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While log-Gaussian Cox process regression models are useful tools for modeling point patterns, they can be technically difficult to fit and require users to learn/adopt bespoke software. We show that, for suitably formatted data, we can actually fit these models using generalized additive model software, via a simple line of code, demonstrated on R by the popular mgcv package. We are able to do this because a common and computationally efficient way to fit a log-Gaussian Cox process model is to use a basis function expansion to approximate the Gaussian random field, as is provided by a generic bivariate smoother over geographic space. We further show that if basis functions are parameterized appropriately then we can estimate parameters in the spatial covariance function for the latent random field using a generalized additive model. We use simulation to show that this approach leads to model fits of comparable quality to state-of-the-art software, often more quickly. But we see the main advance from this work as lowering the technology barrier to spatial statistics for applied researchers, many of whom are already familiar with generalized additive model software. [ABSTRACT FROM AUTHOR]

Zero-inflated count data models are widely used in various fields such as ecology, epidemiology, and transportation, where count data with a large proportion of zeros is prevalent. Despite their widespread use, their theoretical properties have not been extensively studied. This study aims to investigate the impact of ignoring heterogeneity in event count intensity and susceptibility probability on zero-inflated count data analysis within the zero-inflated Poisson framework. To address this issue, we propose a novel conditional likelihood approach that uses positive count data only to estimate event count intensity parameters and develop a consistent estimator for estimating the average susceptibility probability. Our approach is compared with the maximum likelihood approach, and we demonstrate our findings through a comprehensive simulation study and real data analysis. The results can also be extended to zero-inflated binomial and geometric models with similar conclusions. These findings contribute to the understanding of the theoretical properties of zero-inflated count data models and provide a practical approach to handling heterogeneity in such models. [ABSTRACT FROM AUTHOR]

Spatial or temporal clustering commonly arises in various biological and ecological applications, for example, species or communities may cluster in groups. In this paper, we develop a new clustered occurrence data model where presence–absence data are modeled under a multivariate negative binomial framework. We account for spatial or temporal clustering by introducing a community parameter in the model that controls the strength of dependence between observations thereby enhancing the estimation of the mean and dispersion parameters. We provide conditions to show the existence of maximum likelihood estimates when cluster sizes are homogeneous and equal to 2 or 3 and consider a composite likelihood approach that allows for additional robustness and flexibility in fitting for clustered occurrence data. The proposed method is evaluated in a simulation study and demonstrated using forest plot data from the Center for Tropical Forest Science. Finally, we present several examples using multiple visit occupancy data to illustrate the difference between the proposed model and those of N‐mixture models. [ABSTRACT FROM AUTHOR]