Harmonisation Template for Cohort B
Preface
Here is the documentation of the data harmonisation step generated using Quarto. To learn more about Quarto books visit https://quarto.org/docs/books.
File Structure
Here is the file structure of the project used to generate the document.
harmonisation/ # Root of the project template.
|
├── .quarto/ (not in repository) # Folder to keep intermediate files/folders
| # generated when Quarto renders the files.
|
├── archive/ # Folder to keep previous books and harmonised data.
| |
│ ├── reports/ # Folder to keep previous versions of
| | | # data harmonisation documentation.
| | |
| | ├── {some_date}_batch/ # Folder to keep {some_date} version of
| | | # data harmonisation documentation.
| | |
| | └── Flowchart.xlsx # Flowchart sheet to record version control.
| |
| └── harmonised/ # Folder to keep previous version of harmonised data.
| |
| ├── {some_date}_batch/ # Folder to keep {some_date} version of
| | # harmonised data.
| |
| └── Flowchart.xlsx # Flowchart sheet to record version control.
|
├── codes/ # Folder to keep R/Quarto scripts
| | # to run data harmonisation.
| |
│ ├── {cohort name}/ # Folder to keep Quarto scripts to run
| | | # data cleaning, harmonisation
| | | # and output them for each cohort.
| | |
| | └── preprocessed_data/ # Folder to keep preprocessed data.
| |
│ ├── harmonisation_summary/ # Folder to keep Quarto scripts to create
| | # data harmonisation summary report.
| |
│ ├── output/ # Folder to keep harmonised data.
| |
| ├── cohort_harmonisation_script.R # R script to render each {cohort name}/ folder.
| | # folder into html, pdf and word document.
| |
| └── harmonisation_summary_script.R # R script to render the {harmonisation_summary}/
| # folder into word document.
│
├── data-raw/ # Folder to keep cohort raw data (.csv, .xlsx, etc.)
| |
│ ├── {cohort name}/ # Folder to keep cohort raw data.
| | |
| | ├── {data_dictionary} # Data dictionary file that correspond to the
| | | # cohort raw data. Can be one from the
| | | # collaborator provide or provided by us.
| | |
| | └── Flowchart.xlsx # Flowchart sheet to record version control.
| |
| ├── data-dictionary/ # Folder to keep data dictionary
| | | # used for harmonising data.
| | |
| | └── Flowchart.xlsx # Flowchart sheet to record version control.
| |
| └── data-input/ # Folder to keep data input file
| | # for collaborators to fill in.
| |
| └── Flowchart.xlsx # Flowchart sheet to record version control.
|
├── docs/ # Folder to keep R functions documentation
| # generated using pkgdown:::build_site_external().
|
├── inst/ # Folder to keep arbitrary additional files
| | # to include in the project.
| |
| └── WORDLIST # File generated by spelling::update_wordlist()
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├── man/ # Folder to keep R functions documentation
| | # generated using devtools::document().
| |
│ ├── {fun-demo}.Rd # Documentation of the demo R function.
| |
│ └── harmonisation-template.Rd # High-level documentation.
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├── R/ # Folder to keep R functions.
| |
│ ├── {fun-demo}.R # Script with R functions.
| |
│ └── harmonisation-package.R # Dummy R file for high-level documentation.
│
├── renv/ (not in repository) # Folder to keep all packages
| # installed in the renv environment.
|
├── reports/ # Folder to keep the most recent data harmonisation
| # documentation.
|
├── templates/ # Folder to keep template files needed to generate
| | # data harmonisation documentation efficiently.
| |
| ├── quarto-yaml/ # Folder to keep template files to generate
| | | # data harmonisation documentation structure
| | | # in Quarto.
| | |
│ | ├── _quarto_{cohort name}.yml # Quarto book template data harmonisation documentation
| | | # for {cohort name}.
| | |
| | └── _quarto_summary.yml # Quarto book template data harmonisation summary.
| |
| └── index-qmd/ # Folder to keep template files to generate
| | # the preface page of the data harmonisation
| | # documentation.
| |
| ├── _index_report.qmd # Preface template for each cohort data harmonisation
| | # report.
| |
| └── _index_summary.qmd # Preface template for data harmonisation
| # summary report.
|
├── tests/ # Folder to keep test unit files.
| # Files will be used by R package testhat.
|
├── .Rbuildignore # List of files/folders to be ignored while
│ # checking/installing the package.
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├── .Renviron (not in repository) # File to set environment variables.
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├── .Rprofile (not in repository) # R code to be run when R starts up.
| # It is run after the .Renviron file is sourced.
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├── .Rhistory (not in repository) # File containing R command history.
|
├── .gitignore # List of files/folders to be ignored while
│ # using the git workflow.
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├── .lintr # Configuration for linting
| # R projects and packages using linter.
|
├── .renvignore # List of files/folders to be ignored when
│ # renv is doing its snapshot.
|
├── DESCRIPTION[*] # Overall metadata of the project.
|
├── LICENSE # Content of the MIT license generated via
| # usethis::use_mit_license().
|
├── LICENSE.md # Content of the MIT license generated via
| # usethis::use_mit_license().
|
├── NAMESPACE # List of functions users can use or imported
| # from other R packages. It is generated
| # by devtools::document().
│
├── README.md # GitHub README markdown file generated by Quarto.
|
├── README.qmd # GitHub README quarto file used to generate README.md.
|
├── _pkgdown.yml # Configuration for R package documentation
| # using pkgdown:::build_site_external().
|
├── _quarto.yml # Configuration for Quarto book generation.
| # It is also the project configuration file.
|
├── csl_file.csl # Citation Style Language (CSL) file to ensure
| # citations follows the Lancet journal.
|
├── custom-reference.docx # Microsoft word template for data harmonisation
| # documentation to Word.
|
├── harmonisation_template.Rproj # RStudio project file.
|
├── index.qmd # Preface page of Quarto book content.
|
├── references.bib # Bibtex file for Quarto book.
|
└── renv.lock # Metadata of R packages installed generated
# using renv::snapshot().
[*] These files are automatically created but user needs to manually add some information.