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Paketmanagement mit packcrat.

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daniel 4 years ago
parent 00670d9dc1
commit f2ae692432
8 changed files with 739 additions and 24 deletions
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  1. 3
      .Rprofile
  2. 2
      .gitignore
  3. 18
      README.md
  4. 2
      VHK.Rproj
  5. 226
      packrat/init.R
  6. 453
      packrat/packrat.lock
  7. 19
      packrat/packrat.opts
  8. 40
      vhk.Rmd

3
.Rprofile
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#### -- Packrat Autoloader (version 0.5.0) -- ####
source("packrat/init.R")
#### -- End Packrat Autoloader -- ####

2
.gitignore vendored
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*.pptx
*-figure/
*-files/
packrat/lib*/
packrat/src/

18
README.md
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Vorhofkatheter-Statistik
========================
Statistische Auswertung der Vorhofkatheter-Datenbank.
Man benötigt:
* [R](https://www.r-project.org)
* [packrat](http://rstudio.github.io/packrat/)
Die Datei `vhk.csv` wird von der Abfrage `qryExportToCsv` generiert.
Es gibt kein traditionelles R-Skript, sondern eine R-Markdown-Datei,
die den Code zum Erzeugen der Abbildungen enthält. Als Präsentationsformat
eignen sich HTML mit Slidy und PDF am besten. HTML mit ioslides kann vom
in der Klinik immer noch installierten Internet Explorer nicht dargestellt
werden, und der PowerPoint-Export klappt auch nicht so gut (Stand 1/2019).

2
VHK.Rproj
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@ -14,3 +14,5 @@ LaTeX: pdfLaTeX
AutoAppendNewline: Yes
StripTrailingWhitespace: Yes
BuildType: Makefile

226
packrat/init.R
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local({
## Helper function to get the path to the library directory for a
## given packrat project.
getPackratLibDir <- function(projDir = NULL) {
path <- file.path("packrat", "lib", R.version$platform, getRversion())
if (!is.null(projDir)) {
## Strip trailing slashes if necessary
projDir <- sub("/+$", "", projDir)
## Only prepend path if different from current working dir
if (!identical(normalizePath(projDir), normalizePath(getwd())))
path <- file.path(projDir, path)
}
path
}
## Ensure that we set the packrat library directory relative to the
## project directory. Normally, this should be the working directory,
## but we also use '.rs.getProjectDirectory()' if necessary (e.g. we're
## rebuilding a project while within a separate directory)
libDir <- if (exists(".rs.getProjectDirectory"))
getPackratLibDir(.rs.getProjectDirectory())
else
getPackratLibDir()
## Unload packrat in case it's loaded -- this ensures packrat _must_ be
## loaded from the private library. Note that `requireNamespace` will
## succeed if the package is already loaded, regardless of lib.loc!
if ("packrat" %in% loadedNamespaces())
try(unloadNamespace("packrat"), silent = TRUE)
if (suppressWarnings(requireNamespace("packrat", quietly = TRUE, lib.loc = libDir))) {
# Check 'print.banner.on.startup' -- when NA and RStudio, don't print
print.banner <- packrat::get_opts("print.banner.on.startup")
if (print.banner == "auto" && is.na(Sys.getenv("RSTUDIO", unset = NA))) {
print.banner <- TRUE
} else {
print.banner <- FALSE
}
return(packrat::on(print.banner = print.banner))
}
## Escape hatch to allow RStudio to handle bootstrapping. This
## enables RStudio to provide print output when automagically
## restoring a project from a bundle on load.
if (!is.na(Sys.getenv("RSTUDIO", unset = NA)) &&
is.na(Sys.getenv("RSTUDIO_PACKRAT_BOOTSTRAP", unset = NA))) {
Sys.setenv("RSTUDIO_PACKRAT_BOOTSTRAP" = "1")
setHook("rstudio.sessionInit", function(...) {
# Ensure that, on sourcing 'packrat/init.R', we are
# within the project root directory
if (exists(".rs.getProjectDirectory")) {
owd <- getwd()
setwd(.rs.getProjectDirectory())
on.exit(setwd(owd), add = TRUE)
}
source("packrat/init.R")
})
return(invisible(NULL))
}
## Bootstrapping -- only performed in interactive contexts,
## or when explicitly asked for on the command line
if (interactive() || "--bootstrap-packrat" %in% commandArgs(TRUE)) {
needsRestore <- "--bootstrap-packrat" %in% commandArgs(TRUE)
message("Packrat is not installed in the local library -- ",
"attempting to bootstrap an installation...")
## We need utils for the following to succeed -- there are calls to functions
## in 'restore' that are contained within utils. utils gets loaded at the
## end of start-up anyhow, so this should be fine
library("utils", character.only = TRUE)
## Install packrat into local project library
packratSrcPath <- list.files(full.names = TRUE,
file.path("packrat", "src", "packrat")
)
## No packrat tarballs available locally -- try some other means of installation
if (!length(packratSrcPath)) {
message("> No source tarball of packrat available locally")
## There are no packrat sources available -- try using a version of
## packrat installed in the user library to bootstrap
if (requireNamespace("packrat", quietly = TRUE) && packageVersion("packrat") >= "0.2.0.99") {
message("> Using user-library packrat (",
packageVersion("packrat"),
") to bootstrap this project")
}
## Couldn't find a user-local packrat -- try finding and using devtools
## to install
else if (requireNamespace("devtools", quietly = TRUE)) {
message("> Attempting to use devtools::install_github to install ",
"a temporary version of packrat")
library(stats) ## for setNames
devtools::install_github("rstudio/packrat")
}
## Try downloading packrat from CRAN if available
else if ("packrat" %in% rownames(available.packages())) {
message("> Installing packrat from CRAN")
install.packages("packrat")
}
## Fail -- couldn't find an appropriate means of installing packrat
else {
stop("Could not automatically bootstrap packrat -- try running ",
"\"'install.packages('devtools'); devtools::install_github('rstudio/packrat')\"",
"and restarting R to bootstrap packrat.")
}
# Restore the project, unload the temporary packrat, and load the private packrat
if (needsRestore)
packrat::restore(prompt = FALSE, restart = TRUE)
## This code path only reached if we didn't restart earlier
unloadNamespace("packrat")
requireNamespace("packrat", lib.loc = libDir, quietly = TRUE)
return(packrat::on())
}
## Multiple packrat tarballs available locally -- try to choose one
## TODO: read lock file and infer most appropriate from there; low priority because
## after bootstrapping packrat a restore should do the right thing
if (length(packratSrcPath) > 1) {
warning("Multiple versions of packrat available in the source directory;",
"using packrat source:\n- ", shQuote(packratSrcPath))
packratSrcPath <- packratSrcPath[[1]]
}
lib <- file.path("packrat", "lib", R.version$platform, getRversion())
if (!file.exists(lib)) {
dir.create(lib, recursive = TRUE)
}
message("> Installing packrat into project private library:")
message("- ", shQuote(lib))
surround <- function(x, with) {
if (!length(x)) return(character())
paste0(with, x, with)
}
## Invoke install.packages() in clean R session
peq <- function(x, y) paste(x, y, sep = " = ")
installArgs <- c(
peq("pkgs", surround(packratSrcPath, with = "'")),
peq("lib", surround(lib, with = "'")),
peq("repos", "NULL"),
peq("type", surround("source", with = "'"))
)
fmt <- "utils::install.packages(%s)"
installCmd <- sprintf(fmt, paste(installArgs, collapse = ", "))
## Write script to file (avoid issues with command line quoting
## on R 3.4.3)
installFile <- tempfile("packrat-bootstrap", fileext = ".R")
writeLines(installCmd, con = installFile)
on.exit(unlink(installFile), add = TRUE)
fullCmd <- paste(
surround(file.path(R.home("bin"), "R"), with = "\""),
"--vanilla",
"--slave",
"-f",
surround(installFile, with = "\"")
)
system(fullCmd)
## Tag the installed packrat so we know it's managed by packrat
## TODO: should this be taking information from the lockfile? this is a bit awkward
## because we're taking an un-annotated packrat source tarball and simply assuming it's now
## an 'installed from source' version
## -- InstallAgent -- ##
installAgent <- "InstallAgent: packrat 0.5.0"
## -- InstallSource -- ##
installSource <- "InstallSource: source"
packratDescPath <- file.path(lib, "packrat", "DESCRIPTION")
DESCRIPTION <- readLines(packratDescPath)
DESCRIPTION <- c(DESCRIPTION, installAgent, installSource)
cat(DESCRIPTION, file = packratDescPath, sep = "\n")
# Otherwise, continue on as normal
message("> Attaching packrat")
library("packrat", character.only = TRUE, lib.loc = lib)
message("> Restoring library")
if (needsRestore)
packrat::restore(prompt = FALSE, restart = FALSE)
# If the environment allows us to restart, do so with a call to restore
restart <- getOption("restart")
if (!is.null(restart)) {
message("> Packrat bootstrap successfully completed. ",
"Restarting R and entering packrat mode...")
return(restart())
}
# Callers (source-erers) can define this hidden variable to make sure we don't enter packrat mode
# Primarily useful for testing
if (!exists(".__DONT_ENTER_PACKRAT_MODE__.") && interactive()) {
message("> Packrat bootstrap successfully completed. Entering packrat mode...")
packrat::on()
}
Sys.unsetenv("RSTUDIO_PACKRAT_BOOTSTRAP")
}
})

453
packrat/packrat.lock
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PackratFormat: 1.4
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packrat/packrat.opts
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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
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@ -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")
```

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