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clipboard update

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dr. M.S. (Matthijs) Berends 2018-07-23 15:09:19 +02:00
parent 8421638b60
commit 03a3cb397b
3 changed files with 24 additions and 7 deletions
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5
R/clipboard.R
View File

@ -14,6 +14,7 @@
#' @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
@ -58,6 +59,7 @@
#' clipboard_export()
#' }
clipboard_import <- function(sep = '\t',
quote = "",
header = TRUE,
dec = ".",
na = c("", "NA", "NULL"),
@ -68,6 +70,7 @@ clipboard_import <- function(sep = '\t',
date_names = 'en',
date_format = '%Y-%m-%d',
time_format = '%H:%M',
remove_ASCII_escape_char = FALSE,
tz = Sys.timezone(),
encoding = "UTF-8",
info = TRUE) {
@ -80,6 +83,7 @@ clipboard_import <- function(sep = '\t',
# 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,
@ -108,6 +112,7 @@ clipboard_import <- function(sep = '\t',
decimal_mark = dec,
tz = tz,
encoding = encoding,
remove_ASCII_escape_char = remove_ASCII_escape_char,
na = na)
if (info == TRUE) {
cat('OK\n')

7
R/misc.R
View File

@ -119,6 +119,7 @@ tbl_parse_guess <- function(tbl,
decimal_mark = '.',
tz = Sys.timezone(),
encoding = "UTF-8",
remove_ASCII_escape_char = FALSE,
na = c("", "NA", "NULL")) {
date_format <- date_generic(date_format)
@ -139,8 +140,10 @@ tbl_parse_guess <- function(tbl,
if (any(tbl %>% pull(i) %>% class() %in% c('factor', 'character'))) {
# get values
distinct_val <- tbl %>% pull(i) %>% unique() %>% sort()
# remove ASCII escape character: https://en.wikipedia.org/wiki/Escape_character#ASCII_escape_character
tbl[, i] <- tbl %>% pull(i) %>% gsub('\033', ' ', ., fixed = TRUE)
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)
}
# look for RSI, shouldn't all be "" and must be valid antibiotic interpretations
if (!all(distinct_val[!is.na(distinct_val)] == '')
& all(distinct_val[!is.na(distinct_val)] %in% c('', 'I', 'I;I', 'R', 'R;R', 'S', 'S;S'))) {

19
man/clipboard.Rd
View File

@ -6,11 +6,12 @@
\alias{clipboard_export}
\title{Import/export from clipboard}
\usage{
clipboard_import(sep = "\\t", 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", tz = Sys.timezone(), encoding = "UTF-8",
info = TRUE)
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 = Sys.timezone(),
encoding = "UTF-8", info = TRUE)
clipboard_export(x, sep = "\\t", dec = ".", na = "", header = TRUE,
info = TRUE)
@ -21,6 +22,12 @@ clipboard_export(x, sep = "\\t", dec = ".", na = "", header = TRUE,
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}
@ -50,6 +57,8 @@ or an object created by \code{\link[=date_names]{date_names()}}.}
\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