Related papers: Multi-species count transformation models
Discrete data such as counts of microbiome taxa resulting from next-generation sequencing are routinely encountered in bioinformatics. Taxa count data in microbiome studies are typically high-dimensional, over-dispersed, and can only reveal…
In the companion paper of this set (Capitan and Cuesta, 2010) we have developed a full analytical treatment of the model of species assembly introduced in Capitan et al. (2009). This model is based on the construction of an assembly graph…
Topic modeling is a popular method used to describe biological count data. With topic models, the user must specify the number of topics $K$. Since there is no definitive way to choose $K$ and since a true value might not exist, we develop…
We investigate the replicator dynamics with "sparse" symmetric interactions which represent specialist-specialist interactions in ecological communities. By considering a large self interaction $u$, we conduct a perturbative expansion which…
General circulation models (GCMs) are essential tools for climate studies. Such climate models may have varying accuracy across the input domain, but no model is uniformly best. One can improve climate model prediction performance by…
This paper develops a Bayesian graphical model for fusing disparate types of count data. The motivating application is the study of bacterial communities from diverse high dimensional features, in this case transcripts, collected from…
Occupancy modeling is a common approach to assess spatial and temporal species distribution patterns, while explicitly accounting for measurement errors common in detection-nondetection data. Numerous extensions of the basic single species…
Models of the spatial distribution of animals provide useful tools to help ecologists quantify species-environment relationships, and they are increasingly being used to help determine the impacts of climate and habitat changes on species.…
In the last decade, stochastic models have shown to be very useful for quantitative modelling of social processes. Here, a configurational master equation for the description of behavioral changes by pair interactions of individuals is…
Ecologists often interpret variation in the spatial distribution of populations in terms of responses to environmental features, but disentangling the effects of individual variables can be difficult if latent effects and spatial and…
A flexible semiparametric class of models is introduced that offers an alternative to classical regression models for count data as the Poisson and negative binomial model, as well as to more general models accounting for excess zeros that…
North Atlantic right whales are an endangered species; their entire population numbers approximately 372 individuals, and they are subject to major anthropogenic threats. They feed on zooplankton species whose distribution shifts in a…
This is the second of two papers dedicated to the relationship between population models of competition and biodiversity. Here we consider species assembly models where the population dynamics is kept far from fixed points through the…
An analytical approximation is derived for the Zero Sum Multinomial distribution which gives the Species Abundance Distribution in Neutral Community Models. The obtained distribution function describes well computer simulation results on…
1.) Spatio-temporal datasets that are difficult to analyze are common in ecological surveys. There are software packages available to analyze these datasets, but many of them require advanced coding skills. There is a growing need for easy…
In fisheries ecology, species abundance data are often collected by multiple surveys, each with unique characteristics. This article is motivated by a dataset of Atlantic sea scallop abundance records along the northeast coast of the United…
Understanding covariate-varying interdependencies among features is of great interest in various applications. Motivated by microbiome studies where microbial abundances and interactions vary with environmental factors, we develop a…
The distributions of species lifetimes and species in space are related, since species with good local survival chances have more time to colonize new habitats and species inhabiting large areas have higher chances to survive local…
Stochastic models that incorporate birth, death and immigration (also called birth-death and innovation models) are ubiquitous and applicable to many research topics such as quantifying species sizes in ecological populations, describing…
The number of species can be estimated by sampling individuals from a species assemblage. The problem of estimating generalized species accumulation curve is addressed in a nonparametric Poisson mixture model. A likelihood-based estimator…