Joint species distribution modelling with the r-package Hmsc

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Tikhonov , G , Opedal , O H , Abrego , N , Lehikoinen , A , de Jonge , M M J , Oksanen , J & Ovaskainen , O 2020 , ' Joint species distribution modelling with the r-package Hmsc ' , Methods in Ecology and Evolution , vol. 11 , no. 3 , pp. 442-447 .

Title: Joint species distribution modelling with the r-package Hmsc
Author: Tikhonov, Gleb; Opedal, Oystein H.; Abrego, Nerea; Lehikoinen, Aleksi; de Jonge, Melinda M. J.; Oksanen, Jari; Ovaskainen, Otso
Contributor: University of Helsinki, Research Centre for Ecological Change
University of Helsinki, Research Centre for Ecological Change
University of Helsinki, Department of Agricultural Sciences
University of Helsinki, Helsinki Institute of Sustainability Science (HELSUS)
University of Helsinki, Finnish Museum of Natural History
University of Helsinki, Organismal and Evolutionary Biology Research Programme
Date: 2020-03-01
Language: eng
Number of pages: 6
Belongs to series: Methods in Ecology and Evolution
ISSN: 2041-210X
Abstract: Joint Species Distribution Modelling (JSDM) is becoming an increasingly popular statistical method for analysing data in community ecology. Hierarchical Modelling of Species Communities (HMSC) is a general and flexible framework for fitting JSDMs. HMSC allows the integration of community ecology data with data on environmental covariates, species traits, phylogenetic relationships and the spatio-temporal context of the study, providing predictive insights into community assembly processes from non-manipulative observational data of species communities. The full range of functionality of HMSC has remained restricted to Matlab users only. To make HMSC accessible to the wider community of ecologists, we introduce Hmsc 3.0, a user-friendly r implementation. We illustrate the use of the package by applying Hmsc 3.0 to a range of case studies on real and simulated data. The real data consist of bird counts in a spatio-temporally structured dataset, environmental covariates, species traits and phylogenetic relationships. Vignettes on simulated data involve single-species models, models of small communities, models of large species communities and models for large spatial data. We demonstrate the estimation of species responses to environmental covariates and how these depend on species traits, as well as the estimation of residual species associations. We demonstrate how to construct and fit models with different types of random effects, how to examine MCMC convergence, how to examine the explanatory and predictive powers of the models, how to assess parameter estimates and how to make predictions. We further demonstrate how Hmsc 3.0 can be applied to normally distributed data, count data and presence-absence data. The package, along with the extended vignettes, makes JSDM fitting and post-processing easily accessible to ecologists familiar with r.
Subject: community ecology
community modelling
community similarity
hierarchical modelling of species communities
joint species distribution modelling
multivariate data
species distribution modelling
1181 Ecology, evolutionary biology

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