ryanoisin / ComputationalTreatment

Code repository for "Improving Treatments for Mental Disorders using Computational Models"

Reproducibility ARchive

Reproducibility archive for the paper Ryan, O., Haslbeck, J. M. B. & Robinaugh ,D. J. (preprint) "Improving Treatments for Mental Disorders using Computational Models". Preprint here

Overview

Simulation

The folder /Simulation contains all files to reproduce the simulated treatments reported in the paper. The folder contains the following files and folders:

• SimScript.R contains the script for simulating the baseline and all five treatment arms for 16 subjects. The run time of this script is below 6h parallelized across 16 cores with 2.5GHZ.
• submit_jobs.sh is a bash script to call SimScript.R on the (now defunct) Surf LISA supercomputer system of the University of Amsterdam
• submit_all.sh is a bash script to call submit_jobs.sh 32 times, which gives us 512 subjects. We report the first 500 in the paper.
• The folder output contains 32 output files of SimScript.R which each contain the data of 16 subjects

Creating Figures

• sim_preprocess.R contains functions to map the minute-to-minute data of components to weekly symptom scores, and create other processed output stored in /Files/
• analysis_figures.R contains the code to re-create all figures relating to the results of the simulation study
• example_PanicModel.R contains code to simulate an example time series for a single individual using the panic model. This is used to create Figure 3 in the manuscript.