corncob - Count Regression for Correlated Observations with the Beta-Binomial

Statistical modeling for correlated count data using the beta-binomial distribution, described in Martin et al. (2020) <doi:10.1214/19-AOAS1283>. It allows for both mean and overdispersion covariates.

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9.85 score 108 stars 1 dependents 392 scripts 606 downloads

breakaway - Species Richness Estimation and Modeling

Understanding the drivers of microbial diversity is an important frontier of microbial ecology, and investigating the diversity of samples from microbial ecosystems is a common step in any microbiome analysis. 'breakaway' is the premier package for statistical analysis of microbial diversity. 'breakaway' implements the latest and greatest estimates of species richness, described in Willis and Bunge (2015) <doi:10.1111/biom.12332>, Willis et al. (2017) <doi:10.1111/rssc.12206>, and Willis (2016) <arXiv:1604.02598>, as well as the most commonly used estimates, including the objective Bayes approach described in Barger and Bunge (2010) <doi:10.1214/10-BA527>.

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8.21 score 68 stars 265 scripts 440 downloads

rigr - Regression, Inference, and General Data Analysis Tools in R

A set of tools to streamline data analysis. Learning both R and introductory statistics at the same time can be challenging, and so we created 'rigr' to facilitate common data analysis tasks and enable learners to focus on statistical concepts. We provide easy-to-use interfaces for descriptive statistics, one- and two-sample inference, and regression analyses. 'rigr' output includes key information while omitting unnecessary details that can be confusing to beginners. Heteroscedasticity-robust ("sandwich") standard errors are returned by default, and multiple partial F-tests and tests for contrasts are easy to specify. A single regression function can fit both linear and generalized linear models, allowing students to more easily make connections between different classes of models.

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regressionstatistics

7.49 score 10 stars 51 scripts 977 downloads

radEmu - Using Relative Abundance Data to Estimate of Multiplicative Differences in Mean Absolute Abundance

A differential abundance method for the analysis of microbiome data. 'radEmu' estimates fold-differences in the abundance of taxa across samples relative to "typical" fold-differences. Notably, it does not require pseudocounts, nor choosing a denominator taxon. For more details, see Clausen et al. (2026) <doi:10.1093/biomet/asag009>.

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dametagenomicsmicrobiomestatistics

7.18 score 65 stars 72 scripts 244 downloads