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changepointGA - Changepoint Detection via Modified Genetic Algorithms

The Genetic Algorithm (GA) is used to perform changepoint analysis in time series data. The package also includes an extended island version of GA, as described in Lu, Lund, and Lee (2010, <doi:10.1214/09-AOAS289>). By mimicking the principles of natural selection and evolution, GA provides a powerful stochastic search technique for solving combinatorial optimization problems. In 'changepointGA', each chromosome represents a changepoint configuration, including the number and locations of changepoints, hyperparameters, and model parameters. The package employs genetic operators—selection, crossover, and mutation—to iteratively improve solutions based on the given fitness (objective) function. The structured and consensus-guided island model GA additionally incorporates cross-island consensus guidance and optional objective-based local refinement. Key features of 'changepointGA' include encoding changepoint configurations in an integer format, enabling dynamic and simultaneous estimation of model hyperparameters, changepoint configurations, and associated parameters. The detailed algorithmic implementation can be found in the package vignettes and in the paper of Li and Lu (2024, <doi:10.48550/arXiv.2410.15571>).

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openblascpp

5.56 score 2 dependents 4 scripts 613 downloads

GAReg - Genetic Algorithms in Regression

Provides a genetic algorithm framework for regression problems requiring discrete optimization over model spaces with unknown or varying dimension, where gradient-based methods and exhaustive enumeration are impractical. Uses a compact chromosome representation for tasks including spline knot placement and best-subset variable selection, with constraint-preserving crossover and mutation, exact uniform initialization under spacing constraints, steady-state replacement, and optional island-model parallelization from Lu, Lund, and Lee (2010, <doi:10.1214/09-AOAS289>). The computation is built on the 'GA' engine of Scrucca (2017, <doi:10.32614/RJ-2017-008>) and 'changepointGA' engine from Li and Lu (2024, <doi:10.48550/arXiv.2410.15571>). In challenging high-dimensional settings, 'GAReg' enables efficient search and delivers near-optimal solutions when alternative algorithms are not well-justified.

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4.85 score 1 stars 331 downloads

CAFT - Rank-Based Compositional Analysis using Log-Linear Models for Microbiome Data with Zero Cells

Provides rank-based compositional differential abundance analysis for microbiome count data with zero cells using the compositional accelerated failure time model of Satten, Li and Zhao (2025) "CAFT: A Compositional Log-Linear Model for Microbiome Data with Zero Cells" <doi:10.1101/2025.11.26.690468>. Zero counts are treated as censored observations below sample-specific detection limits, avoiding the use of pseudocounts. The package implements estimation and hypothesis testing procedures for assessing associations between microbial taxa and covariates while accounting for the compositional structure of sequencing count data. It supports taxon-level differential abundance analysis, estimation of regression effects under censoring induced by detection limits, and inference based on rank-based methods that remain applicable in the presence of excess zeros. Functions are provided for model fitting, significance testing, extraction of effect estimates, and summarization of results across taxa. The package also provides optional bootstrap calibration of taxon-level p-values for sensitivity analysis in small-taxon settings.

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4.65 score 4 scripts 349 downloads