%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
  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 files

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

• List of assays.

# Code to save data

# saveBinary(ass,ta,"assays")

Conclusions

Describe here the conclusions of the analyses.

Validation

Describe here the process used to validate the statistical analysis performed above.

Depending on an estimation of risk, the validation is typically 1) no validation, 2) a review of report objects, 3) a standard code review, 4) extended code review, or 5) double coding of the analyses.

Example: Validation of these analyses by double coding was performed in task %TASK%_validation.

## Create a validation task
vt <- initTask(project="%PROJECT%", package="%PACKAGE%", taskname="%TASK%_validation")
initTaskRmd(vt)

\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.