Complete Case Analysis for Censored Covariates

Marissa C. Ashner and Tanya P. Garcia

Code for simulations, tables, and figures for the manuscript Understanding the implications of a complete case analysis for regression models with a right-censored covariate (https://doi.org/10.1080/00031305.2023.2282629).

In the R subdirectory, you will find the following:

• simulation_study_functions_cc.R: This script defines the functions used to generate data, run a simulation, and report the results for requested simulation settings.
• main_cc.R: This script defines the functions used to estimate the parameters and the variance of the parameters using a complete case analysis or an oracle analysis.
• simulation_study_cc.R: You can run a simulation study from inside this script. You can change the settings in the script to run with a certain number of simulations, sample size, number of fully observed covariates, true parameter values, starting values, mean function, censoring rate, censoring mechanism, sigma2, and output file name.
• dag_cc.R: This script recreates the Directed Acyclic Graph (DAG) that is in the manuscript.
• cc_tables.R: This script recreates the simulation results tables that are in the manuscript main text and supplementary materials.

Note: These scripts assume your working directory is inside the R subdirectory.

In the main directory, you will find the following:

• cc_simulation_study.sh: This is a bash script, which includes an example of another way to run simulation_study_cc.R from the command line instead of running the simulations inside the R script itself. To use this on the command line, you would edit the parameters in the file, save, and run the command bash cc_simulation_study.sh in the terminal.

Note: Some syntax in this file may change depending on the environment you are running it in. This is just an example of a bash file based on the computing cluster that was used to run the simulations.

In the simulation_output_may2023 subdirectory, you will find the simulation output files needed to recreate the tables in R/cc_tables.R.

In the Figures and Tables subdirectory, you will find the output files for the tables and figures from R/cc_tables.R and R/cc_dag.R.