%PROJECT% - %PACKAGE%'

In D4TAlink.light: GDP - Workflow Management

# ===================== HELPER CODE ==========================
if(FALSE) {
  library(D4TAlink.light)
  #library(D4TAlink)
  setTaskSponsor("%SPONSOR%")
  setTaskStructure(pathsDefault)
  try(setTaskRoot("%ROOT%"))

  # load the task
  task <- loadTask(project="%PROJECT%", package="%PACKAGE%", taskname="%TASK%")

  # render the task
  shell.exec(renderTaskRmd(task,suffix="%SUFFIX%"))

  # archive the task to the home directory
  archiveTask(task,zf<-paste0("~/",task$task,".zip"),overwrite=FALSE)

  # settings for new repository
  oro <- getTaskRoot() 
  setTaskRoot("/PATH/TO/NEW/REPOSITORY")
  ost <- getTaskStructure() 
  setTaskStructure(pathsDefault)

  # copy the task to a new repository
  newtask <- restoreTask(zf)
  print(list.files(getTaskPaths(newtask)$data,
                   full.names=FALSE,recursive=TRUE))

  #restore old settings
  setTaskRoot(oro) 
  setTaskStructure(ost)
}
# ============================================================

options(warn=1)
knitr::opts_chunk$set(
  fig.cap = TRUE,
    eval = TRUE, 
    echo = FALSE,
    comment = "#",
  message = FALSE,
    error = TRUE, 
  warning = TRUE,
    dpi = 150,
  dev.args = list(pointsize=8)
)
library(officedown)
library(officer)

# Load libraries
library(D4TAlink.light)
#library(D4TAlink)
setTaskSponsor("%SPONSOR%")
setTaskStructure(pathsDefault)
# try(setTaskRoot("%ROOT%"))

# Load task
task <- loadTask(project="%PROJECT%", package="%PACKAGE%", taskname="%TASK%",quiet=TRUE)
# if task does not exist on repository, create it 
if(is.null(task)) {
  task <- initTask(project="%PROJECT%",
                   package="%PACKAGE%",
                   taskname="%TASK%",
                   sponsor="%SPONSOR%",
                   author="%AUTHOR%")
}

options(warn = 2)

\newpage

Scope

In this section the scope / rationale of the task should be explained.

Input

The section list the information and data sources.

• List of patients (see email by JD dated 2022-05-01 17:12).
• List of assays (see task 20220102_loadAssays).

# Code to load input data

# ta <- loadTask(task$project,task$package,"20220102_loadAssays)
# ass <- readBinary(ta,"assays")

Methods and Results

The results-section contains more details regarding the results of task X.

# Chunk that contains the analysis R code.

Table

head(data.frame(l=letters,L=LETTERS))

Plot

boxplot(1:8)

Output

The section contains detailed information on output (incl. location).

• List of assays.

# Code to save data

# saveBinary(ass,ta,"assays")

\newpage

References

1. R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.

\newpage

Appendices

Session information

# In the appendix the session information is being printed for reproducibility.

sessionInfo()

List of figures

List of tables

D4TAlink.light documentation built on April 4, 2025, 1:02 a.m.