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Tinker Taylor py is a framework for modelling and fitting neuroscientific models to the responses of people to probabilistic decision making tasks.

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Tinker Taylor py

TTpy is a framework for modelling and fitting the responses of people to probabilistic decision making tasks.

Any questions can either be submitted as issues or e-mailed to d.hunt (at) gold.ac.uk

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Prerequisites

This code has been tested using Python 3.7. Apart from the standard Python libraries it also depends on the SciPy libraries and a few others listed in requirements.txt. For those installing Python for the first time I would recommend the Anaconda Python distribution.

Installation

For now this is just Python code that you download and use, not a package.

Usage

The framework can been run with a run script, live in a terminal or Python command-line (or jupyter notebook).

A task simulation can be simply created by running simulation.run(). Equally, for fitting participant data, the function is dataFitting.run('./path/to/data/').

More complex example running scripts can be found in ./runScripts/. Here, a number of scripts have been created as templates: runScript_sim.py for simulating the probSelect task and runScript_fit.py for fitting the data generated from runScript_sim.py, stored in the ./tests/test_sim folder. The output of this fit can also be found ./tests/test_fit folder.

A new method of passing in the fitting or simulation configuration is to use a YAML configuration file. This is done, for both simulations and data fitting, using the function start.run_config For example, to run the YAML configuration equivalent to the runScript_sim.py from a command line would be :start.run_config('./runScripts/runScripts_sim.yaml'). For the fitting example, the configuration equivalent to runScript_fit.py would be :start.run_config('./runScripts/runScripts_fit.yaml').

Documentation

Documentation Status

The documentation can be found on readthedocs or in ./doc/_build/html, with the top level file being index.html.

To update the documentation you will need to install Sphinx and a set of extensions. The list of extensions can be found in ./doc/conf.py. The list of extensions can be found in ./doc/requirements.txt. To update the documentation follow the instruction in ./doc/readme.md

License

This project is licenced under the MIT license.

History

This repository first began as a clone of the original repository from Bitbucket.

Testing

Testing is done using pytest. The tests can be found in ./tests/

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Tinker Taylor py is a framework for modelling and fitting neuroscientific models to the responses of people to probabilistic decision making tasks.

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