MBRarefy: data-adaptive multi-bin rarefying for alpha diversity association analysis

Mo Li

Home/Archive/arXiv

arXiv · 2606.21000

MBRarefy: data-adaptive multi-bin rarefying for alpha diversity association analysis

Mo Li

View original source ↗Read source document ↗Export metadata ↓

Abstract

Summary: This paper presents MBRarefy, an R package that provides a reproducible workflow for alpha diversity analysis under confounding from heterogeneous library sizes. Building on the multi-bin rarefying approach in Li et al (2024), MBRarefy supports alpha diversity association analysis with repeated rarefying, bin-wise testing, and cross-bin meta-analysis. A key new feature is automated, data-adaptive selection of library size bin thresholds via a genetic algorithm (GA), which replaces ad hoc cutpoints with an objective optimization procedure based on the rarefying-derived profiles. The package also supports routine data-management tasks, including file-based sample-wise processing and standardized output generation, enabling users to execute the full analysis pipeline from raw count files to combined inferential results. Availability and implementation: The R package MBRarefy is freely available on GitHub at https://github.com/mli171/MBRarefy.

Explore related subjects

stat.CO stat.ME

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Mo Li. 2026-06-19. MBRarefy: data-adaptive multi-bin rarefying for alpha diversity association analysis. https://arxiv.org/abs/2606.21000

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Extended One-Liners for the Gamma, Poisson, and Binomial Distributions

We demonstrate explicit transformations of three independent uniforms with exact Gamma$(a,1)$, $a>0$, Poisson$(\lambda)$, $\lambda>0$, and Binomial$(N,p)$, $N\geq 1$, $0\leq p \leq 1$ laws using only elementary operations.

stat.CO↗

arXiv2026

Estimating Hierarchically Rank Structured Covariance Matrices

We consider the problem of estimating a high-dimensional covariance matrix from a very limited number of samples. This problem is ubiquitous in computational fluid dynamics, where a small number of fluid snapshots must be used to construct a Gramian matrix determining a reduced-order model, as well as in computational geoscience, where a small ensemble of Earth system forecasts must be used to estimate the covariance matrix associated with the forecast uncertainty. It is common practice to regularize the small-sample covariance by imposing a "localization" structure that enforces a physically realistic correlation length scale, imposing a sparsity constraint, "shrinking" towards a prescribed target, or attenuating small correlations. We propose an alternate technique that regularizes the small-sample covariance by imposing hierarchical rank structure. Compared to regularization methods that assume sparsity such as spatial localization, hierarchical rank structure accommodates a wider range of covariance matrices, roughly corresponding to situations where long-range correlations vary more smoothly than short-range ones. It also results in a data-sparse matrix format that permits highly efficient matrix-vector products. We present theory and algorithms which show how to efficiently estimate a high-dimensional, hierarchically rank structured covariance matrix from limited samples. Through an error analysis and numerical experiments with a variety of model problems, we demonstrate that these techniques are effective at reducing sampling errors, and that in many cases they achieve smaller estimation error than conventional techniques.

stat.CO↗

arXiv2026

Optimal Slice-Adaptive Tuning of Hybrid Slice Sampling

Slice sampling is a Markov chain Monte Carlo algorithm that draws its next state uniformly from a "slice"---a super-level set of the target density function---at each iteration, thereby providing automatic local adaptivity to the scale of the target. In practice the exact slice is not known, so general-purpose implementations use an approximate slice that is grown from a starting interval of length $w>0$, with a computational cost that depends on $w$. This work presents an analysis of the average per-iteration number of target density evaluations, as a function of $w$, of hybrid slice sampling with various slice-finding schemes for targets with contiguous slices. The paper uses the results of the analysis to develop automated, slice-adaptive tuning schemes along with suboptimality bounds and asymptotic convergence guarantees. Simulations demonstrate that the tuning schemes reliably yield near-optimal slice-adaptive tuning with essentially no dependence on the initial setting of $w$.

stat.CO↗