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.

Author
Emanuele Giorgi, Peter J. Diggle
Date of publication
2016-10-17 00:44:51
Maintainer
Emanuele Giorgi <e.giorgi@lancaster.ac.uk>
License
GPL (>= 2)
Version
1.4

View on CRAN

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