addm-toolbox 0.1.12

A toolbox for data analysis using the attentional drift-diffusion model.

This toolbox can be used to perform model fitting and to generate simulations for the attentional drift-diffusion model (aDDM), as well as for the classic version of the drift-diffusion model (DDM) without an attentional component.

Prerequisites

aDDM-Toolbox supports Python 2.7 (and Python 3.6 tentatively – please report any bugs). The following libraries are required:

• deap

• future

• matplotlib

• numpy

• pandas

• scipy

Installing

$ pip install addm_toolbox

Running tests

To make sure everything is working correctly after installation, try (from a UNIX shell, not the Python interpreter):

$ addm_toolbox_tests

This should take a while to finish, so maybe go get a cup of tea :)

Getting started

To get a feel for how the algorithm works, try:

$ addm_demo --display-figures

You can see all the arguments available for the demo using:

$ addm_demo --help

Here is a list of useful scripts which can be similarly run from a UNIX shell:

• addm_demo

• ddm_pta_test

• addm_pta_test

• addm_pta_mle

• addm_pta_map

• addm_simulate_true_distributions

• addm_basinhopping

• addm_genetic_algorithm

• ddm_mla

• addm_mla

You can also have a look directly at the code in the following modules:

• addm.py contains the aDDM implementation, with functions to generate model simulations and obtain the likelihood for a given data trial.

• ddm.py is equivalent to addm.py but for the DDM.

• addm_pta_test.py generates an artificial data set for a given set of aDDM parameters and attempts to recover these parameters through maximum a posteriori estimation.

• ddm_pta_test.py is equivalent to addm_pta_test.py but for the DDM.

• addm_pta_mle.py fits the aDDM to a data set by performing maximum likelihood estimation.

• addm_pta_map.py performs model comparison for the aDDM by obtaining a posterior distribution over a set of models.

• simulate_addm_true_distributions.py generates aDDM simulations using empirical data for the fixations.

Common issues

If you get errors while using the toolbox under Python 3, try it with Python 2.7.

If you get a Python RuntimeError with the message “Python is not installed as a framework.”, try creating the file ~/.matplotlib/matplotlibrc and adding the following code:

backend: TkAgg

Authors

• Gabriela Tavares - [e-mail], goptavares

License

This project is licensed under the GNU GENERAL PUBLIC LICENSE - see the COPYING file for details.

Acknowledgments

This toolbox was developed as part of a research project in the Rangel Neuroeconomics Lab at the California Institute of Technology.