Defining and evaluating predictions of joint species distribution models

David P. Wilkinson, Nick Golding, Gurutzeta Guillera-Arroita, Reid Tingley, Michael A. McCarthy

Research output: Contribution to journalArticleResearchpeer-review

1 Citation (Scopus)


Joint species distribution models (JSDMs) simultaneously model the distributions of multiple species, while accounting for residual co-occurrence patterns. Despite increasing adoption of JSDMs in the literature, the question of how to define and evaluate JSDM predictions has only begun to be explored. We define four different JSDM prediction types that correspond to different aspects of species distribution and community assemblage processes. Marginal predictions are environment-only predictions akin to predictions from single-species models; joint predictions simultaneously predict entire community assemblages; and conditional marginal and conditional joint predictions are made at the species or assemblage level, conditional on the known occurrence state of one or more species at a site. We define five different classes of metrics that can be used to evaluate these types of predictions: threshold-dependent, threshold-independent, community dissimilarity, species richness and likelihood metrics. We illustrate different prediction types and evaluation metrics using a case study in which we fit a JSDM to a frog occurrence dataset collected in Melbourne, Australia. Joint species distribution models present opportunities to investigate the facets of species distribution and community assemblage processes that are not possible to explore with single-species models. We show that there are a variety of different metrics available to evaluate JSDM predictions, and that choice of prediction type and evaluation metric should closely match the questions being investigated.

Original languageEnglish
Pages (from-to)394-404
Number of pages11
JournalMethods in Ecology and Evolution
Issue number3
Publication statusPublished - Mar 2021


  • biotic interactions
  • community assemblage
  • evaluation metrics
  • joint species distribution models
  • prediction
  • species richness

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