Paketmanagement mit packcrat.
This commit is contained in:
parent
00670d9dc1
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3
.Rprofile
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3
.Rprofile
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#### -- Packrat Autoloader (version 0.5.0) -- ####
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source("packrat/init.R")
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#### -- End Packrat Autoloader -- ####
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2
.gitignore
vendored
2
.gitignore
vendored
@ -7,3 +7,5 @@
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*.pptx
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*-figure/
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*-files/
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packrat/lib*/
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packrat/src/
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18
README.md
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18
README.md
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Vorhofkatheter-Statistik
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========================
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Statistische Auswertung der Vorhofkatheter-Datenbank.
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Man benötigt:
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* [R](https://www.r-project.org)
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* [packrat](http://rstudio.github.io/packrat/)
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Die Datei `vhk.csv` wird von der Abfrage `qryExportToCsv` generiert.
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Es gibt kein traditionelles R-Skript, sondern eine R-Markdown-Datei,
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die den Code zum Erzeugen der Abbildungen enthält. Als Präsentationsformat
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eignen sich HTML mit Slidy und PDF am besten. HTML mit ioslides kann vom
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in der Klinik immer noch installierten Internet Explorer nicht dargestellt
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werden, und der PowerPoint-Export klappt auch nicht so gut (Stand 1/2019).
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@ -14,3 +14,5 @@ LaTeX: pdfLaTeX
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AutoAppendNewline: Yes
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StripTrailingWhitespace: Yes
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BuildType: Makefile
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226
packrat/init.R
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226
packrat/init.R
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local({
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## Helper function to get the path to the library directory for a
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## given packrat project.
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getPackratLibDir <- function(projDir = NULL) {
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path <- file.path("packrat", "lib", R.version$platform, getRversion())
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if (!is.null(projDir)) {
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## Strip trailing slashes if necessary
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projDir <- sub("/+$", "", projDir)
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## Only prepend path if different from current working dir
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if (!identical(normalizePath(projDir), normalizePath(getwd())))
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path <- file.path(projDir, path)
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}
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path
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}
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## Ensure that we set the packrat library directory relative to the
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## project directory. Normally, this should be the working directory,
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## but we also use '.rs.getProjectDirectory()' if necessary (e.g. we're
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## rebuilding a project while within a separate directory)
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libDir <- if (exists(".rs.getProjectDirectory"))
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getPackratLibDir(.rs.getProjectDirectory())
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else
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getPackratLibDir()
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## Unload packrat in case it's loaded -- this ensures packrat _must_ be
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## loaded from the private library. Note that `requireNamespace` will
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## succeed if the package is already loaded, regardless of lib.loc!
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if ("packrat" %in% loadedNamespaces())
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try(unloadNamespace("packrat"), silent = TRUE)
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if (suppressWarnings(requireNamespace("packrat", quietly = TRUE, lib.loc = libDir))) {
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# Check 'print.banner.on.startup' -- when NA and RStudio, don't print
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print.banner <- packrat::get_opts("print.banner.on.startup")
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if (print.banner == "auto" && is.na(Sys.getenv("RSTUDIO", unset = NA))) {
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print.banner <- TRUE
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} else {
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print.banner <- FALSE
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}
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return(packrat::on(print.banner = print.banner))
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}
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## Escape hatch to allow RStudio to handle bootstrapping. This
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## enables RStudio to provide print output when automagically
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## restoring a project from a bundle on load.
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if (!is.na(Sys.getenv("RSTUDIO", unset = NA)) &&
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is.na(Sys.getenv("RSTUDIO_PACKRAT_BOOTSTRAP", unset = NA))) {
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Sys.setenv("RSTUDIO_PACKRAT_BOOTSTRAP" = "1")
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setHook("rstudio.sessionInit", function(...) {
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# Ensure that, on sourcing 'packrat/init.R', we are
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# within the project root directory
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if (exists(".rs.getProjectDirectory")) {
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owd <- getwd()
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setwd(.rs.getProjectDirectory())
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on.exit(setwd(owd), add = TRUE)
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}
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source("packrat/init.R")
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})
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return(invisible(NULL))
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}
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## Bootstrapping -- only performed in interactive contexts,
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## or when explicitly asked for on the command line
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if (interactive() || "--bootstrap-packrat" %in% commandArgs(TRUE)) {
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needsRestore <- "--bootstrap-packrat" %in% commandArgs(TRUE)
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message("Packrat is not installed in the local library -- ",
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"attempting to bootstrap an installation...")
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## We need utils for the following to succeed -- there are calls to functions
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## in 'restore' that are contained within utils. utils gets loaded at the
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## end of start-up anyhow, so this should be fine
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library("utils", character.only = TRUE)
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## Install packrat into local project library
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packratSrcPath <- list.files(full.names = TRUE,
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file.path("packrat", "src", "packrat")
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)
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## No packrat tarballs available locally -- try some other means of installation
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if (!length(packratSrcPath)) {
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message("> No source tarball of packrat available locally")
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## There are no packrat sources available -- try using a version of
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## packrat installed in the user library to bootstrap
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if (requireNamespace("packrat", quietly = TRUE) && packageVersion("packrat") >= "0.2.0.99") {
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message("> Using user-library packrat (",
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packageVersion("packrat"),
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") to bootstrap this project")
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}
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## Couldn't find a user-local packrat -- try finding and using devtools
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## to install
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else if (requireNamespace("devtools", quietly = TRUE)) {
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message("> Attempting to use devtools::install_github to install ",
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"a temporary version of packrat")
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library(stats) ## for setNames
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devtools::install_github("rstudio/packrat")
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}
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## Try downloading packrat from CRAN if available
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else if ("packrat" %in% rownames(available.packages())) {
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message("> Installing packrat from CRAN")
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install.packages("packrat")
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}
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## Fail -- couldn't find an appropriate means of installing packrat
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else {
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stop("Could not automatically bootstrap packrat -- try running ",
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"\"'install.packages('devtools'); devtools::install_github('rstudio/packrat')\"",
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"and restarting R to bootstrap packrat.")
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}
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# Restore the project, unload the temporary packrat, and load the private packrat
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if (needsRestore)
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packrat::restore(prompt = FALSE, restart = TRUE)
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## This code path only reached if we didn't restart earlier
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unloadNamespace("packrat")
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requireNamespace("packrat", lib.loc = libDir, quietly = TRUE)
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return(packrat::on())
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}
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## Multiple packrat tarballs available locally -- try to choose one
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## TODO: read lock file and infer most appropriate from there; low priority because
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## after bootstrapping packrat a restore should do the right thing
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if (length(packratSrcPath) > 1) {
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warning("Multiple versions of packrat available in the source directory;",
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"using packrat source:\n- ", shQuote(packratSrcPath))
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packratSrcPath <- packratSrcPath[[1]]
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}
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lib <- file.path("packrat", "lib", R.version$platform, getRversion())
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if (!file.exists(lib)) {
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dir.create(lib, recursive = TRUE)
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}
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message("> Installing packrat into project private library:")
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message("- ", shQuote(lib))
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surround <- function(x, with) {
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if (!length(x)) return(character())
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paste0(with, x, with)
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}
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## Invoke install.packages() in clean R session
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peq <- function(x, y) paste(x, y, sep = " = ")
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installArgs <- c(
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peq("pkgs", surround(packratSrcPath, with = "'")),
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peq("lib", surround(lib, with = "'")),
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peq("repos", "NULL"),
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peq("type", surround("source", with = "'"))
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)
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fmt <- "utils::install.packages(%s)"
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installCmd <- sprintf(fmt, paste(installArgs, collapse = ", "))
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## Write script to file (avoid issues with command line quoting
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## on R 3.4.3)
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installFile <- tempfile("packrat-bootstrap", fileext = ".R")
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writeLines(installCmd, con = installFile)
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on.exit(unlink(installFile), add = TRUE)
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fullCmd <- paste(
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surround(file.path(R.home("bin"), "R"), with = "\""),
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"--vanilla",
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"--slave",
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"-f",
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surround(installFile, with = "\"")
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)
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system(fullCmd)
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## Tag the installed packrat so we know it's managed by packrat
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## TODO: should this be taking information from the lockfile? this is a bit awkward
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## because we're taking an un-annotated packrat source tarball and simply assuming it's now
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## an 'installed from source' version
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## -- InstallAgent -- ##
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installAgent <- "InstallAgent: packrat 0.5.0"
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## -- InstallSource -- ##
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installSource <- "InstallSource: source"
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packratDescPath <- file.path(lib, "packrat", "DESCRIPTION")
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DESCRIPTION <- readLines(packratDescPath)
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DESCRIPTION <- c(DESCRIPTION, installAgent, installSource)
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cat(DESCRIPTION, file = packratDescPath, sep = "\n")
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# Otherwise, continue on as normal
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message("> Attaching packrat")
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library("packrat", character.only = TRUE, lib.loc = lib)
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message("> Restoring library")
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if (needsRestore)
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packrat::restore(prompt = FALSE, restart = FALSE)
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# If the environment allows us to restart, do so with a call to restore
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restart <- getOption("restart")
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if (!is.null(restart)) {
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message("> Packrat bootstrap successfully completed. ",
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"Restarting R and entering packrat mode...")
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return(restart())
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}
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# Callers (source-erers) can define this hidden variable to make sure we don't enter packrat mode
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# Primarily useful for testing
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if (!exists(".__DONT_ENTER_PACKRAT_MODE__.") && interactive()) {
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message("> Packrat bootstrap successfully completed. Entering packrat mode...")
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packrat::on()
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}
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Sys.unsetenv("RSTUDIO_PACKRAT_BOOTSTRAP")
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}
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})
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453
packrat/packrat.lock
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453
packrat/packrat.lock
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@ -0,0 +1,453 @@
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PackratFormat: 1.4
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PackratVersion: 0.5.0
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RVersion: 3.5.2
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Repos: CRAN=https://cloud.r-project.org
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Package: BH
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Source: CRAN
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Version: 1.66.0-1
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Hash: 4cc8883584b955ed01f38f68bc03af6d
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Package: DBI
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Source: CRAN
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Version: 1.0.0
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Hash: 6abedd7919c4457604c0aa44529a6683
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Package: R6
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Source: CRAN
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Version: 2.3.0
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Hash: 8eccabbf292b5aba632985cde6406fc3
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Package: RColorBrewer
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Source: CRAN
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Version: 1.1-2
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Hash: c0d56cd15034f395874c870141870c25
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Package: Rcpp
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Source: CRAN
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Version: 1.0.0
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Hash: c7273c0f0bc9f5e41f4c52a8cf571f0f
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Package: assertthat
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Source: CRAN
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Version: 0.2.0
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Hash: e8805df54c65ac96d50235c44a82615c
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Package: backports
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Source: CRAN
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Version: 1.1.3
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Hash: a0b8191e6bd2fe71aadd4678bb8f3c98
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Package: base64enc
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Source: CRAN
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Version: 0.1-3
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Hash: c590d29e555926af053055e23ee79efb
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Package: bindr
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Source: CRAN
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Version: 0.1.1
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Hash: 76578c5f543a6ecbc1365d6445f9ebf7
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Package: bindrcpp
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Source: CRAN
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Version: 0.2.2
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Hash: 8ce499301f0dc5c7ff69f0b42e33f5c1
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Requires: Rcpp, bindr, plogr
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Package: broom
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Source: CRAN
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Version: 0.5.1
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Hash: f170bc989c523e039487511e87c1854f
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Requires: backports, dplyr, generics, purrr, reshape2, stringr, tibble,
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tidyr
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Package: callr
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Source: CRAN
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Version: 3.1.1
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Hash: 461cdebafe2c1cfc23ddc37527633185
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Requires: R6, processx
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Package: cellranger
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Source: CRAN
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Version: 1.1.0
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Hash: be9d203e7849f73818b36f93e9273c2c
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Requires: rematch, tibble
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Package: cli
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Source: CRAN
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Version: 1.0.1
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Hash: a742a3229dbf7085c3a737af10e5065b
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Requires: assertthat, crayon
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Package: clipr
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Source: CRAN
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Version: 0.4.1
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Hash: caf20ae357bfa2ed50e0e7db267f69ce
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Package: colorspace
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Source: CRAN
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Version: 1.3-2
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Hash: 0bf8618b585fa98eb23414cd3ab95118
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Package: crayon
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Source: CRAN
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Version: 1.3.4
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Hash: ff2840dd9b0d563fc80377a5a45510cd
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Package: curl
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Source: CRAN
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Version: 3.2
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Hash: 82a7cf5bb702ef52329b6d23ea6132a7
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Package: dbplyr
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Source: CRAN
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Version: 1.2.2
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Hash: f09ea2f1a5c31d86b061d7121fab5db8
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Requires: DBI, R6, assertthat, dplyr, glue, purrr, rlang, tibble,
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tidyselect
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Package: digest
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Source: CRAN
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Version: 0.6.18
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Hash: 65f62365ec69ddd17230d2ffe891a6ab
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Package: dplyr
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Source: CRAN
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Version: 0.7.8
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Hash: d6e576944199cba782a471015a822848
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Requires: BH, R6, Rcpp, assertthat, bindrcpp, glue, magrittr,
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pkgconfig, plogr, rlang, tibble, tidyselect
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Package: evaluate
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Source: CRAN
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Version: 0.12
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Hash: c32505adba4f6eca5aa20dd32300b019
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Package: fansi
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Source: CRAN
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Version: 0.4.0
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Hash: f147621f72b561485bfffcae78c4f5d5
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Package: forcats
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Source: CRAN
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Version: 0.3.0
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Hash: 770f3834b97a2c429bdecb7a5f27eb25
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Requires: magrittr, rlang, tibble
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Package: fs
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Source: CRAN
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Version: 1.2.6
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Hash: 8ffb8b293a18e26e435465307cc47f75
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Requires: Rcpp
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Package: generics
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Source: CRAN
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||||
Version: 0.0.2
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Hash: 4aaf002dd434e8c854611c5d11a1d58e
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Package: ggplot2
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Source: CRAN
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Version: 3.1.0
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Hash: ef541b05dda10b209d509b5bbaf46ea3
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Requires: digest, gtable, lazyeval, plyr, reshape2, rlang, scales,
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tibble, viridisLite, withr
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Package: glue
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Source: CRAN
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Version: 1.3.0
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Hash: 1fbde6dec830370be696eee8ef31c9e4
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Package: gtable
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Source: CRAN
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Version: 0.2.0
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Hash: cd78381a9d3fea966ac39bd0daaf5554
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Package: haven
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Source: CRAN
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Version: 2.0.0
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||||
Hash: 3180a95083d9ef6da3fafc38e0519e2f
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Requires: Rcpp, forcats, hms, readr, tibble
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Package: highr
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Source: CRAN
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Version: 0.7
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||||
Hash: 20757f5c393ed0ecf96c9e8e6d8d514c
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Package: hms
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||||
Source: CRAN
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||||
Version: 0.4.2
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||||
Hash: b4096a4f6a6736138e9a825c2baaacf0
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||||
Requires: pkgconfig, rlang
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|
||||
Package: htmltools
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||||
Source: CRAN
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||||
Version: 0.3.6
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||||
Hash: 9707abea0a9b7406e98fb1242e97e1f6
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||||
Requires: Rcpp, digest
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||||
|
||||
Package: httr
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||||
Source: CRAN
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||||
Version: 1.4.0
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||||
Hash: 62d62d3ffcc9a34411b6e35a813f72dd
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||||
Requires: R6, curl, jsonlite, mime, openssl
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||||
|
||||
Package: jsonlite
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||||
Source: CRAN
|
||||
Version: 1.6
|
||||
Hash: 5f969e213e966135393e3e304abf3f49
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|
||||
Package: knitr
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||||
Source: CRAN
|
||||
Version: 1.21
|
||||
Hash: 05d92a30fe7f149fef5e82428cbbe0d7
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||||
Requires: evaluate, highr, markdown, stringr, xfun, yaml
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|
||||
Package: labeling
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||||
Source: CRAN
|
||||
Version: 0.3
|
||||
Hash: ecf589b42cd284b03a4beb9665482d3e
|
||||
|
||||
Package: lazyeval
|
||||
Source: CRAN
|
||||
Version: 0.2.1
|
||||
Hash: 88926ad9c43581fd0822a37c8ed09f05
|
||||
|
||||
Package: lubridate
|
||||
Source: CRAN
|
||||
Version: 1.7.4
|
||||
Hash: a7c783782f0e50be33b31f859c11333e
|
||||
Requires: Rcpp, stringr
|
||||
|
||||
Package: magrittr
|
||||
Source: CRAN
|
||||
Version: 1.5
|
||||
Hash: bdc4d48c3135e8f3b399536ddf160df4
|
||||
|
||||
Package: markdown
|
||||
Source: CRAN
|
||||
Version: 0.9
|
||||
Hash: 730f688930cef3223d59bd8aef679ab9
|
||||
Requires: mime
|
||||
|
||||
Package: mime
|
||||
Source: CRAN
|
||||
Version: 0.6
|
||||
Hash: 2ed8f98b8284ad733f3907fc6e2f1334
|
||||
|
||||
Package: modelr
|
||||
Source: CRAN
|
||||
Version: 0.1.2
|
||||
Hash: f691854a99ac7814f3853d499408d9a3
|
||||
Requires: broom, dplyr, magrittr, purrr, rlang, tibble, tidyr
|
||||
|
||||
Package: munsell
|
||||
Source: CRAN
|
||||
Version: 0.5.0
|
||||
Hash: 38d0efee9bb99bef143bde41c4ce715c
|
||||
Requires: colorspace
|
||||
|
||||
Package: openssl
|
||||
Source: CRAN
|
||||
Version: 1.1
|
||||
Hash: 82c893294829c4badc3d4133b66d1428
|
||||
|
||||
Package: packrat
|
||||
Source: CRAN
|
||||
Version: 0.5.0
|
||||
Hash: 498643e765d1442ba7b1160a1df3abf9
|
||||
|
||||
Package: pillar
|
||||
Source: CRAN
|
||||
Version: 1.3.1
|
||||
Hash: 9ed4c2a5d3047bfba3e852ad5e806d91
|
||||
Requires: cli, crayon, fansi, rlang, utf8
|
||||
|
||||
Package: pkgconfig
|
||||
Source: CRAN
|
||||
Version: 2.0.2
|
||||
Hash: b0fd6ed908e150b77e5f00c6478bd58c
|
||||
|
||||
Package: plogr
|
||||
Source: CRAN
|
||||
Version: 0.2.0
|
||||
Hash: 81a8008a5e7858552503935f1abe48aa
|
||||
|
||||
Package: plyr
|
||||
Source: CRAN
|
||||
Version: 1.8.4
|
||||
Hash: ec185c885aab7ec91693d78c20cb5d1a
|
||||
Requires: Rcpp
|
||||
|
||||
Package: prettyunits
|
||||
Source: CRAN
|
||||
Version: 1.0.2
|
||||
Hash: 49286102a855640daaa38eafe8b1ec30
|
||||
Requires: assertthat, magrittr
|
||||
|
||||
Package: processx
|
||||
Source: CRAN
|
||||
Version: 3.2.1
|
||||
Hash: fdc6a66626b75f96ee28ffc770d9ebd7
|
||||
Requires: R6, ps
|
||||
|
||||
Package: progress
|
||||
Source: CRAN
|
||||
Version: 1.2.0
|
||||
Hash: 0ff5f631b66daf57857f28062f3e6f30
|
||||
Requires: R6, crayon, hms, prettyunits
|
||||
|
||||
Package: ps
|
||||
Source: CRAN
|
||||
Version: 1.3.0
|
||||
Hash: 1d4cae95887ffe5b1a22bea5994476cd
|
||||
|
||||
Package: purrr
|
||||
Source: CRAN
|
||||
Version: 0.2.5
|
||||
Hash: 8b0c16db10c7e20b70cd37779a673a8b
|
||||
Requires: magrittr, rlang, tibble
|
||||
|
||||
Package: readr
|
||||
Source: CRAN
|
||||
Version: 1.3.1
|
||||
Hash: ed1b5520a0df4007bc971658ee543b00
|
||||
Requires: BH, R6, Rcpp, clipr, crayon, hms, tibble
|
||||
|
||||
Package: readxl
|
||||
Source: CRAN
|
||||
Version: 1.2.0
|
||||
Hash: 3d49de1375021e909463ce4bdb613327
|
||||
Requires: Rcpp, cellranger, progress, tibble
|
||||
|
||||
Package: rematch
|
||||
Source: CRAN
|
||||
Version: 1.0.1
|
||||
Hash: ad4faf59e7611117ff165817074c50c7
|
||||
|
||||
Package: reprex
|
||||
Source: CRAN
|
||||
Version: 0.2.1
|
||||
Hash: b30c7fbcb528a71d7ffcd07c9982589d
|
||||
Requires: callr, clipr, fs, rlang, rmarkdown, whisker, withr
|
||||
|
||||
Package: reshape2
|
||||
Source: CRAN
|
||||
Version: 1.4.3
|
||||
Hash: c950c8ac85b81209635acb3ce21b4cce
|
||||
Requires: Rcpp, plyr, stringr
|
||||
|
||||
Package: rlang
|
||||
Source: CRAN
|
||||
Version: 0.3.0.1
|
||||
Hash: 35fb7a51d5d756c56f793ed9c381fb84
|
||||
|
||||
Package: rmarkdown
|
||||
Source: CRAN
|
||||
Version: 1.11
|
||||
Hash: a30b0c41b60d981f41dc8c98f2136297
|
||||
Requires: base64enc, evaluate, htmltools, jsonlite, knitr, mime,
|
||||
stringr, tinytex, yaml
|
||||
|
||||
Package: rstudioapi
|
||||
Source: CRAN
|
||||
Version: 0.8
|
||||
Hash: 9ba7fe76dcaf96966c449527ca04bb78
|
||||
|
||||
Package: rvest
|
||||
Source: CRAN
|
||||
Version: 0.3.2
|
||||
Hash: c69f7526520bad66fd2111ebe8b1364b
|
||||
Requires: httr, magrittr, selectr, xml2
|
||||
|
||||
Package: scales
|
||||
Source: CRAN
|
||||
Version: 1.0.0
|
||||
Hash: 7d9b717abcec656ae7c5c982d72b75e5
|
||||
Requires: R6, RColorBrewer, Rcpp, labeling, munsell, viridisLite
|
||||
|
||||
Package: selectr
|
||||
Source: CRAN
|
||||
Version: 0.4-1
|
||||
Hash: b12802c11e35dec9d16a74d30ed0f3ed
|
||||
Requires: R6, stringr
|
||||
|
||||
Package: stringi
|
||||
Source: CRAN
|
||||
Version: 1.2.4
|
||||
Hash: 03ab60ef7fa4627b38ad67c95ce6b04c
|
||||
|
||||
Package: stringr
|
||||
Source: CRAN
|
||||
Version: 1.3.1
|
||||
Hash: 9f417a1d899ed1f080942ab36998e8b5
|
||||
Requires: glue, magrittr, stringi
|
||||
|
||||
Package: tibble
|
||||
Source: CRAN
|
||||
Version: 1.4.2
|
||||
Hash: 83895360ce4f8d2ce92eee00526b5b0b
|
||||
Requires: cli, crayon, pillar, rlang
|
||||
|
||||
Package: tidyr
|
||||
Source: CRAN
|
||||
Version: 0.8.2
|
||||
Hash: 9ff92b9b3c11dfcd94d179b75b85c668
|
||||
Requires: Rcpp, dplyr, glue, magrittr, purrr, rlang, stringi, tibble,
|
||||
tidyselect
|
||||
|
||||
Package: tidyselect
|
||||
Source: CRAN
|
||||
Version: 0.2.5
|
||||
Hash: fad1cf10c5c4996fca6ca68e0716d2e6
|
||||
Requires: Rcpp, glue, purrr, rlang
|
||||
|
||||
Package: tidyverse
|
||||
Source: CRAN
|
||||
Version: 1.2.1
|
||||
Hash: 1b090209cb20b6fc6eba75de8b7f0b53
|
||||
Requires: broom, cli, crayon, dbplyr, dplyr, forcats, ggplot2, haven,
|
||||
hms, httr, jsonlite, lubridate, magrittr, modelr, purrr, readr,
|
||||
readxl, reprex, rlang, rstudioapi, rvest, stringr, tibble, tidyr,
|
||||
xml2
|
||||
|
||||
Package: tinytex
|
||||
Source: CRAN
|
||||
Version: 0.9
|
||||
Hash: a4ffe98c58eace5a95644d8fd6ca5a50
|
||||
Requires: xfun
|
||||
|
||||
Package: utf8
|
||||
Source: CRAN
|
||||
Version: 1.1.4
|
||||
Hash: f3f97ce59092abc8ed3fd098a59e236c
|
||||
|
||||
Package: viridisLite
|
||||
Source: CRAN
|
||||
Version: 0.3.0
|
||||
Hash: 78bb072c4f9e729a283d4c40ec93f9c6
|
||||
|
||||
Package: whisker
|
||||
Source: CRAN
|
||||
Version: 0.3-2
|
||||
Hash: 803d662762e532705c2c066a82d066e7
|
||||
|
||||
Package: withr
|
||||
Source: CRAN
|
||||
Version: 2.1.2
|
||||
Hash: d534108bcd5f34ec73e9eb523751ba20
|
||||
|
||||
Package: xfun
|
||||
Source: CRAN
|
||||
Version: 0.4
|
||||
Hash: 76004125b45195c0330ec71904849995
|
||||
|
||||
Package: xml2
|
||||
Source: CRAN
|
||||
Version: 1.2.0
|
||||
Hash: 3f00e5347a6d7ccad2237fe1bc1df6d0
|
||||
Requires: Rcpp
|
||||
|
||||
Package: yaml
|
||||
Source: CRAN
|
||||
Version: 2.2.0
|
||||
Hash: a5ad5616d83d89f8d84cbf3cf4034e13
|
||||
19
packrat/packrat.opts
Normal file
19
packrat/packrat.opts
Normal file
@ -0,0 +1,19 @@
|
||||
auto.snapshot: TRUE
|
||||
use.cache: TRUE
|
||||
print.banner.on.startup: auto
|
||||
vcs.ignore.lib: TRUE
|
||||
vcs.ignore.src: TRUE
|
||||
external.packages:
|
||||
local.repos:
|
||||
load.external.packages.on.startup: TRUE
|
||||
ignored.packages:
|
||||
ignored.directories:
|
||||
data
|
||||
inst
|
||||
quiet.package.installation: TRUE
|
||||
snapshot.recommended.packages: FALSE
|
||||
snapshot.fields:
|
||||
Imports
|
||||
Depends
|
||||
LinkingTo
|
||||
symlink.system.packages: TRUE
|
||||
40
vhk.Rmd
40
vhk.Rmd
@ -99,57 +99,49 @@ raw_data %>% mutate(Duration = RemovalDate - Date) %>%
|
||||
### Variante A: Absolute Zahlen
|
||||
```{r removal_reasons, message=FALSE}
|
||||
raw_data %>% filter(!is.na(RemovalDate), !is.na(RemovalReason)) %>%
|
||||
mutate(ExplYear = ExplYear %% 100) %>%
|
||||
group_by(ExplYear) %>%
|
||||
mutate(ImplYear = ImplYear %% 100) %>%
|
||||
group_by(ImplYear) %>%
|
||||
count(RemovalReason) %>%
|
||||
ggplot(aes(x = ExplYear, y = n)) +
|
||||
ggplot(aes(x = ImplYear, y = n)) +
|
||||
geom_point() + geom_line() +
|
||||
scale_x_continuous(breaks = scales::pretty_breaks()) +
|
||||
scale_y_continuous(breaks = scales::pretty_breaks()) +
|
||||
facet_wrap(vars(RemovalReason)) +
|
||||
labs(x = NULL, y = "Anzahl entfernter Katheter")
|
||||
labs(x = "Implantationsjahr", y = "Anzahl entfernter Katheter")
|
||||
```
|
||||
|
||||
### Variante B: auf die Zahl der in dem Jahr gelegten Katheter bezogen
|
||||
```{r removal_reasons_normalized, message=FALSE}
|
||||
# Zur Berechnung dieses Index muß man zunächst für jeden explantierten Katheter
|
||||
# berechnen, wie viele Katheter im *ex*plantationsjahr *im*plantiert wurden.
|
||||
impl_per_year = raw_data %>% mutate(ImplYear = year(Date)) %>% count(ImplYear)
|
||||
|
||||
raw_data %>%
|
||||
select(ImplYear, ExplYear, RemovalDate, RemovalReason) %>%
|
||||
select(ImplYear, RemovalDate, RemovalReason) %>%
|
||||
mutate(ImplYear = ImplYear %% 100) %>%
|
||||
left_join(impl_per_year, by = c("ExplYear" = "ImplYear")) %>% # creates column "n"
|
||||
filter(!is.na(RemovalDate), !is.na(RemovalReason)) %>%
|
||||
group_by(ExplYear) %>%
|
||||
add_count(RemovalReason) %>% # creates column "nn"
|
||||
ungroup() %>%
|
||||
select(ExplYear, RemovalReason, n, nn) %>%
|
||||
group_by(ImplYear) %>%
|
||||
add_count(ImplYear) %>%
|
||||
add_count(RemovalReason) %>%
|
||||
mutate(i = nn/n) %>%
|
||||
group_by(ExplYear, RemovalReason) %>%
|
||||
# summarize(i = sum(i)) %>%
|
||||
distinct() %>%
|
||||
ggplot(aes(x = ExplYear, y = i)) +
|
||||
filter(!is.na(RemovalDate), !is.na(RemovalReason)) %>%
|
||||
ggplot(aes(x = ImplYear, y = i)) +
|
||||
geom_point() + geom_line() +
|
||||
scale_x_continuous(breaks = scales::pretty_breaks()) +
|
||||
scale_y_continuous(breaks = scales::pretty_breaks()) +
|
||||
facet_wrap(vars(RemovalReason)) +
|
||||
labs(x = NULL, y = "Anzahl entfernter Katheter / gelegter Katheter")
|
||||
labs(x = "Implantationsjahr", y = "Anzahl entfernter Katheter / gelegter Katheter")
|
||||
```
|
||||
|
||||
## Wann treten Infektionen auf?
|
||||
```{r infections, message=FALSE}
|
||||
raw_data %>% filter(!is.na(RemovalDate), RemovalReason == "Infektion") %>%
|
||||
mutate(Duration = RemovalDate - Date, Month = as.integer(Duration) %/% 30) %>%
|
||||
ggplot(aes(x = Month)) +
|
||||
mutate(Duration = RemovalDate - Date, Week = as.integer(Duration) %/% 7 + 1) %>%
|
||||
filter(Week <= 56) %>%
|
||||
ggplot(aes(x = Week)) +
|
||||
geom_bar(width = 0.9) +
|
||||
# raw_data %>% filter(!is.na(RemovalDate), RemovalReason == "Infektion") %>%
|
||||
coord_cartesian(xlim = c(0, 56)) +
|
||||
scale_x_continuous(breaks = seq(from = 0, to = 56, by = 4)) +
|
||||
scale_y_continuous(breaks = seq(from = 0, to = 10, by = 1)) +
|
||||
facet_grid(rows = vars(ImplYear)) +
|
||||
labs(x = "Woche nach Implantation", y = "Anzahl wg. Infektion entfernter Katheter",
|
||||
title = "Liegedauer infizierter Katheter nach Implantationsjahr")
|
||||
title = "Liegedauer infizierter Katheter nach Implantationsjahr",
|
||||
subtitle = "Die Graphik berücksichtigt nur Infektionen im ersten Jahr")
|
||||
```
|
||||
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user