A python toolbox for analyzing and plotting free recall data
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Latest commit 30e1c78 Oct 16, 2017 @jeremymanning jeremymanning remove month from bibtex entry
(it messes with bibliography entries in some styles)

README.md

DOI JOSS

Quail logo

Overview

Quail is a Python package that facilitates analyses of behavioral data from memory experiments. (The current focus is on free recall experiments.) Key features include:

  • Serial position curves (probability of recalling items presented at each presentation position)
  • Probability of Nth recall curves (probability of recalling items at each presentation position as the Nth recall in the recall sequence)
  • Lag-Conditional Response Probability curves (probability of transitioning between items in the recall sequence, as a function of their relative presentation positions)
  • Clustering metrics (e.g. single-number summaries of how often participants transition from recalling a word to another related word, where "related" can be user-defined.)
  • Many nice plotting functions
  • Convenience functions for loading in data
  • Automatically parse speech data (audio files) using wrappers for the Google Cloud Speech to Text API

The intended user of this toolbox is a memory researcher who seeks an easy way to analyze and visualize data from free recall psychology experiments.

The toolbox name is inspired by Douglas Quail, the main character from the Philip K. Dick short story We Can Remember It for You Wholesale (the inspiration for the film Total Recall).

Try it!

Check out our repo of Jupyter notebooks.

Installation

To install quail in the recommended way, run:

pip install quail

To install directly from this repo (not recommended, but you'll get the "bleeding edge" version of the code):

git clone https://github.com/ContextLab/quail.git

Then, navigate to the folder and type:

pip install -e .

(this assumes you have pip installed on your system)

This will work on clean systems, but if you encounter issues you may need to run:

sudo pip install --upgrade --ignore-installed -e .

Requirements

  • python 2.7, 3.4+
  • pandas>=0.18.0
  • seaborn>=0.7.1
  • matplotlib>=1.5.1
  • scipy>=0.17.1
  • numpy>=1.10.4
  • future
  • pytest (for development)

If installing from github (instead of pip), you must also install the requirements: pip install -r requirements.txt

Documentation

Check out our readthedocs: here.

We also have a repo with example notebooks from the paper here.

Citing

Please cite as:

Heusser AC, Fitzpatrick PC, Field CE, Ziman K, Manning JR (2017) Quail: A Python toolbox for analyzing and plotting free recall data. The Journal of Open Source Software, 2(18) https://doi.org/10.21105%2Fjoss.00424

Here is a bibtex formatted reference:

@ARTICLE {HeusEtal2017b,
	doi = {10.21105/joss.00424},
	url = {https://doi.org/10.21105%2Fjoss.00424},
	year = 2017,
	publisher = {The Open Journal},
	volume = {2},
	number = {18},
	author = {Andrew C. Heusser and Paxton C. Fitzpatrick and Campbell E. Field and Kirsten Ziman and Jeremy R. Manning},
	title = {Quail: A Python toolbox for analyzing and plotting free recall data},
	journal = {The Journal of Open Source Software}
}

Contributing

(Some text borrowed from Matplotlib contributing guide.)

Submitting a bug report

If you are reporting a bug, please do your best to include the following:

  1. A short, top-level summary of the bug. In most cases, this should be 1-2 sentences.
  2. A short, self-contained code snippet to reproduce the bug, ideally allowing a simple copy and paste to reproduce. Please do your best to reduce the code snippet to the minimum required.
  3. The actual outcome of the code snippet
  4. The expected outcome of the code snippet

Contributing code

The preferred way to contribute to quail is to fork the main repository on GitHub, then submit a pull request.

  • If your pull request addresses an issue, please use the title to describe the issue and mention the issue number in the pull request description to ensure a link is created to the original issue.

  • All public methods should be documented on our readthedocs API page.

  • Each high-level plotting function should have a simple example in the examples folder. This should be as simple as possible to demonstrate the method.

  • Changes (both new features and bugfixes) should be tested using pytest. Add tests for your new feature to the tests/ repo folder.

Support

If you have a question, comment or concern about the software, please post a question to Stack Overflow, or send us an email at contextualdynamics@gmail.com.

Testing

Build Status

To test quail, install pytest (pip install pytest) and run pytest in the quail folder

Examples

See here for more examples.

Create an egg!

Eggs are the fundamental data structure in quail. They are comprised of lists of presented words, lists of recalled words, and a few other optional components.

import quail

# presented words
presented_words = [['cat', 'bat', 'hat', 'goat'],['zoo', 'animal', 'zebra', 'horse']]

# recalled words
recalled_words = [['bat', 'cat', 'goat', 'hat'],['animal', 'horse', 'zoo']]

# create egg
egg = quail.Egg(pres=presented_words, rec=recalled_words)

Analyze some data

#load data
egg = quail.load_example_data()

#analysis
analyzed_data = quail.analyze(egg, analysis='accuracy', listgroup=['average']*8)

Plot Accuracy

analyzed_data = quail.analyze(egg, analysis='accuracy', listgroup=['average']*8)
ax = quail.plot(analyzed_data, title='Recall Accuracy')

Plot Accuracy

Plot Serial Position Curve

analyzed_data = quail.analyze(egg, analysis='spc', listgroup=['average']*8)
ax = quail.plot(analyzed_data, title='Serial Position Curve')

Plot SPC

Plot Probability of First Recall

analyzed_data = quail.analyze(egg, analysis='pfr', listgroup=['average']*8)
ax = quail.plot(analyzed_data, title='Probability of First Recall')

Plot PFR

Plot Lag-CRP

analyzed_data = quail.analyze(egg, analysis='lagcrp', listgroup=['average']*8)
ax = quail.plot(analyzed_data, title='Lag-CRP')

Plot Lag-CRP

Plot Memory Fingerprint

analyzed_data = quail.analyze(egg, analysis='fingerprint', listgroup=['average']*8)
ax = quail.plot(analyzed_data, title='Memory Fingerprint')

Plot Fingerprint