Multivariate ecological models
Conditional Random Fields (CRF) models use species’ occurrences or abundances as outcome variables and allow variance to be partitioned among both abiotic and biotic effects. Some major advantages of these models are that they can:
Produce directly interpretable coefficients that allow users to determine the relative importances (i.e. effect sizes) of biotic associations and environmental covariates in driving abundances or occurrence probabilities
Identify association strengths, rather than simply determining whether they are “significantly different from zero”
Estimate how associations are predicted to change across environmental gradients.
Clark, NJ, Tozer, S, Wood, C, Firestone, SM, Stevenson, M, Caraguel, C, Chaber, AL, Heller, J and Soares Magalhães, RJ. 2020. Unravelling animal exposure profiles of human Q fever cases in Queensland, Australia using natural language processing. Transboundary and Emerging Diseases. DOI: https://doi.org/10.1111/tbed.13565.
Clark, NJ, Owada, K, Ruberanziza, E, Ortu, G, Umulisa, I, Bayisenge, U, Mbonigaba, JB, Mucaca, JB, Lancaster, W, Fenwick, A, Soares Magalhaes, RJ and Mbituyumuremyi, A. 2020. Parasite associations predict infection risk: incorporating co-infections in predictive models for neglected tropical diseases. Parasites & Vectors 13:1-16.
Clark, NJ, Kerry, JT and Fraser, CI. 2020. Rapid winter warming could disrupt coastal marine fish community structure. Nature Climate Change. DOI: 10.1038/s41558-41020-40838-41555.
Fountain‐Jones, NM, Clark, NJ, Kinsley, AC, Carstensen, M, Forester, J, Johnson, TJ, Miller, E, Moore, S, Wolf, TM and Craft, ME. 2019. Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition. Journal of Animal Ecology 89:817-828.Peel, AJ, Wells, K, Giles, J, Boyd, V, Burroughs, A, Edson, D, Crameri, G, Baker, ML, Field, H, Wang, LF, McCallum, H, Plowright, RK and Clark, NJ. 2019. Synchronous shedding of multiple bat paramyxoviruses coincides with peak periods of Hendra virus spillover. Emerging Microbes & Infections 8:1314-1323.