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

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...

Functions

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

Files

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

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

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

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