Geostatistical Modelling of Spatially Referenced Prevalence Data

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Documentation for package ‘PrevMap’ version 1.5.4

• DESCRIPTION file.

Help Pages

adjust.sigma2	Adjustment factor for the variance of the convolution of Gaussian noise
autocor.plot	Plot of the autocorrelgram for posterior samples
binary.probit.Bayes	Bayesian estimation for the two-levels binary probit model
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
coef.PrevMap.ps	Extract model coefficients from geostatistical linear model with preferentially sampled locations
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.Bayes.SPDE	Control settings for the MCMC algorithm used for Bayesian inference using SPDE
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
galicia	Heavy metal biomonitoring in Galicia
galicia.boundary	Boundary of Galicia
glgm.LA	Maximum Likelihood estimation for generalised linear geostatistical models via the Laplace approximation
Laplace.sampling	Langevin-Hastings MCMC for conditional simulation
Laplace.sampling.lr	Langevin-Hastings MCMC for conditional simulation (low-rank approximation)
Laplace.sampling.SPDE	Independence sampler for conditional simulation of a Gaussian process using SPDE
linear.model.Bayes	Bayesian estimation for the geostatistical linear Gaussian model
linear.model.MLE	Maximum Likelihood estimation for the geostatistical linear Gaussian model
lm.ps.MCML	Monte Carlo Maximum Likelihood estimation of the geostatistical linear model with preferentially sampled locations
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.pred.PrevMap.ps	Plot of a predicted surface of geostatistical linear fits with preferentially sampled locations
plot.PrevMap.diagnostic	Plot of the variogram-based diagnostics
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
point.map	Point map
poisson.log.MCML	Monte Carlo Maximum Likelihood estimation for the Poisson model
set.par.ps	Define the model coefficients of a geostatistical linear model with preferentially sampled locations
shape.matern	Profile likelihood for the shape parameter of the Matern covariance function
spat.corr.diagnostic	Diagnostics for residual spatial correlation
spatial.pred.binomial.Bayes	Bayesian spatial prediction for the binomial logistic and binary probit models
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
spatial.pred.lm.ps	Spatial predictions for the geostatistical Linear Gaussian model using plug-in of ML estimates
spatial.pred.poisson.MCML	Spatial predictions for the Poisson model with log link function, using plug-in of MCML estimates
summary.Bayes.PrevMap	Summarizing Bayesian model fits
summary.PrevMap	Summarizing likelihood-based model fits
summary.PrevMap.ps	Summarizing fits of geostatistical linear models with preferentially sampled locations
trace.plot	Trace-plots for posterior samples
trace.plot.MCML	Trace-plots of the importance sampling distribution samples from the MCML method
trend.plot	Plot of trends
variog.diagnostic.glgm	Variogram-based validation for generalized linear geostatistical model fits (Binomial and Poisson)
variog.diagnostic.lm	Variogram-based validation for linear geostatistical model fits
variogram	The empirical variogram