dlimIM_simulations

The repository contains scripts to recreate the simulations and analyses in "Distributed Lag Interaction Model with Index Modification" in press in Biostatistics (Demateis et al.).

There are 3 folders, one containing simulation scripts and the others containing analysis scripts (one for each respective analysis).
Information on data sharing and processing is available in the README files in the Analysis_CO/DataPrep and Analysis_PROGRESS folders.

Simulation folder:

First, run the modifier_correlation_structures.R script. Then, run the simulation.R script on a HPC using the submit_all.sh script (in terminal, run $sbatch submit_all.sh). The rest of the files in this folder are used to create figures/tables for this simulation.

Analysis_CO folder:

First, follow instructions in the Analyais_CO/DataPrep folder for obtaining and processing data. This produces a file called co_birth_danielle_index.rda to be used with the analysis script. Then, run analysis_script_CO.R on a HPC using the submit_analysis.sh script (in terminal, run $sbatch submit_analysis.sh). Now, you can use maintext_figure2_table2.R to create figures/tables. For additional supplemental figures, run analysis_script_CO_single_modifier_models.R on a HPC using the submit_single_modifier.sh script (in terminal, fun $sbtach submit_single_modifier.sh). Now, the supplement_figures_8to12_table2.R will be able to create all supplemental figures/tables.

Information on obtaining data and creating the analysis file is in the folder Analysis_CO/DataPrep. The README file in that folder contains additional details.

Analysis_PROGRESS folder:

See information in the README of this folder on obtaining data. First, run analysis_script_PROGRESS.R. The rest of the files in this folder are used to create figures/tables for this simulation.

Information on data sharing for the PROGESS data is available in the README file in the folder Analysis_PROGRESS.

Packages

This uses the following packages:

• data.table version 1.17.0
• dlim version 0.1.0
• dlimIM version 0.1.1
• dplyr version 1.1.4
• elevatr version 0.99.0
• ggplot2 version 3.5.2
• gridExtra version 2.3
• MASS version 7.3.61
• Matrix version 1.7.1
• mgcv version 1.9.1
• ncdf4 version 1.24
• sf version 1.0.20
• tidyverse version 2.0.0
• tidycensus version 1.7.1
• tigris version 2.2.1
• viridis version 0.6.5
• xtable version 1.8.4

All packages are on CRAN with the exception of dlimIM which is available at github.com/ddemateis/dlimIM and DOI:10.5281/zenodo.15354392.