Joint species distribution modelling with the r-package Hmsc

Gleb Tikhonov; Øystein H Opedal; Nerea Abrego; Aleksi Lehikoinen; Melinda M J de Jonge; Jari Oksanen; Otso Ovaskainen

doi:10.1111/2041-210X.13345

Joint species distribution modelling with the r-package Hmsc

Methods Ecol Evol. 2020 Mar;11(3):442-447. doi: 10.1111/2041-210X.13345. Epub 2020 Jan 23.

Authors

Gleb Tikhonov^{1

2}, Øystein H Opedal^{2

3}, Nerea Abrego⁴, Aleksi Lehikoinen⁵, Melinda M J de Jonge⁶, Jari Oksanen⁷, Otso Ovaskainen^{2

3}

Affiliations

¹ Department of Computer Science Aalto University Espoo Finland.
² Organismal and Evolutionary Biology Research Programme University of Helsinki Helsinki Finland.
³ Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology Trondheim Norway.
⁴ Department of Agricultural Sciences University of Helsinki Helsinki Finland.
⁵ The Helsinki Lab of Ornithology Finnish Museum of Natural History University of Helsinki Helsinki Finland.
⁶ Department of Environmental Science Institute for Water and Wetland Research Radboud University Nijmegen The Netherlands.
⁷ Botany Unit Finnish Museum of Natural History University of Helsinki Helsinki Finland.

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.

Keywords: community ecology; community modelling; community similarity; hierarchical modelling of species communities; joint species distribution modelling; multivariate data; species distribution modelling.