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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include=FALSE, echo=FALSE,message=FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
out.width = "100%")
```
# spOccupancy <a href='https://www.jeffdoser.com/files/spoccupancy-web/'><img src="man/figures/logo.png" align="right" height="139" width="120"/></a>
[](https://CRAN.R-project.org/package=spOccupancy)
[](https://CRAN.R-project.org/package=spOccupancy)
[](https://codecov.io/gh/doserjef/spOccupancy?branch=main)
spOccupancy fits single-species, multi-species, and integrated spatial occupancy models using Markov chain Monte Carlo (MCMC). Models are fit using Pólya-Gamma data augmentation. Spatial models are fit using either Gaussian processes or Nearest Neighbor Gaussian Processes (NNGP) for large spatial datasets. The package provides functionality for data integration of multiple single-species occupancy data sets using a joint likelihood framework. For multi-species models, spOccupancy provides functions to account for residual species correlations in a joint species distribution model framework while accounting for imperfect detection. `spOccupancy` also provides functions for multi-season (i.e., spatio-temporal) single-species occupancy models. Below we give a very brief introduction to some of the package's functionality, and illustrate just one of the model fitting functions. For more information, see the resources referenced at the bottom of this page.
## Installation
```{r, echo = FALSE}
set.seed(100)
```
You can install the released version of `spOccupancy` from [CRAN](https://CRAN.R-project.org) with:
```{r, eval = FALSE}
install.packages("spOccupancy")
```
## Functionality
| `spOccupancy` Function | Description |
| ---------------------- | -------------------------------------------------------------------------|
| `PGOcc()` | Single-species occupancy model |
| `spPGOcc()` | Single-species spatial occupancy model |
| `intPGOcc()` | Single-species occupancy model with multiple data sources |
| `spIntPGOcc()` | Single-species spatial occupancy model with multiple data sources |
| `msPGOcc()` | Multi-species occupancy model |
| `spMsPGOcc()` | Multi-species spatial occupancy model |
| `lfJSDM()` | Joint species distribution model without imperfect detection |
| `sfJSDM()` | Spatial joint species distribution model without imperfect detection |
| `lfMsPGOcc()` | Multi-species occupancy model with species correlations |
| `sfMsPGOcc()` | Multi-species spatial occupancy model with species correlations |
| `intMsPGOcc()` | Multi-species occupancy model with multiple data sources |
| `tPGOcc()` | Single-species multi-season occupancy model |
| `stPGOcc()` | Single-species multi-season spatio-temporal occupancy model |
| `svcPGBinom()` | Single-species spatially-varying coefficient GLM |
| `svcPGOcc()` | Single-species spatially-varying coefficient occupancy model |
| `svcTPGBinom()` | Single-species spatially-varying coefficient multi-season GLM |
| `svcTPGOcc()` | Single-species spatially-varying coefficient multi-season occupancy model|
| `svcMsPGOcc()` | Multi-species spatially-varying coefficient occupancy model |
| `tMsPGOcc()` | Multi-species, multi-season occupancy model |
| `stMsPGOcc()` | Multi-species, multi-season spatial occupancy model |
| `svcTMsPGOcc()` | Multi-species, multi-season spatially-varying coefficient occupancy model|
| `postHocLM()` | Fit a linear (mixed) model using estimates from a previous model fit |
| `ppcOcc()` | Posterior predictive check using Bayesian p-values |
| `waicOcc()` | Compute Widely Applicable Information Criterion (WAIC) |
| `updateMCMC()` | Update an existing model object with more MCMC samples (in development) |
| `simOcc()` | Simulate single-species occupancy data |
| `simTOcc()` | Simulate single-species multi-season occupancy data |
| `simBinom()` | Simulate detection-nondetection data with perfect detection |
| `simTBinom()` | Simulate multi-season detection-nondetection data with perfect detection |
| `simMsOcc()` | Simulate multi-species occupancy data |
| `simTMsOcc()` | Simulate multi-species, multi-season occupancy data |
| `simIntOcc()` | Simulate single-species occupancy data from multiple data sources |
| `simIntMsOcc()` | Simulate multi-species occupancy data from multiple data sources |
## Example usage
### Load package and data
To get started with `spOccupancy` we load the package and an example data set. We use data on twelve foliage-gleaning birds from the [Hubbard Brook Experimental Forest](https://hubbardbrook.org/), which is available in the `spOccupancy` package as the `hbef2015` object. Here we will only work with one bird species, the black-throated blue warbler (BTBW), and so we subset the `hbef2015` object to only include this species.
```{r}
library(spOccupancy)
data(hbef2015)
sp.names <- dimnames(hbef2015$y)[[1]]
btbwHBEF <- hbef2015
btbwHBEF$y <- btbwHBEF$y[sp.names == "BTBW", , ]
```
### Fit a spatial occupancy model using `spPGOcc()`
Below we fit a single-species spatial occupancy model to the BTBW data using a Nearest Neighbor Gaussian Process. We use the default priors and initial values for the occurrence (`beta`) and detection (`alpha`) coefficients, the spatial variance (`sigma.sq`), the spatial decay parameter (`phi`), the spatial random effects (`w`), and the latent occurrence values (`z`). We assume occurrence is a function of linear and quadratic elevation along with a spatial random intercept. We model detection as a function of linear and quadratic day of survey and linear time of day the survey occurred.
```{r}
# Specify model formulas
btbw.occ.formula <- ~ scale(Elevation) + I(scale(Elevation)^2)
btbw.det.formula <- ~ scale(day) + scale(tod) + I(scale(day)^2)
```
We run the model using an adaptive MCMC sampler with a target acceptance rate of 0.43. We run 3 chains of the model each for 10,000 iterations split into 400 batches each of length 25. For each chain, we discard the first 2000 iterations as burn-in and use a thinning rate of 4 for a resulting 6000 samples from the joint posterior. We fit the model using 5 nearest neighbors and an exponential correlation function. We also specify the `k.fold` argument to perform 2-fold cross-validation after fitting the full model. Run `?spPGOcc` for more detailed information on all function arguments.
```{r}
# Run the model
out <- spPGOcc(occ.formula = btbw.occ.formula,
det.formula = btbw.det.formula,
data = btbwHBEF, n.batch = 400, batch.length = 25,
accept.rate = 0.43, cov.model = "exponential",
NNGP = TRUE, n.neighbors = 5, n.burn = 2000,
n.thin = 4, n.chains = 3, verbose = FALSE, k.fold = 2)
```
This will produce a large output object, and you can use `str(out)` to get an overview of what's in there. Here we use the `summary()` function to print a concise but informative summary of the model fit.
```{r}
summary(out)
```
### Posterior predictive check
The function `ppcOcc` performs a posterior predictive check on the resulting list from the call to `spPGOcc`. For binary data, we need to perform Goodness of Fit assessments on some binned form of the data rather than the raw binary data. Below we perform a posterior predictive check on the data grouped by site with a Freeman-Tukey fit statistic, and then use the `summary` function to summarize the check with a Bayesian p-value.
```{r}
ppc.out <- ppcOcc(out, fit.stat = 'freeman-tukey', group = 1)
summary(ppc.out)
```
### Model selection using WAIC and k-fold cross-validation
The `waicOcc` function computes the Widely Applicable Information Criterion (WAIC) for use in model selection and assessment (note that due to Monte Carlo error your results will differ slightly).
```{r}
waicOcc(out)
```
Alternatively, we can perform k-fold cross-validation (CV) directly in our call to `spPGOcc` using the `k.fold` argument and compare models using a deviance scoring rule. We fit the model with `k.fold = 2` and so below we access the deviance scoring rule from the 2-fold cross-validation. If we have additional candidate models to compare this model with, then we might select for inference the one with the lowest value of this CV score.
```{r}
out$k.fold.deviance
```
### Prediction
Prediction is possible using the `predict` function, a set of occurrence covariates at the new locations, and the spatial coordinates of the new locations. The object `hbefElev` contains elevation data across the entire Hubbard Brook Experimental Forest. Below we predict BTBW occurrence across the forest, which are stored in the `out.pred` object.
```{r, eval = FALSE}
# First standardize elevation using mean and sd from fitted model
elev.pred <- (hbefElev$val - mean(btbwHBEF$occ.covs[, 1])) / sd(btbwHBEF$occ.covs[, 1])
coords.0 <- as.matrix(hbefElev[, c('Easting', 'Northing')])
X.0 <- cbind(1, elev.pred, elev.pred^2)
out.pred <- predict(out, X.0, coords.0, verbose = FALSE)
```
## Learn more
The `vignette("modelFitting")` provides a more detailed description and tutorial of the core functions in `spOccupancy`. For full statistical details on the MCMC samplers for core functions in `spOccupancy`, see `vignette("mcmcSamplers")`. In addition, see [the introductory spOccupancy paper](https://doi.org/10.1111/2041-210X.13897) that describes the package in more detail (Doser et al. 2022). For a detailed description and tutorial of joint species distribution models in `spOccupancy` that account for residual species correlations, see `vignette("factorModels")`, `vignette("mcmcFactorModels")`, and our [open-access paper](https://doi.org/10.1002/ecy.4137) (Doser et al. 2023). For a description and tutorial of multi-season (spatio-temporal) occupancy models in `spOccupancy`, see `vignette("spaceTimeModels")`. For a tutorial on spatially-varying coefficient models in `spOccupancy`, see `vignette("svcModels")` and `vignette(mcmcSVCModels)` and our associated papers that describe the [methods](https://www.jeffdoser.com/files/pubs/doser2024JABES.pdf) (Doser et al. 2024A) and [applications to ecology](https://onlinelibrary.wiley.com/doi/epdf/10.1111/geb.13814) (Doser et al. 2024B) in much more detail.
## References
Doser, J. W., Finley, A. O., Kery, M., and Zipkin, E. F. (2022a). spOccupancy: An R package for single-species, multi-species, and integrated spatial occupancy models. Methods in Ecology and Evolution. 13(8) 1670-1678. https://doi.org/10.1111/2041-210X.13897.
Doser, J. W., Finley, A. O., and Banerjee, S. (2023). Joint species distribution models with imperfect detection for high-dimensional spatial data. Ecology, 104(9), e4137. https://doi.org/10.1002/ecy.4137.
Doser, J. W., Finley, A. O., Saunders, S. P., Kéry, M., Weed, A. S., & Zipkin, E. F. (2024A). Modeling complex species-environment relationships through spatially-varying coefficient occupancy models. Journal of Agricultural, Biological and Environmental Statistics. https://doi.org/10.1007/s13253-023-00595-6.
Doser, J. W., Kéry, M., Saunders, S. P., Finley, A. O., Bateman, B. L., Grand, J., Reault, S., Weed, A. S., & Zipkin, E. F. (2024B). Guidelines for the use of spatially varying coefficients in species distribution models. Global Ecology and Biogeography, 33, e13814. https://doi.org/10.1111/geb.13814