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Numerous modelling techniques exist to estimate abundance of plant and animal populations. The most accurate methods account for multiple complexities found in ecological data, such as observational biases, spatial autocorrelation, and species correlations. There is, however, a lack of user‐friendly and computationally efficient software to implement the various models, particularly for large data sets.

Determining the spatial distributions of species and communities is a key task in ecology and conservation efforts. Joint species distribution models are a fundamental tool in community ecology that use multi‐species detection–nondetection data to estimate species distributions and biodiversity metrics. The analysis of such data is complicated by residual correlations between species, imperfect detection, and spatial autocorrelation. While many methods exist to accommodate each of these complexities, there are few examples in the literature that address and explore all three complexities simultaneously. Here we developed a spatial factor multi‐species occupancy model to explicitly account for species correlations, imperfect detection, and spatial autocorrelation. The proposed model uses a spatial factor dimension reduction approach and Nearest Neighbor Gaussian Processes to ensure computational efficiency for data sets with both a large number of species (e.g., >100) and spatial locations (e.g., 100,000). We compared the proposed model performance to five alternative models, each addressing a subset of the three complexities. We implemented the proposed and alternative models in thespOccupancysoftware, designed to facilitate application via an accessible, well documented, and open‐source R package. Using simulations, we found that ignoring the three complexities when present leads to inferior model predictive performance, and the impacts of failing to account for one or more complexities will depend on the objectives of a given study. Using a case study on 98 bird species across the continental US, the spatial factor multi‐species occupancy model had the highest predictive performance among the alternative models. Our proposed framework, together with its implementation inspOccupancy, serves as a user‐friendly tool to understand spatial variation in species distributions and biodiversity while addressing common complexities in multi‐species detection–nondetection data.

A key challenge in spatial data science is the analysis for massive spatially‐referenced data sets. Such analyses often proceed from Gaussian process specifications that can produce rich and robust inference, but involve dense covariance matrices that lack computationally exploitable structures. Recent developments in spatial statistics offer a variety of massively scalable approaches. Bayesian inference and hierarchical models, in particular, have gained popularity due to their richness and flexibility in accommodating spatial processes. Our current contribution is to provide computationally efficient exact algorithms for spatial interpolation of massive data sets using scalable spatial processes. We combine low‐rank Gaussian processes with efficient sparse approximations. Following recent work by Zhang et al. (2019), we model the low‐rank process using a Gaussian predictive process (GPP) and the residual process as a sparsity‐inducing nearest‐neighbor Gaussian process (NNGP). A key contribution here is to implement these models using exact conjugate Bayesian modeling to avoid expensive iterative algorithms. Through the simulation studies, we evaluate performance of the proposed approach and the robustness of our models, especially for long range prediction. We implement our approaches for remotely sensed light detection and ranging (LiDAR) data collected over the US Forest Service Tanana Inventory Unit (TIU) in a remote portion of Interior Alaska.