Mixed Models Python Packages

formulae

Formulas for mixed-effects models in Python

jamma

JAMMA (Highly-Accelerated Multi-method Mixed-model Association) -- a fast and modern Python and C reimplementation of GEMMA for large-scale GWAS.

pygapit-ng

Python implementation of GAPIT 3.5 for GWAS and genomic prediction, with disk-backed NumPy, HDF5, and Zarr workflows.

mixedlm-rs

Fast linear mixed-effects models for Python - lme4 speed, statsmodels API, no R required

pyreml

General-purpose linear mixed model solver

decision-tree-morfist

Multi-target Random Forest implementation that can mix both classification and regression tasks.

pymmeans

Estimated marginal means, contrasts, and small-sample mixed-model inference for Python — a native port of R's emmeans and pbkrtest.

pilotr

pilotr: a cross-language toolkit for simulating experimental and behavioral data, with integrated power and design analysis

mixmil

Code for the paper: Mixed Models with Multiple Instance Learning