PrevMap: Geostatistical Modelling of Spatially Referenced Prevalence Data
Version 1.4

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("PrevMap")

Popular man pages

binomial.logistic.Bayes: Bayesian estimation for the binomial logistic model
discrete.sample: Spatially discrete sampling
Laplace.sampling: Langevin-Hastings MCMC for conditional simulation
linear.model.MLE: Maximum Likelihood estimation for the geostatistical linear...
loaloa: Loa loa prevalence data from 197 village surveys
loglik.linear.model: Profile log-likelihood or fixed parameters likelihood...
matern.kernel: Matern kernel
See all...

All man pages Function index File listing

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...

Functions

Laplace.sampling Man page Source code
Laplace.sampling.SPDE Man page Source code
Laplace.sampling.lr Man page Source code
adjust.sigma2 Man page Source code
autocor.plot Man page Source code
binary.geo.Bayes Source code
binary.geo.Bayes.lr Source code
binary.probit.Bayes Man page Source code
binomial.geo.Bayes Source code
binomial.geo.Bayes.SPDE Source code
binomial.geo.Bayes.lr Source code
binomial.logistic.Bayes Man page Source code
binomial.logistic.MCML Man page Source code
coef.PrevMap Man page Source code
coef.PrevMap.ps Man page Source code
cond.sim.ps Source code
continuous.sample Man page Source code
contour.pred.PrevMap Man page Source code
control.mcmc.Bayes Man page Source code
control.mcmc.Bayes.SPDE Man page Source code
control.mcmc.MCML Man page Source code
control.prior Man page Source code
control.profile Man page Source code
create.ID.coords Man page Source code
data_sim Man page
dens.plot Man page Source code
discrete.sample Man page Source code
galicia Man page
galicia.boundary Man page
geo.MCML Source code
geo.MCML.SPDE Source code
geo.MCML.lr Source code
geo.linear.Bayes Source code
geo.linear.Bayes.lr Source code
geo.linear.MLE Source code
geo.linear.MLE.SPDE Source code
geo.linear.MLE.lr Source code
linear.model.Bayes Man page Source code
linear.model.MLE Man page Source code
lm.ps.MCML Man page Source code
loaloa Man page
loglik.ci Man page Source code
loglik.linear.model Man page Source code
matern.kernel Man page Source code
maxim.integrand Source code
maxim.integrand.SPDE Source code
maxim.integrand.lr Source code
plot.pred.PrevMap Man page Source code
plot.pred.PrevMap.ps Man page Source code
plot.profile.PrevMap Man page Source code
plot.shape.matern Man page Source code
poisson.log.MCML Man page Source code
print.summary.Bayes.PrevMap Source code
print.summary.PrevMap Source code
print.summary.PrevMap.ps Source code
set.par.ps Man page Source code
shape.matern Man page Source code
spatial.pred.binomial.Bayes Man page Source code
spatial.pred.binomial.MCML Man page Source code
spatial.pred.linear.Bayes Man page Source code
spatial.pred.linear.MLE Man page Source code
spatial.pred.lm.ps Man page Source code
spatial.pred.poisson.MCML Man page Source code
summary.Bayes.PrevMap Man page Source code
summary.PrevMap Man page Source code
summary.PrevMap.ps Man page Source code
trace.plot Man page Source code
trace.plot.MCML Man page Source code

Files

inst
inst/doc
inst/doc/PrevMap.ltx
inst/doc/PrevMap.pdf
NAMESPACE
data
data/loaloa.rdata
data/data_sim.rdata
data/galicia.boundary.rdata
data/galicia.rdata
R
R/foo.R
R/galicia.R
R/data_sim.R
R/loaloa.R
R/galicia.boundary.R
vignettes
vignettes/jss.dtx
vignettes/PrevMap.ltx
vignettes/jsslogo.jpg
vignettes/biblio.bib
vignettes/Images
vignettes/Images/loaloa_profile_kappa.png
vignettes/Images/loaloa_profile.png
vignettes/Images/loaloa_pred.png
vignettes/Images/acf_loaloa.png
vignettes/Images/loaloa1.png
vignettes/Images/data_sim_pred.png
vignettes/Images/sim_loc.png
vignettes/Images/diagnostic.png
vignettes/Images/autocorrelogram.png
MD5
build
build/vignette.rds
DESCRIPTION
man
man/summary.Bayes.PrevMap.Rd
man/coef.PrevMap.ps.Rd
man/Laplace.sampling.SPDE.Rd
man/spatial.pred.lm.ps.Rd
man/data_sim.Rd
man/plot.pred.PrevMap.Rd
man/spatial.pred.binomial.Bayes.Rd
man/plot.profile.PrevMap.Rd
man/spatial.pred.linear.Bayes.Rd
man/Laplace.sampling.lr.Rd
man/spatial.pred.poisson.MCML.Rd
man/dens.plot.Rd
man/control.prior.Rd
man/linear.model.Bayes.Rd
man/lm.ps.MCML.Rd
man/spatial.pred.linear.MLE.Rd
man/binomial.logistic.MCML.Rd
man/contour.pred.PrevMap.Rd
man/galicia.Rd
man/create.ID.coords.Rd
man/Laplace.sampling.Rd
man/continuous.sample.Rd
man/poisson.log.MCML.Rd
man/loglik.linear.model.Rd
man/spatial.pred.binomial.MCML.Rd
man/shape.matern.Rd
man/trace.plot.Rd
man/binomial.logistic.Bayes.Rd
man/plot.shape.matern.Rd
man/galicia.boundary.Rd
man/coef.PrevMap.Rd
man/loglik.ci.Rd
man/control.mcmc.MCML.Rd
man/plot.pred.PrevMap.ps.Rd
man/loaloa.Rd
man/set.par.ps.Rd
man/control.mcmc.Bayes.Rd
man/summary.PrevMap.Rd
man/trace.plot.MCML.Rd
man/summary.PrevMap.ps.Rd
man/matern.kernel.Rd
man/adjust.sigma2.Rd
man/control.profile.Rd
man/autocor.plot.Rd
man/control.mcmc.Bayes.SPDE.Rd
man/discrete.sample.Rd
man/linear.model.MLE.Rd
man/binary.probit.Bayes.Rd
PrevMap documentation built on May 20, 2017, 12:18 a.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.