Scholarly Work - Ecology
Permanent URI for this collectionhttps://scholarworks.montana.edu/handle/1/8716
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Item Evaluating and presenting uncertainty in model‐based unconstrained ordination(2019-12) Hoegh, Andrew; Roberts, David W.Variability in ecological community composition is often analyzed by recording the presence or abundance of taxa in sample units, calculating a symmetric matrix of pairwise distances or dissimilarities among sample units and then mapping the resulting matrix to a low‐dimensional representation through methods collectively called ordination. Unconstrained ordination only uses taxon composition data, without any environmental or experimental covariates, to infer latent compositional gradients associated with the sampling units. Commonly, such distance‐based methods have been used for ordination, but recently there has been a shift toward model‐based approaches. Model‐based unconstrained ordinations are commonly formulated using a Bayesian latent factor model that permits uncertainty assessment for parameters, including the latent factors that correspond to gradients in community composition. While model‐based methods have the additional benefit of addressing uncertainty in the estimated gradients, typically the current practice is to report point estimates without summarizing uncertainty. To demonstrate the uncertainty present in model‐based unconstrained ordination, the well‐known spider and dune data sets were analyzed and shown to have large uncertainty in the ordination projections. Hence to understand the factors that contribute to the uncertainty, simulation studies were conducted to assess the impact of additional sampling units or species to help inform future ordination studies that seek to minimize variability in the latent factors. Accurate reporting of uncertainty is an important part of transparency in the scientific process; thus, a model‐based approach that accounts for uncertainty is valuable. An R package, UncertainOrd, contains visualization tools that accurately represent estimates of the gradients in community composition in the presence of uncertainty.Item Identifying occupancy model inadequacies: can residuals separately assess detection and presence?(2019-04) Wright, Wilson J.; Irvine, Kathryn M.; Higgs, Megan D.Occupancy models are widely applied to estimate species distributions, but few methods exist for model checking. Thorough model assessments can uncover inadequacies and allow for deeper ecological insight by exploring structure in the observed data not accounted for by a model. We introduce occupancy model residual definitions that utilize the posterior distribution of the partially latent occupancy states. Residual-based assessments are valuable because they can target specific assumptions and identify ways to improve a model, such as adding spatial correlation or meaningful covariates. Our approach defines separate residuals for occupancy and detection, and we use simulation to examine whether missing structure for modeling detection probabilities can be distinguished from that for occupancy probabilities. In many scenarios, our residual diagnostics were able to separate inadequacies at the different model levels successfully, but we describe other situations when this may not be the case. Applying Moran\'s I residual diagnostics to assess models for silver-haired (Lasionycteris noctivagans) and little brown (Myotis lucifugus) bats only provided evidence of residual spatial correlation among detections. Targeting specific model assumptions using carefully chosen residual diagnostics is valuable for any analysis, and we remove previous barriers for occupancy analyses-lack of examples and practical advice.