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

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Documentation for package ‘SDALGCP2’ version 0.1.0

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

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