diff --git a/.travis.yml b/.travis.yml
index 4acc29fb..187650ed 100755
--- a/.travis.yml
+++ b/.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
- - if [ $TRAVIS_OS_NAME = osx ]; then Rscript -e 'covr::codecov()'; fi
+ - Rscript -e 'covr::codecov()'
notifications:
email:
recipients:
diff --git a/DESCRIPTION b/DESCRIPTION
index 1f96b3bc..9c0ac43f 100755
--- a/DESCRIPTION
+++ b/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)
diff --git a/NAMESPACE b/NAMESPACE
index dd4ddc09..1a1b00cb 100755
--- a/NAMESPACE
+++ b/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)
diff --git a/NEWS.md b/NEWS.md
index 750b7b65..e1d30d34 100755
--- a/NEWS.md
+++ b/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
diff --git a/R/clipboard.R b/R/clipboard.R
deleted file mode 100644
index 315ccbda..00000000
--- a/R/clipboard.R
+++ /dev/null
@@ -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{
}
-#' \cr
-#' \strong{The resulting data contains the right RSI-classes:} \cr
-#' \cr
-#' \code{> data$amox} \cr
-#' \out{
}\figure{clipboard_rsi.png}\out{
}
-#' }
-#' @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")
- }
-
-}
-
diff --git a/R/misc.R b/R/misc.R
index f5097fa3..83cfd2ef 100755
--- a/R/misc.R
+++ b/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
-}
diff --git a/README.md b/README.md
index 1920a06d..27e12dec 100755
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# `AMR`
+# `AMR`
### 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).
diff --git a/man/clipboard.Rd b/man/clipboard.Rd
deleted file mode 100644
index 0cbdf030..00000000
--- a/man/clipboard.Rd
+++ /dev/null
@@ -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{