mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 18:06:12 +01:00
fix clipboard on linux
This commit is contained in:
parent
abcb4accbd
commit
c182a9673d
1
.gitignore
vendored
1
.gitignore
vendored
@ -3,3 +3,4 @@
|
||||
.RData
|
||||
.Ruserdata
|
||||
AMR.Rproj
|
||||
tests/testthat/Rplots.pdf
|
||||
|
10
.travis.yml
10
.travis.yml
@ -3,15 +3,9 @@
|
||||
# Setting up R deps
|
||||
language: r
|
||||
r: 3.2
|
||||
r_packages:
|
||||
- covr
|
||||
- testthat
|
||||
- dplyr
|
||||
- rvest
|
||||
- xml2
|
||||
- reshape2
|
||||
r_packages: covr
|
||||
|
||||
# system deps
|
||||
# system deps, install xclip for clipboard support
|
||||
os:
|
||||
- linux
|
||||
- osx
|
||||
|
@ -1,6 +1,6 @@
|
||||
Package: AMR
|
||||
Version: 0.1.2
|
||||
Date: 2018-03-27
|
||||
Date: 2018-04-02
|
||||
Title: Antimicrobial Resistance Analysis
|
||||
Authors@R: c(
|
||||
person(
|
||||
|
@ -30,15 +30,27 @@ clipboard_import <- function(sep = '\t',
|
||||
on.exit(close(file))
|
||||
}
|
||||
|
||||
import_tbl <- read.delim(file = file,
|
||||
sep = sep,
|
||||
header = header,
|
||||
strip.white = TRUE,
|
||||
dec = dec,
|
||||
na.strings = na,
|
||||
fileEncoding = 'UTF-8',
|
||||
encoding = 'UTF-8',
|
||||
stringsAsFactors = FALSE)
|
||||
import_tbl <- tryCatch(read.delim(file = file,
|
||||
sep = sep,
|
||||
header = header,
|
||||
strip.white = TRUE,
|
||||
dec = dec,
|
||||
na.strings = na,
|
||||
fileEncoding = 'UTF-8',
|
||||
encoding = 'UTF-8',
|
||||
stringsAsFactors = FALSE),
|
||||
error = function(e) {
|
||||
FALSE
|
||||
})
|
||||
|
||||
if (import_tbl == FALSE) {
|
||||
cat("No clipboard content found.")
|
||||
if (Sys.info()['sysname'] %like% "Linux") {
|
||||
cat(" These functions do not work without X11 installed.")
|
||||
}
|
||||
cat("\n")
|
||||
return(invisible())
|
||||
}
|
||||
|
||||
# use tibble, so column types will be translated correctly
|
||||
import_tbl <- as_tibble(import_tbl)
|
||||
@ -86,18 +98,22 @@ clipboard_export <- function(x,
|
||||
on.exit(close(file))
|
||||
}
|
||||
|
||||
write.table(x = x,
|
||||
file = file,
|
||||
sep = sep,
|
||||
na = na,
|
||||
row.names = FALSE,
|
||||
col.names = header,
|
||||
dec = dec,
|
||||
quote = FALSE)
|
||||
tryCatch(write.table(x = x,
|
||||
file = file,
|
||||
sep = sep,
|
||||
na = na,
|
||||
row.names = FALSE,
|
||||
col.names = header,
|
||||
dec = dec,
|
||||
quote = FALSE),
|
||||
error = function(e) {
|
||||
FALSE
|
||||
})
|
||||
|
||||
if (info == TRUE) {
|
||||
cat("Successfully exported to clipboard:", NROW(x), "obs. of", NCOL(x), "variables.\n")
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
is_Windows <- function() {
|
||||
@ -105,6 +121,10 @@ is_Windows <- function() {
|
||||
}
|
||||
check_xclip <- function() {
|
||||
if (!isTRUE(file.exists(Sys.which("xclip")[1L]))) {
|
||||
if (Sys.info()['sysname'] %like% "Linux") {
|
||||
stop("Please install Linux package xclip first.")
|
||||
} else {
|
||||
stop("Please install package xclip first (use `brew install xclip on macOS`).")
|
||||
}
|
||||
}
|
||||
}
|
||||
|
2
R/data.R
2
R/data.R
@ -125,7 +125,7 @@
|
||||
#'
|
||||
#' # Add first isolates to our dataset:
|
||||
#' my_data <- my_data %>%
|
||||
#' mutate(first_isolates = first_isolate(my_data, date, patient_id, bactid))
|
||||
#' mutate(first_isolates = first_isolate(my_data, "date", "patient_id", "bactid"))
|
||||
#'
|
||||
#' # -------- #
|
||||
#' # ANALYSIS #
|
||||
|
@ -20,12 +20,12 @@
|
||||
#'
|
||||
#' Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type.
|
||||
#' @param tbl a \code{data.frame} containing isolates.
|
||||
#' @param col_date column name of the result date (or date that is was received on the lab), supports tidyverse-like quotation
|
||||
#' @param col_patient_id column name of the unique IDs of the patients, supports tidyverse-like quotation
|
||||
#' @param col_bactid column name of the unique IDs of the microorganisms (should occur in the \code{\link{microorganisms}} dataset), supports tidyverse-like quotation
|
||||
#' @param col_date column name of the result date (or date that is was received on the lab)
|
||||
#' @param col_patient_id column name of the unique IDs of the patients
|
||||
#' @param col_bactid column name of the unique IDs of the microorganisms (should occur in the \code{\link{microorganisms}} dataset)
|
||||
#' @param col_testcode column name of the test codes. Use \code{col_testcode = NA} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored. Supports tidyverse-like quotation.
|
||||
#' @param col_specimen column name of the specimen type or group, supports tidyverse-like quotation
|
||||
#' @param col_icu column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU), supports tidyverse-like quotation
|
||||
#' @param col_specimen column name of the specimen type or group
|
||||
#' @param col_icu column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU)
|
||||
#' @param col_keyantibiotics column name of the key antibiotics to determine first \emph{weighted} isolates, see \code{\link{key_antibiotics}}. Supports tidyverse-like quotation.
|
||||
#' @param episode_days episode in days after which a genus/species combination will be determined as 'first isolate' again
|
||||
#' @param testcodes_exclude character vector with test codes that should be excluded (case-insensitive)
|
||||
@ -36,8 +36,8 @@
|
||||
#' @param ignore_I logical to determine whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantibiotics"}, see Details
|
||||
#' @param points_threshold points until the comparison of key antibiotics will lead to inclusion of an isolate when \code{type = "points"}, see Details
|
||||
#' @param info print progress
|
||||
#' @param col_genus (deprecated, use \code{col_bactid} instead) column name of the genus of the microorganisms, supports tidyverse-like quotation
|
||||
#' @param col_species (deprecated, use \code{col_bactid} instead) column name of the species of the microorganisms, supports tidyverse-like quotation
|
||||
#' @param col_genus (deprecated, use \code{col_bactid} instead) column name of the genus of the microorganisms
|
||||
#' @param col_species (deprecated, use \code{col_bactid} instead) column name of the species of the microorganisms
|
||||
#' @details \strong{WHY THIS IS SO IMPORTANT} \cr
|
||||
#' To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode \href{https://www.ncbi.nlm.nih.gov/pubmed/17304462}{[1]}. If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all \emph{S. aureus} isolates would be overestimated, because you included this MRSA more than once. It would be \href{https://en.wikipedia.org/wiki/Selection_bias}{selection bias}.
|
||||
#'
|
||||
@ -57,11 +57,9 @@
|
||||
#'
|
||||
#' library(dplyr)
|
||||
#' my_patients$first_isolate <- my_patients %>%
|
||||
#' left_join_microorganisms() %>%
|
||||
#' first_isolate(col_date = date,
|
||||
#' col_patient_id = patient_id,
|
||||
#' col_genus = genus,
|
||||
#' col_species = species)
|
||||
#' first_isolate(col_date = "date",
|
||||
#' col_patient_id = "patient_id",
|
||||
#' col_bactid = "bactid")
|
||||
#'
|
||||
#' \dontrun{
|
||||
#'
|
||||
@ -122,16 +120,10 @@ first_isolate <- function(tbl,
|
||||
col_genus = NA,
|
||||
col_species = NA) {
|
||||
|
||||
# support tidyverse-like quotation
|
||||
# col_date <- quasiquotate(deparse(substitute(col_date)), col_date)
|
||||
# col_patient_id <- quasiquotate(deparse(substitute(col_patient_id)), col_patient_id)
|
||||
# col_bactid <- quasiquotate(deparse(substitute(col_bactid)), col_bactid)
|
||||
# col_genus <- quasiquotate(deparse(substitute(col_genus)), col_genus)
|
||||
# col_species <- quasiquotate(deparse(substitute(col_species)), col_species)
|
||||
# col_testcode <- quasiquotate(deparse(substitute(col_testcode)), col_testcode)
|
||||
# col_specimen <- quasiquotate(deparse(substitute(col_specimen)), col_specimen)
|
||||
# col_icu <- quasiquotate(deparse(substitute(col_icu)), col_icu)
|
||||
# col_keyantibiotics <- quasiquotate(deparse(substitute(col_keyantibiotics)), col_keyantibiotics)
|
||||
# bactid OR genus+species must be available
|
||||
if (is.na(col_bactid) & (is.na(col_genus) | is.na(col_species))) {
|
||||
stop('`col_bactid or both `col_genus` and `col_species` must be available.')
|
||||
}
|
||||
|
||||
# check if columns exist
|
||||
check_columns_existance <- function(column, tblname = tbl) {
|
||||
@ -141,7 +133,7 @@ first_isolate <- function(tbl,
|
||||
|
||||
if (!is.na(column)) {
|
||||
if (!(column %in% colnames(tblname))) {
|
||||
stop('Column ', column, ' not found.')
|
||||
stop('Column `', column, '` not found.')
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -156,7 +148,7 @@ first_isolate <- function(tbl,
|
||||
check_columns_existance(col_keyantibiotics)
|
||||
|
||||
if (!is.na(col_bactid)) {
|
||||
tbl <- tbl %>% left_join_microorganisms()
|
||||
tbl <- tbl %>% left_join_microorganisms(by = col_bactid)
|
||||
col_genus <- "genus"
|
||||
col_species <- "species"
|
||||
}
|
||||
|
@ -41,7 +41,7 @@ clipboard_export(x, sep = "\\t", dec = ".", na = "", header = TRUE,
|
||||
data.frame
|
||||
}
|
||||
\description{
|
||||
These are helper functions around \code{\link{read.table}} and \code{\link{write.table}} to import from and export to clipboard. 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.
|
||||
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.
|
||||
}
|
||||
\details{
|
||||
For \code{clipboard_export}, the reserved clipboard size for exporting will be set automatically to 125\% of the object size of \code{x}. This way, it is possible to export data with thousands of rows as the only limit will be your systems RAM.
|
||||
|
@ -14,17 +14,17 @@ first_isolate(tbl, col_date, col_patient_id, col_bactid = NA,
|
||||
\arguments{
|
||||
\item{tbl}{a \code{data.frame} containing isolates.}
|
||||
|
||||
\item{col_date}{column name of the result date (or date that is was received on the lab), supports tidyverse-like quotation}
|
||||
\item{col_date}{column name of the result date (or date that is was received on the lab)}
|
||||
|
||||
\item{col_patient_id}{column name of the unique IDs of the patients, supports tidyverse-like quotation}
|
||||
\item{col_patient_id}{column name of the unique IDs of the patients}
|
||||
|
||||
\item{col_bactid}{column name of the unique IDs of the microorganisms (should occur in the \code{\link{microorganisms}} dataset), supports tidyverse-like quotation}
|
||||
\item{col_bactid}{column name of the unique IDs of the microorganisms (should occur in the \code{\link{microorganisms}} dataset)}
|
||||
|
||||
\item{col_testcode}{column name of the test codes. Use \code{col_testcode = NA} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored. Supports tidyverse-like quotation.}
|
||||
|
||||
\item{col_specimen}{column name of the specimen type or group, supports tidyverse-like quotation}
|
||||
\item{col_specimen}{column name of the specimen type or group}
|
||||
|
||||
\item{col_icu}{column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU), supports tidyverse-like quotation}
|
||||
\item{col_icu}{column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU)}
|
||||
|
||||
\item{col_keyantibiotics}{column name of the key antibiotics to determine first \emph{weighted} isolates, see \code{\link{key_antibiotics}}. Supports tidyverse-like quotation.}
|
||||
|
||||
@ -46,9 +46,9 @@ first_isolate(tbl, col_date, col_patient_id, col_bactid = NA,
|
||||
|
||||
\item{info}{print progress}
|
||||
|
||||
\item{col_genus}{(deprecated, use \code{col_bactid} instead) column name of the genus of the microorganisms, supports tidyverse-like quotation}
|
||||
\item{col_genus}{(deprecated, use \code{col_bactid} instead) column name of the genus of the microorganisms}
|
||||
|
||||
\item{col_species}{(deprecated, use \code{col_bactid} instead) column name of the species of the microorganisms, supports tidyverse-like quotation}
|
||||
\item{col_species}{(deprecated, use \code{col_bactid} instead) column name of the species of the microorganisms}
|
||||
}
|
||||
\value{
|
||||
A vector to add to table, see Examples.
|
||||
@ -73,11 +73,9 @@ my_patients <- septic_patients
|
||||
|
||||
library(dplyr)
|
||||
my_patients$first_isolate <- my_patients \%>\%
|
||||
left_join_microorganisms() \%>\%
|
||||
first_isolate(col_date = date,
|
||||
col_patient_id = patient_id,
|
||||
col_genus = genus,
|
||||
col_species = species)
|
||||
first_isolate(col_date = "date",
|
||||
col_patient_id = "patient_id",
|
||||
col_bactid = "bactid")
|
||||
|
||||
\dontrun{
|
||||
|
||||
|
@ -39,7 +39,7 @@ library(dplyr)
|
||||
|
||||
# Add first isolates to our dataset:
|
||||
my_data <- my_data \%>\%
|
||||
mutate(first_isolates = first_isolate(my_data, date, patient_id, bactid))
|
||||
mutate(first_isolates = first_isolate(my_data, "date", "patient_id", "bactid"))
|
||||
|
||||
# -------- #
|
||||
# ANALYSIS #
|
||||
|
Binary file not shown.
@ -1,9 +1,9 @@
|
||||
context("clipboard.R")
|
||||
|
||||
test_that("clipboard works", {
|
||||
skip_on_os(c("linux", "solaris"))
|
||||
t1 <<- AMR::antibiotics # why is the <<- needed? Won't work without it...
|
||||
clipboard_export(t1, info = FALSE)
|
||||
t2 <- clipboard_import()
|
||||
skip_if(is.null(t1) | is.null(t2), message = "No clipboard content found: skipping.")
|
||||
expect_equal(t1, t2)
|
||||
})
|
||||
|
Loading…
Reference in New Issue
Block a user