A simulation of bias introduced by missing confounder data

Author

Janick Weberpals

Description

Objective

The objective of this repository is to flexibly simulate de novo datasets with different missingness scenarios. The simulated datasets approximate the distributions of the empirical cohort used in the HDMI project.

Dependencies

This is a quarto project and R package dependencies are managed through the renv package. All packages and their versions can be viewed in the lockfile renv.lock. All required packages and the appropriate versions can be installed by running the following command:

Show the code 
renv::restore()
Important

The dependencies are managed through Posit’s repository package manager (RSPM) version for your underlying OS distribution. If you use a different operating system than MacOS, please head over to the RSPM setup website and follow these steps:

  1. Go to the RSPM setup website

  2. Choose the operating system (if Linux, also choose the Linux distribution)

  3. Go to Repository URL: and copy-paste the URL to the options statement in the .Rprofile file

    options(repos = c(REPO_NAME = “URL”))

Reproducibility

Follow these steps in RStudio to reproduce this study:

Note
  1. Install all necessary dependencies (see above)
  2. In RStudio, run all scripts via quarto render or Build > Render Book (make sure quarto is installed)

Repository structure and files

Directory overview

.
├── README.md
├── _quarto.yml
├── cc_bias_simulation.Rproj
├── functions
│   ├── format_methods.R
│   ├── generate_NA_cont.R
│   ├── generate_NA_discrete.R
│   ├── generate_data.R
│   ├── ps_analysis_mids.R
│   ├── rsimsum_ggplot.R
│   └── run_simulation.R
├── index.qmd
├── index.rmarkdown
├── public
│   ├── index.html
│   ├── robots.txt
│   ├── scripts
│   ├── search.json
│   ├── site_libs
│   └── sitemap.xml
├── renv
│   ├── activate.R
│   ├── library
│   └── settings.json
├── renv.lock
├── scripts
│   ├── 01_data_generation.qmd
│   ├── 02_missingness_generation.qmd
│   ├── 03_run_simulation.html.md
│   ├── 03_run_simulation.md
│   ├── 03_run_simulation.qmd
│   └── 03_run_simulation_files
├── site_libs
│   ├── bootstrap
│   ├── clipboard
│   ├── crosstalk-1.2.1
│   ├── htmltools-fill-0.5.8.1
│   ├── htmlwidgets-1.6.4
│   ├── jquery-3.5.1
│   ├── plotly-binding-4.10.4
│   ├── plotly-htmlwidgets-css-2.11.1
│   ├── plotly-main-2.11.1
│   ├── quarto-html
│   ├── quarto-nav
│   ├── quarto-search
│   └── typedarray-0.1
└── update_README.R
  • .Rprofile - defines paths, activates renv, options for Posit R package manager
  • scripts - main R/RMarkdown scripts
  • functions - helper functions called in scripts
  • renv/renv.lock - renv directories to manage R dependencies and versions used in this simulation
  • docs - output of Quarto scripts
  • README - essential information about the project (README.Rmd renders to README.md via update_README.R after each quarto render command)