Related papers: A Bayesian theory for estimation of biodiversity
A Bayesian nonparametric approach to the study of species diversity based on choosing a random discrete distribution as a prior model for the unknown relative abundances of species has been recently introduced in Lijoi et al. (2007, 2008).…
We derive explicit Bayesian nonparametric analysis for a species sampling model with finitely many types of Gibbs form of type $\alpha= -1$ recently introduced in Gnedin (2009). Our results complement existing analysis under Gibbs priors of…
Global species richness is a key biodiversity metric. Despite recent efforts to estimate global species richness, the resulting estimates have been highly uncertain and often logically inconsistent. Estimates lower down either the taxonomic…
We present an alternative approach to the Bayesian nonparametric analysis of conditional species richness under two-parameter Poisson Dirichlet priors. We rely on a known characterization by deletion of classes property and on results for…
In Bayesian nonparametric inference, random discrete probability measures are commonly used as priors within hierarchical mixture models for density estimation and for inference on the clustering of the data. Recently, it has been shown…
This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100036). Approximate Bayesian computation (ABC) has grown into a standard methodology that manages Bayesian…
We describe a new and computationally efficient Bayesian methodology for inferring species trees and demographics from unlinked binary markers. Likelihood calculations are carried out using diffusion models of allele frequency dynamics…
Tsallis entropy is a generalized diversity index first derived in Patil and Taillie (1982) and then rediscovered in community ecology by Keylock (2005). Bayesian nonparametric estimation of Shannon entropy and Simpson's diversity under…
Given a sample of size $n$ from a population of individuals belonging to different species with unknown proportions, a popular problem of practical interest consists in making inference on the probability $D_{n}(l)$ that the $(n+1)$-th draw…
This paper proposes a novel approach for statistical modelling of a continuous random variable $X$ on $[0, 1)$, based on its digit representation $X=.X_1X_2\ldots$. In general, $X$ can be coupled with a latent random variable $N$ so that…
We derive ensembles of decision trees through a nonparametric Bayesian model, allowing us to view random forests as samples from a posterior distribution. This insight provides large gains in interpretability, and motivates a class of…
Given i.i.d. data from an unknown distribution, we consider the problem of predicting future items. An adaptive way to estimate the probability density is to recursively subdivide the domain to an appropriate data-dependent granularity. A…
To understand biological diversification, it is important to account for large-scale processes that affect the evolutionary history of groups of co-distributed populations of organisms. Such events predict temporally clustered divergences…
Quantitative methods for studying biodiversity have been traditionally rooted in the classical theory of finite frequency tables analysis. However, with the help of modern experimental tools, like high throughput sequencing, we now begin to…
Given i.i.d. data from an unknown distribution, we consider the problem of predicting future items. An adaptive way to estimate the probability density is to recursively subdivide the domain to an appropriate data-dependent granularity. A…
We present a robust Bayesian method to analyze forestry data when samples are selected with probability proportional to length from a finite population of unknown size. Specifically, we use Bayesian predictive inference to estimate the…
Discrete random probability measures and the exchangeable random partitions they induce are key tools for addressing a variety of estimation and prediction problems in Bayesian inference. Indeed, many popular nonparametric priors, such as…
Biological data objects often have both of the following features: (i) they are functions rather than single numbers or vectors, and (ii) they are correlated due to phylogenetic relationships. In this paper we give a flexible statistical…
Many of the mathematical frameworks describing natural selection are equivalent to Bayes Theorem, also known as Bayesian updating. By definition, a process of Bayesian Inference is one which involves a Bayesian update, so we may conclude…
To study population dynamics, ecologists and wildlife biologists use relative abundance data, which are often subject to temporal preferential sampling. Temporal preferential sampling occurs when sampling effort varies across time. To…