MARCQI simulation tool

This tool was created to generate fake patient data with any given causal relationships.

Organization

figures contains the figures for the paper generation contains the code for simulating patients plotting contains the code for generating the figures sources contains pdfs of the sources used to obtain the simulation numbers

Usage

Build System

The simulation build system uses gradle. There are two steps to simulation: generation and analysis. Running gradle generate in the generation directory runs the main method in Generate.java, which is for generating patient data. Running gradle analyze in the generation directory runs the main method in Analyze.java, which is for analyzing the generated patient data with TETRAD. The generation/analysis source code is found in generation/src/main/java/revgen.

Data storage

Due to the volume of data generated, it is infeasable to store it in separate files per simulation. Instead, it is configured to store the results in a MySQL database. A database schema that can be used for the current configuration is included in the root of the project, schema.sql. That can be used to create a schema in a new MySQL database from the MySQL CLI as follows:

create database test; use test; source source.sql

The table schema will need to be edited accordingly if new variables are to be added.

Code

All classes are documented internally, but I have also included an outline of each class here for reference.

Generate.java

Generate.java contains the main method that is run to generate patient data.

Analyze.java

Analyze.java contains the main method that is run to analyze generated patient data with TETRAD.

Run.java

The Run class represents the largest grouping of simulation data. Each Run contains multiple ParameterSets. Every time Generate.java is run, it creates a new Run in the database.

ParameterSet.java

The ParameterSet class is a structure that contains parameters that are used to generate patient data.

Simulation.java

The Simulation class represents a single simulated set of patient data. Each simulation uses one ParameterSet to generate its patient data.

Case.java

The Case class represents one patient and its associated variables. Each case belongs to one simulation.

CaseGenerator.java

The CaseGenerator class returns generated cases using a given parameter set.