hierarch

A Hierarchical Resampling Package for Python

Version 2.0.0

hierarch is a package for hierarchical resampling (bootstrapping, permutation) of datasets in Python. Resampling is batched and vectorized with numpy, so cluster-aware bootstraps and permutations are drawn without Python-level loops over the hierarchy.

hierarch has several functions to assist in performing resampling-based (and therefore distribution-free) hypothesis tests, confidence interval calculations, and power analyses on hierarchical data.

Table of Contents

1. Introduction
2. Setup
3. Documentation
4. Citation

Introduction

Design-based randomization tests represents the platinum standard for significance analyses [1, 2, 3] - that is, they produce probability statements that depend only on the experimental design, not at all on less-than-verifiable assumptions about the probability distributions of the data-generating process. Researchers can use hierarch to quickly perform automated design-based randomization tests for experiments with arbitrary levels of hierarchy.

[1] Tukey, J.W. (1993). Tightening the Clinical Trial. Controlled Clinical Trials, 14(4), 266-285.

[2] Millard, S.P., Krause, A. (2001). Applied Statistics in the Pharmaceutical Industry. Springer.

[3] Berger, V.W. (2000). Pros and cons of permutation tests in clinical trials. Statistics in Medicine, 19(10), 1319-1328.

Setup

Dependencies

• numpy
• pandas (for importing data)
• scipy (for power analysis)
• formulaic (for building design matrices from formulas)

Installation

The easiest way to install hierarch is via PyPi.

pip install hierarch

Alternatively, you can install from Anaconda.

conda install -c rkulk111 hierarch

Documentation

Check out our user guide at readthedocs.

Citation

If hierarch helps you analyze your data, please consider citing it. The manuscript also contains a set of simulations validating hierarchical randomization tests in a variety of conditions.

Kulkarni RU, Wang CL, Bertozzi CR (2022) Analyzing nested experimental designs—A user-friendly resampling method to determine experimental significance. PLoS Comput Biol 18(5): e1010061. https://doi.org/10.1371/journal.pcbi.1010061