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:
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).
Check out our repo of Jupyter notebooks.
To install quail in the recommended way, run:
pip install quail
This will install quail with basic functionality. To install with speech decoding dependencies (Note: you will still need to install ffmpeg manually on your computer since it is not pip installable. For instructions, see here):
pip install quail[speech-decoding]
For CDL users, you can install speech decoding and efficient learning capabilities like this:
pip install quail[speech-decoding, efficient-learning]
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 .
If installing from github (instead of pip), you must also install the requirements:
pip install -r requirements.txt
Check out our readthedocs: here.
We also have a repo with example notebooks from the paper here.
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}
}
(Some text borrowed from Matplotlib contributing guide.)
If you are reporting a bug, please do your best to include the following:
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.
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.
To test quail, install pytest (pip install pytest
) and run pytest
in the quail folder
See here for more examples.
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)
#load data
egg = quail.load_example_data()
#analysis
analyzed_data = quail.analyze(egg, analysis='accuracy', listgroup=['average']*8)
analyzed_data = quail.analyze(egg, analysis='accuracy', listgroup=['average']*8)
ax = quail.plot(analyzed_data, title='Recall Accuracy')
analyzed_data = quail.analyze(egg, analysis='spc', listgroup=['average']*8)
ax = quail.plot(analyzed_data, title='Serial Position Curve')
analyzed_data = quail.analyze(egg, analysis='pfr', listgroup=['average']*8)
ax = quail.plot(analyzed_data, title='Probability of First Recall')
analyzed_data = quail.analyze(egg, analysis='lagcrp', listgroup=['average']*8)
ax = quail.plot(analyzed_data, title='Lag-CRP')
analyzed_data = quail.analyze(egg, analysis='fingerprint', listgroup=['average']*8)
ax = quail.plot(analyzed_data, title='Memory Fingerprint')