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synced 2024-12-25 19:26:13 +01:00
removed clipboard functions as it violated CRAN policies
This commit is contained in:
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2b0080995e
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768fe17324
@ -35,12 +35,6 @@ matrix:
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r_packages: covr
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cache: packages
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cran: https://cran.rstudio.com
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before_install:
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# needed for clipboard function:
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# - if [ $TRAVIS_OS_NAME = linux ]; then sudo apt-get -qq update; fi
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# - if [ $TRAVIS_OS_NAME = linux ]; then sudo apt-get install -y xclip; fi
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- if [ $TRAVIS_OS_NAME = osx ]; then brew install xclip; fi
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- if [ $TRAVIS_OS_NAME = osx ]; then brew install libgit2; fi
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install:
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- Rscript -e "install.packages(c('devtools', 'backports', 'clipr', 'curl', 'data.table', 'dplyr', 'hms', 'knitr', 'readr', 'rlang', 'rvest', 'xml2', 'covr', 'ggplot2', 'rmarkdown', 'testthat', 'tidyr'))"
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@ -48,8 +42,7 @@ install:
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# postrun
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after_success:
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# only run codecov on osx, so clipboard functions can be checked
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- if [ $TRAVIS_OS_NAME = osx ]; then Rscript -e 'covr::codecov()'; fi
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- Rscript -e 'covr::codecov()'
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notifications:
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email:
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recipients:
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 0.3.0.9009
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Version: 0.3.0.9010
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Date: 2018-09-27
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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@ -46,13 +46,11 @@ Depends:
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R (>= 3.1.0)
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Imports:
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backports,
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clipr,
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curl,
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data.table (>= 1.9.0),
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dplyr (>= 0.7.0),
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hms,
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knitr (>= 1.0.0),
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readr,
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rlang (>= 0.2.0),
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rvest (>= 0.3.2),
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xml2 (>= 1.0.0)
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@ -57,8 +57,6 @@ export(as.rsi)
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export(atc_ddd)
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export(atc_groups)
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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(count_I)
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export(count_IR)
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export(count_R)
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@ -159,8 +157,6 @@ exportMethods(skewness.default)
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exportMethods(skewness.matrix)
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exportMethods(summary.mic)
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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(data.table,as.data.table)
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importFrom(data.table,data.table)
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@ -200,8 +196,6 @@ importFrom(graphics,hist)
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importFrom(graphics,plot)
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importFrom(graphics,text)
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importFrom(knitr,kable)
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importFrom(readr,locale)
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importFrom(readr,parse_guess)
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importFrom(rvest,html_children)
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importFrom(rvest,html_node)
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importFrom(rvest,html_nodes)
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@ -217,7 +211,4 @@ importFrom(stats,sd)
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importFrom(utils,View)
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importFrom(utils,browseVignettes)
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importFrom(utils,installed.packages)
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importFrom(utils,object.size)
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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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2
NEWS.md
2
NEWS.md
@ -54,9 +54,9 @@
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* Function `ab_property` and its aliases: `ab_name`, `ab_tradenames`, `ab_certe`, `ab_umcg` and `ab_trivial_nl`
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* Introduction to AMR as a vignette
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* Removed clipbaord functions as it violated the CRAN policy
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#### Changed
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* Added almost 200 microorganisms to the `microorganisms` data set and removed the few viruses it contained
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* Added three antimicrobial agents to the `antibiotics` data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)
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* Added 163 trade names to the `antibiotics` data set, it now contains 298 different trade names in total, e.g.:
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```r
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165
R/clipboard.R
165
R/clipboard.R
@ -1,165 +0,0 @@
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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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#' This also supports automatic column type transformation, with AMR 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 base::data.frame
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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 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.
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#' @param remove_ASCII_escape_char remove ASCII escape character
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#' @param info print info to console
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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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#' The parameter \code{stringsAsFactors} defaults to \code{FALSE}, as opposed to most base \R methods.
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#'
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#' The parameters \code{date_format} and \code{time_format} also support generic date and time formats like \code{"dd-mm-yyyy"} like Excel.
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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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#' @examples
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#' \dontrun{
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#'
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#' df1 <- data.frame(a = letters[1:12],
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#' b = runif(n = 12, min = 1000, max = 2000),
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#' stringsAsFactors = FALSE)
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#' clipboard_export(df1)
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#' df2 <- clipboard_import()
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#' identical(df1, df2)
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#'
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#' # send frequency table to clipboard (e.g. for pasting in Excel)
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#' septic_patients %>%
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#' freq(age) %>%
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#' format() %>% # this will format the percentages
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#' clipboard_export()
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#' }
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clipboard_import <- function(sep = '\t',
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quote = "",
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header = TRUE,
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dec = ".",
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na = c("", "NA", "NULL"),
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stringsAsFactors = FALSE,
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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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remove_ASCII_escape_char = FALSE,
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tz = "UTC",
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encoding = "UTF-8",
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info = TRUE) {
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if (!clipr::clipr_available() & Sys.info()['sysname'] == "Linux") {
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# try to support on X11, by setting the R variable DISPLAY
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Sys.setenv(DISPLAY = "localhost:10.0")
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}
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# this will fail when clipr is (still) not available
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import_tbl <- clipr::read_clip_tbl(file = file,
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sep = sep,
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quote = quote,
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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 = stringsAsFactors)
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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 data by guessing column types...')
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}
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import_tbl <- tbl_parse_guess(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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remove_ASCII_escape_char = remove_ASCII_escape_char,
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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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# and transform back to data.frame
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import_tbl <- as.data.frame(import_tbl, stringsAsFactors = stringsAsFactors)
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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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if (!clipr::clipr_available() & Sys.info()['sysname'] == "Linux") {
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# try to support on X11, by setting the R variable DISPLAY
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Sys.setenv(DISPLAY = "localhost:10.0")
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}
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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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96
R/misc.R
96
R/misc.R
@ -110,99 +110,3 @@ 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
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}
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# based on readr::parse_guess
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tbl_parse_guess <- 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 = "UTC",
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encoding = "UTF-8",
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remove_ASCII_escape_char = FALSE,
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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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if (remove_ASCII_escape_char == TRUE) {
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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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}
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if (tbl %>% pull(i) %>% is.rsi.eligible()) {
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# look for RSI
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tbl[, i] <- as.rsi(tbl[, i])
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}
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}
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# convert to MIC class when ends on `_mic`
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if (colnames(tbl)[i] %like% '_mic$') {
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tbl[, i] <- as.mic(tbl[, i])
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}
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}
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tbl
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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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@ -1,4 +1,4 @@
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# `AMR`
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# `AMR` <img src="man/figures/logo_amr.png" align="right" height="120px" />
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### 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.
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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).
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139
man/clipboard.Rd
139
man/clipboard.Rd
@ -1,139 +0,0 @@
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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", quote = "", header = TRUE, dec = ".",
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na = c("", "NA", "NULL"), stringsAsFactors = FALSE, startrow = 1,
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as_vector = TRUE, guess_col_types = TRUE, date_names = "en",
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date_format = "\%Y-\%m-\%d", time_format = "\%H:\%M",
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remove_ASCII_escape_char = FALSE, tz = "UTC", encoding = "UTF-8",
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info = TRUE)
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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{
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\item{sep}{the field separator character. Values on each line of the
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file are separated by this character. If \code{sep = ""} (the
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default for \code{read.table}) the separator is \sQuote{white space},
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that is one or more spaces, tabs, newlines or carriage returns.}
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\item{quote}{the set of quoting characters. To disable quoting
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altogether, use \code{quote = ""}. See \code{\link{scan}} for the
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behaviour on quotes embedded in quotes. Quoting is only considered
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for columns read as character, which is all of them unless
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\code{colClasses} is specified.}
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\item{header}{a logical value indicating whether the file contains the
|
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names of the variables as its first line. If missing, the value is
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determined from the file format: \code{header} is set to \code{TRUE}
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if and only if the first row contains one fewer field than the
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number of columns.}
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\item{dec}{the character used in the file for decimal points.}
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\item{na}{the string to use for missing values in the data.}
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\item{stringsAsFactors}{logical: should character vectors be converted
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to factors? The \sQuote{factory-fresh} default is \code{TRUE}, but
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this can be changed by setting \code{\link{options}(stringsAsFactors
|
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= FALSE)}.}
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\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.}
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|
||||
\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}
|
||||
BIN
man/figures/logo_amr.png
Normal file
BIN
man/figures/logo_amr.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 56 KiB |
3547
man/figures/logo_amr.svg
Normal file
3547
man/figures/logo_amr.svg
Normal file
File diff suppressed because it is too large
Load Diff
|
After Width: | Height: | Size: 222 KiB |
@ -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)
|
||||
})
|
||||
@ -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")
|
||||
})
|
||||
|
||||
Loading…
Reference in New Issue
Block a user