Data Analysis with Bootstrapped ESTimation
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README.md

DABEST (Python)

Travis CI PyPI version

About

DABEST is a package for Data Analysis using Bootstrap-Coupled ESTimation.

Estimation statistics is a simple framework that avoids the pitfalls of significance testing. It uses familiar statistical concepts: means, mean differences, and error bars. More importantly, it focuses on the effect size of one's experiment/intervention, as opposed to a false dichotomy engendered by P values.

An estimation plot has two key features.

  1. It presents all datapoints as a swarmplot, which orders each point to display the underlying distribution.

  2. It presents the effect size as a bootstrap 95% confidence interval on a separate but aligned axes.

The five kinds of estimation plots

DABEST powers estimationstats.com, allowing everyone access to high-quality estimation plots.

Requirements

DABEST has been tested on Python 2.7, 3.5, 3.6, and 3.7.

In addition, the following packages are also required:

To obtain these package dependencies easily, it is highly recommended to download the Anaconda distribution of Python.

Installation

You can install this package via pip.

To install, at the command line run

pip install --upgrade dabest

You can also clone this repo locally (see intstructions here).

Then, navigate to the cloned repo in the command line and run

pip install .

Usage

Please refer to the documentation.

How to cite

Moving beyond P values: Everyday data analysis with estimation plots

Joses Ho, Tayfun Tumkaya, Sameer Aryal, Hyungwon Choi, Adam Claridge-Chang

https://doi.org/10.1101/377978

Matlab version

There is also a Matlab version of DABEST.

R version

It is possible to use the R package reticulate to run Python code. Please take a look at this tutorial on how to use reticulate to analyse data in R.

Testing

To test DABEST, you will need to install pytest.

Run pytest in the root directory of the source distribution. This runs the test suite in the folder dabest/tests. The test suite will ensure that the bootstrapping functions and the plotting functions perform as expected.

Bugs

Please report any bugs on the Github issue tracker.

Contributing

All contributions are welcome. Please fork the Github repo and open a pull request.