# Fast Spatially Discrete Approximation to Log-Gaussian Cox Processes for Aggregated Disease Count Data

## Documentation for package ‘SDALGCP2’ version 0.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

coef_plot | Coefficient plot of fixed effects (and sigma^2) with confidence intervals
confint.SDALGCP2 | Wald confidence intervals for an SDALGCP2 fit
control_mcmc | MCMC control settings for the MALA sampler
exceedance | Exceedance probabilities P(risk > threshold)
laplace_sampling | Sample the latent field [S | Y] (Poisson, non-nested) via C++ MALA
liver | Primary biliary cirrhosis incidence in North East England
map_exceedance | Map exceedance probabilities P(risk > threshold)
mcml_fit | Monte Carlo maximum likelihood estimation for the spatial SDA-LGCP
mc_diagnostics | Importance-sampling diagnostics for an MCML fit
model_check | Posterior-predictive model checking for an SDALGCP2 fit
phi_profile | Profile likelihood and confidence interval for the spatial scale phi
plot.sdalgcp | Map an sdalgcp fit
plot.SDALGCP2 | Plot an SDALGCP2 fit (the phi profile deviance)
plot.SDALGCP2_pred | Map a fitted SDALGCP2 prediction
plot.SDALGCP2_ST_pred | Map a spatio-temporal prediction for one time
precompute_corr | Precompute aggregated region-level correlation matrices
predict.sdalgcp | Predict relative risk from an sdalgcp fit
predict.SDALGCP2 | Predict relative risk from a fitted SDALGCP2 model
predict.SDALGCP2_ST | Discrete (region x time) prediction for a spatio-temporal fit
print.SDALGCP2 | Print an SDALGCP2 fit
print.summary.SDALGCP2 | Print a summary of an SDALGCP2 fit
report | One-call panel of post-fit graphics
sdalgcp | Fit a spatially discrete LGCP model for aggregated counts
SDALGCP2 | Fit a spatial SDA-LGCP model
SDALGCP2_misaligned | Fit an SDA-LGCP with covariates measured on a different support
SDALGCP2_raster | Fit an SDA-LGCP with spatially continuous (raster) covariates
SDALGCP2_ST | Fit a spatio-temporal SDA-LGCP model (Kronecker-free)
sdalgcp_control | Control settings for 'sdalgcp'
sdalgcp_data | Simulated aggregated disease-count data
sda_points | Generate candidate sampling points inside each region
summary.SDALGCP2 | Summary of an SDALGCP2 fit