Understanding the cognitive mechanisms of mind-wandering in the depressed mind by modelling an emotional n-back task.
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README.md

README.md

Emotional n-back

This repository contains the code for the models and analyses in my master's thesis: Modelling the Effects of Depression on Working Memory.

Table of contents

Getting started

PRIMs

The models require a customised version of Niels Taatgen's PRIMs cognitive architecture. This application only works with macOS. Download the file PRIMs.app.zip, extract it, and run the application.

Useful links

Models

Files related to running models are provided in the models folder.

Running a single model

Files with a .prims extension contain the actual models. You can load a model by selecting Load Model from the PRIMs menu bar. Use the Step button on the menu bar to step through the model.

Doing multiple model runs at once

Files with a .bprims extension can be used to perform a batch run (simulating more than one participant). Some examples are provided.

To start a batch run, select Run, then Run batch from the PRIMs menu, and select the desired .bprims file.

The Run menu also contains a Run batch with trace option, which works the same, but will also save the entire output trace to a .fulltrace file. Use this option when you want to analyse the model's output with the provided script. (Note that saving the full output trace can take quite some time!)

Saving and loading model states

To save time, you can train a model once and store its state in a .brain file. Use the menu option Save image to save the current state of a model and Load image to reinstate a previous model state.

Data

The output of the models that are discussed in the thesis is provided in the data folder.

Each .fulltrace file contains the full output trace of a single batch run, as produced by PRIMs.

Converting .fulltrace to .csv

Before the output can be analysed, it has to be converted into a sensible format using the python parse script. To convert a .fulltrace file in the 0back/depressed folder, run the following command in the terminal:

python parse_fulltrace_0back.py 0back/depressed

Similarly, a .fulltrace file from a 2-back run in the 2back/control folder is parsed by running:

python parse_fulltrace_2back.py 2back/control

In both cases the script will produce a set of .csv files in the specified folder:

  • *_beh.csv : behavioural results
  • *_mems.csv : list of retrievals from declarative memory
  • *_ops.csv : list of operator executions

Analysis

The analyis directory contains separate R scripts for analysing 0-back and 2-back model runs. These scripts reproduce the accuracy, response rate, and (z-transformed) response time plots shown in the thesis, along with the presented statistical tests, and additional analyses of operator selection.

Notebooks

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