipboard (e.g. for pasting in Excel)
-septic_patients \%>\%
-  freq(age) \%>\%
-  format() \%>\%       # this will format the percentages
-  clipboard_export()
-}
-}
-\keyword{clipboard}
-\keyword{clipboard_export}
-\keyword{clipboard_import}
-\keyword{export}
-\keyword{import}

tests/testthat/test-clipboard.R

@@ -1,24 +0,0 @@
-context("clipboard.R")
-
-test_that("clipboard works", {
-
-  if (!clipr::clipr_available() & Sys.info()['sysname'] == "Linux") {
-    # try to support on X11, by setting the R variable DISPLAY
-    Sys.setenv(DISPLAY = "localhost:10.0")
-  }
-
-  skip_if_not(clipr::clipr_available())
-
-  # clipboard_export(antibiotics)
-  # imp <- clipboard_import(guess_col_types = FALSE,
-  #                         stringsAsFactors = FALSE)
-  # expect_identical(as.data.frame(antibiotics, stringsAsFactors = FALSE),
-  #                  imp)
-
-  clipboard_export(septic_patients[1:100,])
-  imp <- clipboard_import(guess_col_types = TRUE,
-                          stringsAsFactors = FALSE)
-  expect_identical(as.data.frame(tbl_parse_guess(septic_patients[1:100,]),
-                                 stringsAsFactors = FALSE),
-                   imp)
-})

tests/testthat/test-misc.R

@@ -18,8 +18,3 @@ test_that("functions missing in older R versions work", {
   expect_equal(trimws(" test ", "l"), "test ")
   expect_equal(trimws(" test ", "r"), " test")
 })
-
-test_that("generic dates work", {
-  expect_equal(date_generic("yyyy-mm-dd"), "%Y-%m-%d")
-  expect_equal(date_generic("dddd d mmmm yyyy"), "%A %e %B %Y")
-})