Three-Box Foraging Behavioral Analysis

This is where I perform all my analyses of the behavioral data in the three-box foraging task. This repo is organized into the following sections:

data - this folder contains experiment data as well as any data structures generated by the code. Experiment data can be downloaded upon request and placed in data/experiments. Pre-existing data structures useful for analysis may be found under data/analysis.
docs - this folder contains useful documentation about the experiment, results, etc. Some of the pdfs are directly generated from notebooks contained in notebooks.
figures - this folder is used to contain any figures generated by scripts.
notebooks - this folder contains jupyter notebooks that interface with the foraging package to render results and figures.
- start with the Data Cleaning.ipynb notebook first to get an overview of the data and how it's cleaned. Then proceed to the Behavioral Analysis and then the Belief Analysis notebooks.
src - this folder contains the foraging package, which you should install locally in your environment. See steps to setup below.

Dependencies

You can see the full list in the pyproject.toml under the dependencies field.

Here are a couple tested ways to quickly set up an environment

Combine the best of both worlds with this hybrid approach that leverages the scientific computing ecosystem of conda and package management prowess of poetry. To install this package, run the following at the root of this project:

conda create -n <YOUR_ENV> python=3.10
conda activate <YOUR_ENV>
conda install pip
pip install poetry
poetry install

This will build dependencies off pyproject.toml and install packages primarily through pip, including the foraging package itself. If you do not like this, then go to step 2.

conda install conda-lock
conda-lock install --name <YOUR_ENV> conda-lock.yml

This will create a new environment and install dependencies specified in conda-lock.yml.
To install the foraging package, proceed to step 3.

This step assumes you have built a functional environment and are ready to install the package
Cd to the root of this repo and just run pip install . in terminal! To install in development mode, where you may wish to edit the package files, run pip install -e ..