PrevMap: Geostatistical Modelling of Spatially Referenced Prevalence Data

It provides functions for both likelihood-based and Bayesian analysis of spatially referenced prevalence data, and is also an extension of the 'geoR' package.

AuthorEmanuele Giorgi, Peter J. Diggle
Date of publication2016-10-17 00:44:51
MaintainerEmanuele Giorgi <e.giorgi@lancaster.ac.uk>
LicenseGPL (>= 2)
Version1.4

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Man pages

adjust.sigma2: Adjustment factor for the variance of the convolution of...

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...

coef.PrevMap: Extract model coefficients

coef.PrevMap.ps: Extract model coefficients from geostatistical linear model...

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...

control.mcmc.Bayes.SPDE: Control settings for the MCMC algorithm used for Bayesian...

control.mcmc.MCML: Control settings for the MCMC algorithm used for classical...

control.prior: Priors specification

control.profile: Auxliary function for controlling profile log-likelihood in...

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

Laplace.sampling: Langevin-Hastings MCMC for conditional simulation

Laplace.sampling.lr: Langevin-Hastings MCMC for conditional simulation (low-rank...

Laplace.sampling.SPDE: Independence sampler for conditional simulation of a Gaussian...

linear.model.Bayes: Bayesian estimation for the geostatistical linear Gaussian...

linear.model.MLE: Maximum Likelihood estimation for the geostatistical linear...

lm.ps.MCML: Monte Carlo Maximum Likelihood estimation of the...

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...

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...

plot.profile.PrevMap: Plot of the profile log-likelihood for the covariance...

plot.shape.matern: Plot of the profile likelihood for the shape parameter of the...

poisson.log.MCML: Monte Carlo Maximum Likelihood estimation for the Poisson...

set.par.ps: Define the model coefficients of a geostatistical linear...

shape.matern: Profile likelihood for the shape parameter of the Matern...

spatial.pred.binomial.Bayes: Bayesian spatial prediction for the binomial logistic and...

spatial.pred.binomial.MCML: Spatial predictions for the binomial logistic model using...

spatial.pred.linear.Bayes: Bayesian spatial predictions for the geostatistical Linear...

spatial.pred.linear.MLE: Spatial predictions for the geostatistical Linear Gaussian...

spatial.pred.lm.ps: Spatial predictions for the geostatistical Linear Gaussian...

spatial.pred.poisson.MCML: Spatial predictions for the Poisson model with log link...

summary.Bayes.PrevMap: Summarizing Bayesian model fits

summary.PrevMap: Summarizing likelihood-based model fits

summary.PrevMap.ps: Summarizing fits of geostatistical linear models with...

trace.plot: Trace-plots for posterior samples

trace.plot.MCML: Trace-plots of the importance sampling distribution samples...

Files in this package

PrevMap
PrevMap/inst
PrevMap/inst/doc
PrevMap/inst/doc/PrevMap.ltx
PrevMap/inst/doc/PrevMap.pdf
PrevMap/NAMESPACE
PrevMap/data
PrevMap/data/loaloa.rdata
PrevMap/data/data_sim.rdata
PrevMap/data/galicia.boundary.rdata
PrevMap/data/galicia.rdata
PrevMap/R
PrevMap/R/foo.R PrevMap/R/galicia.R PrevMap/R/data_sim.R PrevMap/R/loaloa.R PrevMap/R/galicia.boundary.R
PrevMap/vignettes
PrevMap/vignettes/jss.dtx
PrevMap/vignettes/PrevMap.ltx
PrevMap/vignettes/jsslogo.jpg
PrevMap/vignettes/biblio.bib
PrevMap/vignettes/Images
PrevMap/vignettes/Images/loaloa_profile_kappa.png
PrevMap/vignettes/Images/loaloa_profile.png
PrevMap/vignettes/Images/loaloa_pred.png
PrevMap/vignettes/Images/acf_loaloa.png
PrevMap/vignettes/Images/loaloa1.png
PrevMap/vignettes/Images/data_sim_pred.png
PrevMap/vignettes/Images/sim_loc.png
PrevMap/vignettes/Images/diagnostic.png
PrevMap/vignettes/Images/autocorrelogram.png
PrevMap/MD5
PrevMap/build
PrevMap/build/vignette.rds
PrevMap/DESCRIPTION
PrevMap/man
PrevMap/man/summary.Bayes.PrevMap.Rd PrevMap/man/coef.PrevMap.ps.Rd PrevMap/man/Laplace.sampling.SPDE.Rd PrevMap/man/spatial.pred.lm.ps.Rd PrevMap/man/data_sim.Rd PrevMap/man/plot.pred.PrevMap.Rd PrevMap/man/spatial.pred.binomial.Bayes.Rd PrevMap/man/plot.profile.PrevMap.Rd PrevMap/man/spatial.pred.linear.Bayes.Rd PrevMap/man/Laplace.sampling.lr.Rd PrevMap/man/spatial.pred.poisson.MCML.Rd PrevMap/man/dens.plot.Rd PrevMap/man/control.prior.Rd PrevMap/man/linear.model.Bayes.Rd PrevMap/man/lm.ps.MCML.Rd PrevMap/man/spatial.pred.linear.MLE.Rd PrevMap/man/binomial.logistic.MCML.Rd PrevMap/man/contour.pred.PrevMap.Rd PrevMap/man/galicia.Rd PrevMap/man/create.ID.coords.Rd PrevMap/man/Laplace.sampling.Rd PrevMap/man/continuous.sample.Rd PrevMap/man/poisson.log.MCML.Rd PrevMap/man/loglik.linear.model.Rd PrevMap/man/spatial.pred.binomial.MCML.Rd PrevMap/man/shape.matern.Rd PrevMap/man/trace.plot.Rd PrevMap/man/binomial.logistic.Bayes.Rd PrevMap/man/plot.shape.matern.Rd PrevMap/man/galicia.boundary.Rd PrevMap/man/coef.PrevMap.Rd PrevMap/man/loglik.ci.Rd PrevMap/man/control.mcmc.MCML.Rd PrevMap/man/plot.pred.PrevMap.ps.Rd PrevMap/man/loaloa.Rd PrevMap/man/set.par.ps.Rd PrevMap/man/control.mcmc.Bayes.Rd PrevMap/man/summary.PrevMap.Rd PrevMap/man/trace.plot.MCML.Rd PrevMap/man/summary.PrevMap.ps.Rd PrevMap/man/matern.kernel.Rd PrevMap/man/adjust.sigma2.Rd PrevMap/man/control.profile.Rd PrevMap/man/autocor.plot.Rd PrevMap/man/control.mcmc.Bayes.SPDE.Rd PrevMap/man/discrete.sample.Rd PrevMap/man/linear.model.MLE.Rd PrevMap/man/binary.probit.Bayes.Rd

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