Estimating diversity in networked ecological communities

Bayesian Nonparametric Ordination for the Analysis of Microbial Communities

(2017) Boyu Ren et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Bayesian nonparametric dependent model for partially replicated data: The influence of fuel spills on species diversity

(2016) Julyan Arbel et al.   Annals of Applied Statistics

Improved detection of changes in species richness in high diversity microbial communities

(2016) Amy Willis et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS

iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers)

(2016) T. C. Hsieh et al.   Methods in Ecology and Evolution

Fine-scale hydrological niche differentiation through the lens of multi-species co-occurrence models

(2015) Andrew D. Letten et al.   JOURNAL OF ECOLOGY

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

Microbial Communities on Seafloor Basalts at Dorado Outcrop Reflect Level of Alteration and Highlight Global Lithic Clades

(2015) Michael D. Lee et al.   Frontiers in Microbiology

Microbiome, Metagenomics, and High-Dimensional Compositional Data Analysis

(2015) Hongzhe Li   Annual Review of Statistics and Its Application

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression

(2014) Charles K. Fisher et al.   PLoS One

Model-based approaches to unconstrained ordination

(2014) Francis K.C. Hui et al.   Methods in Ecology and Evolution

Understanding co-occurrence by modelling species simultaneously with a Joint Species Distribution Model (JSDM)

(2014) Laura J. Pollock et al.   Methods in Ecology and Evolution

A Logistic Normal Multinomial Regression Model for Microbiome Compositional Data Analysis

(2013) Fan Xia et al.   BIOMETRICS

Entropy and the species accumulation curve: a novel entropy estimator via discovery rates of new species

(2013) Anne Chao et al.   Methods in Ecology and Evolution

Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth

(2013) Connor O. McCoy et al.   PeerJ

The multinomial diversity model: linking Shannon diversity to multiple predictors

(2012) Glenn De'ath   ECOLOGY

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

New Insights and Faster Computations for the Graphical Lasso

(2011) Daniela M. Witten et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

Modelling community dynamics based on species-level abundance models from detection/nondetection data

(2010) Yuichi Yamaura et al.   JOURNAL OF APPLIED ECOLOGY

Re-parameterization of multinomial distributions and diversity indices

(2010) Zhiyi Zhang et al.   JOURNAL OF STATISTICAL PLANNING AND INFERENCE