Cohesive framework for modeling plant cover class data
Irvine KM, Wright WJ, Shanahan EK, Rodhouse TJ. 2019. Cohesive framework for modeling plant cover class data. Methods in Ecology and Evolution. 10:1749-1760
1. The study of plant distribution and abundance is a fundamental pursuit in ecology and conservation biology. Measuring plant abundance by visually assessing percent cover and recording a cover class is a common field method that yields ordinal data. Statistical models for ordinal data exist but entail cumbersome interpretations and sometimes restrictive assumptions. 2. We propose a Bayesian hierarchical framework for analyzing cover class data that allows for linking ordinal observations to a latent beta distribution and accounts for zero inflation. Harnessing a latent beta distribution supports interpreting changes in abundance in terms of mean percent cover rather than odds ratios of cumulative cover classes as for cumulative link models. The zero augmentation allows for simultaneous inferences on both occurrence (distribution) and abundance. We show how our model can account for true and false zeros, misclassification of cover classes, multiple species, and hierarchical sampling designs by way of empirical examples and simulations. 3. Simulated observation errors, when ignored, led to models overestimating abundance and underestimating occurrence. Based on simulations, we found no substantial difference between mean percent cover estimates when analyzing ordinal cover classes versus continuous percent cover as the response. Our empirical datasets displayed high proba-bility of detection (> 0.85 on average for all species), likely due to the sampling design used and training of observers. Probability of occurrence was slightly underestimated for bareground, Artemisia tridentata, Elycap medusae, and Poa secunda using a model that ignored imperfect detection. Estimated mean percent cover was not substantially impacted by ignoring measurement error for five plant species and bareground. 4. Our modeling framework for cover class data allows for an explicit separation of dis-tribution from abundance and, importantly, allows for interpreting species-environment relationships in terms of variation in mean percent cover as compared to cumulative odds ratios. The beta distribution inherently accommodates heteroskedasticity and skewness, statistical properties that are a consequence of spatially aggregated patterns common to plant survey data. Recording cover classes provides a reliable, efficient way to measure plants and our simulations suggest little loss of information compared to assuming continuous percent cover. We provide JAGS and Stan model code for implementation.
- Type
- Journal Article
- Authors
- Irvine, Kathryn; Wright, Wilson; Shanahan, Erin; Rodhouse, Thomas
- Units
- BICA , GRYN , JODA , UCBN
- Keywords
- beta regression, GRYN journal article, imperfect detection, measurement error, monitoring, observer errors, occupancy models, ordinal models, plant cover, UCBN journal article
- Subjects
- Ecological Framework: Biological Integrity | Invasive Species | Invasive/Exotic plants , Ecological Framework: Biological Integrity | Focal Species or Communities | Grassland/Herbaceous Communities , Ecological Framework: Biological Integrity | Focal Species or Communities | Shrubland Communities , Ecological Framework: Biological Integrity | Focal Species or Communities | Vegetation Complex , Ecological Framework: Biological Integrity | At-risk Biota | T&E Species and Communities