Geostatistical Modelling of Spatially Referenced Prevalence Data

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Documentation for package ‘PrevMap’ version 1.1.4

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adjust.sigma2 Adjustment factor for the variance of the convolution of Gaussian noise
autocor.plot Plot of the autocorrelgram for posterior samples
binomial.logistic.Bayes Bayesian estimation for the binomial logistic model
binomial.logistic.MCML Monte Carlo Maximum Likelihood estimation for the binomial logistic model
coef.PrevMap Extract model coefficients
continuous.sample Spatially continuous sampling
contour.pred.PrevMap Contour plot of a predicted surface
control.mcmc.Bayes Control settings for the MCMC algorithm used for Bayesian inference
control.mcmc.MCML Control settings for the MCMC algorithm used for classical inference on a binomial logistic model
control.prior Priors specification
control.profile Auxliary function for controlling profile log-likelihood in the linear Gaussian model
create.ID.coords ID spatial coordinates
data_sim Simulated binomial data-set over the unit square
dens.plot Density plot for posterior samples
discrete.sample Spatially discrete sampling
Laplace.sampling Langevin-Hastings MCMC for conditional simulation
Laplace.sampling.lr Langevin-Hastings MCMC for conditional simulation (low-rank approximation)
linear.model.Bayes Bayesian estimation for the geostatistical linear Gaussian model
linear.model.MLE Maximum Likelihood estimation for the geostatistical linear Gaussian model
loaloa Loa loa prevalence data from 197 village surveys
loglik.ci Profile likelihood confidence intervals
loglik.linear.model Profile log-likelihood or fixed parameters likelihood evaluation for the covariance parameters in the geostatistical linear model
matern.kernel Matern kernel
plot.pred.PrevMap Plot of a predicted surface
plot.profile.PrevMap Plot of the profile log-likelihood for the covariance parameters of the Matern function
plot.shape.matern Plot of the profile likelihood for the shape parameter of the Matern covariance function
shape.matern Profile likelihood for the shape parameter of the Matern covariance function
spatial.pred.binomial.Bayes Bayesian spatial predictions for the binomial logistic model
spatial.pred.binomial.MCML Spatial predictions for the binomial logistic model using plug-in of MCML estimates
spatial.pred.linear.Bayes Bayesian spatial predictions for the geostatistical Linear Gaussian model
spatial.pred.linear.MLE Spatial predictions for the geostatistical Linear Gaussian model using plug-in of ML estimates
summary.Bayes.PrevMap Summarizing Bayesian model fits
summary.PrevMap Summarizing likelihood-based model fits
trace.plot Trace-plots for posterior samples