simulations/missing-data-benchmarks/README.md

In openpharma/mmrm: Mixed Models for Repeated Measures

Mmrm Simulation

Usage

R simulation

R simulations can be done on any platform where R and snakemake is available. Current snakefile is also compatible with HPC where batch system like lsf is installed.

Make sure the lsf plugin for snakemake is installed.

pip install snakemake-executor-plugin-lsf

Then you can use snakemake to submit jobs.

snakemake --executor lsf all_r_analysis

The data generation step is using a specific seed so reproducibility is ensured.

SAS simulation

The simulation in SAS can be completed on systems where SAS and R are both available. If you don't have machines that both are available, the execution should take two steps.

1. Generate the data using snakemake all_simulated_data (this must run on R machine)
2. Generate the estimate using snakemake all_sas_analysis (this must run on SAS machine)

openpharma/mmrm documentation built on April 14, 2025, 2:10 a.m.