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{
}\figure{clipboard_copy.png}\out{
} -#' \cr -#' \strong{And pasting in R:} \cr -#' \cr -#' \code{> data <- clipboard_import()} \cr -#' \code{> data} \cr -#' \out{
}\figure{clipboard_paste.png}\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{
}\figure{clipboard_copy.png}\out{
} - \cr - \strong{And pasting in R:} \cr - \cr - \code{> data <- clipboard_import()} \cr - \code{> data} \cr - \out{
}\figure{clipboard_paste.png}\out{
} - \cr - \strong{The resulting data contains the right RSI-classes:} \cr - \cr - \code{> data$amox} \cr - \out{
}\figure{clipboard_rsi.png}\out{
} - } -} -\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} diff --git a/man/figures/logo_amr.png b/man/figures/logo_amr.png new file mode 100644 index 00000000..48b92531 Binary files /dev/null and b/man/figures/logo_amr.png differ diff --git a/man/figures/logo_amr.svg b/man/figures/logo_amr.svg new file mode 100644 index 00000000..b3bf9499 --- /dev/null +++ b/man/figures/logo_amr.svg @@ -0,0 +1,3547 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/testthat/test-clipboard.R b/tests/testthat/test-clipboard.R deleted file mode 100644 index 6954c36f..00000000 --- a/tests/testthat/test-clipboard.R +++ /dev/null @@ -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) -}) diff --git a/tests/testthat/test-misc.R b/tests/testthat/test-misc.R index 150f3338..164a9c9f 100755 --- a/tests/testthat/test-misc.R +++ b/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") -})