# Log-Gaussian Cox Process

## Documentation for package ‘lgcp’ version 2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I K L M N O P Q R S T U V W X Y Z misc

lgcp-package | lgcp

## -- A --

add.list | add.list function
addTemporalCovariates | addTemporalCovariates function
affine.fromFunction | affine.fromFunction function
affine.fromSPDF | affine.fromSPDF function
affine.fromXYZ | affine.fromXYZ function
affine.SpatialPolygonsDataFrame | affine.SpatialPolygonsDataFrame function
affine.stppp | affine.stppp function
aggCovInfo | aggCovInfo function
aggCovInfo.ArealWeightedMean | aggCovInfo.ArealWeightedMean function
aggCovInfo.ArealWeightedSum | aggCovInfo.ArealWeightedSum function
aggCovInfo.Majority | aggCovInfo.Majority function
aggregateCovariateInfo | aggregateCovariateInfo function
aggregateformulaList | aggregateformulaList function
andrieuthomsh | andrieuthomsh function
as.array.lgcpgrid | as.array.lgcpgrid function
as.fromXYZ | as.fromXYZ function
as.fromXYZ.fromFunction | as.fromXYZ.fromFunction function
as.im.fromFunction | as.im.fromFunction function
as.im.fromSPDF | as.im.fromSPDF function
as.im.fromXYZ | as.im.fromXYZ function
as.list.lgcpgrid | as.list.lgcpgrid function
as.owin.stapp | as.owin.stapp function
as.owinlist | as.owinlist function
as.owinlist.SpatialPolygonsDataFrame | as.owinlist.SpatialPolygonsDataFrame function
as.owinlist.stapp | as.owinlist.stapp function
as.ppp.mstppp | as.ppp.mstppp function
as.ppp.stppp | as.ppp.stppp function
as.SpatialGridDataFrame | as.SpatialGridDataFrame function
as.SpatialGridDataFrame.fromXYZ | as.SpatialGridDataFrame.fromXYZ function
as.SpatialPixelsDataFrame | as.SpatialPixelsDataFrame function
as.SpatialPixelsDataFrame.lgcpgrid | as.SpatialPixelsDataFrame.lgcpgrid function
as.stppp | as.stppp function
as.stppp.stapp | as.stppp.stapp function
assigninterp | assigninterp function
at | at function
autocorr | autocorr function
autocorrMultitype | autocorrMultitype function

## -- B --

BetaParameters | BetaParameters function
betavals | betavals function
blockcircbase | blockcircbase function
blockcircbaseFunction | blockcircbaseFunction function
bt.scalar | bt.scalar function

## -- C --

checkObsWin | checkObsWin function
chooseCellwidth | chooseCellwidth function
circulant | circulant function
circulant.matrix | circulant.matrix function
circulant.numeric | circulant.numeric function
clearinterp | clearinterp function
computeGradtruncSpatial | computeGradtruncSpatial function
computeGradtruncSpatioTemporal | computeGradtruncSpatioTemporal function
condProbs | condProbs function
constanth | constanth function
constantInTime | constantInTime function
constantInTime.numeric | constantInTime.numeric function
constantInTime.stppp | constantInTime.stppp function
cov.interp.fft | cov.interp.fft function
CovarianceFct | CovarianceFct function
covEffects | covEffects function
CovFunction | CovFunction function
CovFunction.function | CovFunction.function function
CovParameters | CovParameters function
Cvb | Cvb function

## -- D --

d.func | d.func function
density.stppp | density.stppp function
discreteWindow | discreteWindow function
discreteWindow.lgcpPredict | discreteWindow.lgcpPredict function
dump2dir | dump2dir function

## -- E --

eigenfrombase | eigenfrombase function
etavals | etavals function
EvaluatePrior | EvaluatePrior function
exceedProbs | exceedProbs function
exceedProbsAggregated | exceedProbsAggregated function
expectation | expectation function
expectation.lgcpPredict | expectation.lgcpPredict function
expectation.lgcpPredictSpatialOnlyPlusParameters | expectation.lgcpPredictSpatialOnlyPlusParameters function
exponentialCovFct | exponentialCovFct function
extendspatialAtRisk | extendspatialAtRisk function
extract | extract function
extract.lgcpPredict | extract.lgcpPredict function
Extract.mstppp | Extract.mstppp function
Extract.stppp | Extract.stppp function

## -- F --

fftgrid | fftgrid function
fftinterpolate | fftinterpolate function
fftinterpolate.fromFunction | fftinterpolate.fromFunction function
fftinterpolate.fromSPDF | fftinterpolate.fromSPDF function
fftinterpolate.fromXYZ | interpolate.fromXYZ function
fftmultiply | fftmultiply function
formulaList | formulaList function

## -- G --

GAfinalise | GAfinalise function
GAfinalise.MonteCarloAverage | GAfinalise.MonteCarloAverage function
GAfinalise.nullAverage | GAfinalise.nullAverage function
GAinitialise | GAinitialise function
GAinitialise.MonteCarloAverage | GAinitialise.MonteCarloAverage function
GAinitialise.nullAverage | GAinitialise.nullAverage function
GammafromY | GammafromY function
GAreturnvalue | GAreturnvalue function
GAreturnvalue.MonteCarloAverage | GAreturnvalue.MonteCarloAverage function
GAreturnvalue.nullAverage | GAreturnvalue.nullAverage function##'
GAupdate | GAupdate function
GAupdate.MonteCarloAverage | GAupdate.MonteCarloAverage function
GAupdate.nullAverage | GAupdate.nullAverage function
GaussianPrior | GaussianPrior function
gDisjoint_wg | gDisjoint_wg function
genFFTgrid | genFFTgrid function
getCellCounts | getCellCounts function
getCounts | getCounts function
getCovParameters | getCovParameters function
getCovParameters.GPrealisation | getCovParameters.GPrealisation function
getCovParameters.list | getCovParameters.list function
getinterp | getinterp function
getlgcpPredictSpatialINLA | getlgcpPredictSpatialINLA function
getLHSformulaList | getLHSformulaList function
getpolyol | getpolyol function
getRotation | getRotation function
getRotation.default | getRotation.default function
getRotation.stppp | getRotation.stppp function
getup | getup function
getZmat | getZmat function
getZmats | getZmats function
GFfinalise | GFfinalise function
GFfinalise.dump2dir | GFfinalise.dump2dir function
GFfinalise.nullFunction | GFfinalise.nullFunction function
GFinitialise | GFinitialise function
GFinitialise.dump2dir | GFinitialise.dump2dir function
GFinitialise.nullFunction | GFinitialise.nullFunction function
GFreturnvalue | GFreturnvalue function
GFreturnvalue.dump2dir | GFreturnvalue.dump2dir function
GFreturnvalue.nullFunction | GFreturnvalue.nullFunction function
GFupdate | GFupdate function
GFupdate.dump2dir | GFupdate.dump2dir function
GFupdate.nullFunction | GFupdate.nullFunction function
ginhomAverage | ginhomAverage function
gIntersects_pg | gIntersects_pg function
gOverlay | gOverlay function
GPdrv | GPdrv function
GPdrv2 | GPdrv2 function
GPdrv2_Multitype | GPdrv2_Multitype function
GPlist2array | GPlist2array function
GPrealisation | GPrealisation function
grid2spdf | grid2spdf function
grid2spix | grid2spix function
grid2spoly | grid2spoly function
grid2spts | grid2spts function
gridav | gridav function
gridav.lgcpPredict | gridav.lgcpPredict function
gridfun | gridfun function
gridfun.lgcpPredict | gridfun.lgcpPredict function
gridInWindow | gridInWindow function
gTouches_wg | gTouches_wg function
gu | gu function
guessinterp | guessinterp function

## -- H --

hasNext | generic hasNext method
hasNext.iter | hasNext.iter function
hvals | hvals function
hvals.lgcpPredict | hvals.lgcpPredict function

## -- I --

identify.lgcpPredict | identify.lgcpPredict function
identifygrid | identifygrid function
image.lgcpgrid | image.lgcpgrid function
initialiseAMCMC | initialiseAMCMC function
initialiseAMCMC.andrieuthomsh | initaliseAMCMC.andrieuthomsh function
initialiseAMCMC.constanth | initaliseAMCMC.constanth function
integerise | integerise function
integerise.mstppp | integerise.mstppp function
integerise.stppp | integerise.stppp function
intens | intens function
intens.lgcpPredict | intens.lgcpPredict function
intens.lgcpSimMultitypeSpatialPlusParameters | intens.lgcpSimMultitypeSpatialPlusParameters function
intens.lgcpSimSpatialPlusParameters | intens.lgcpSimSpatialPlusParameters function
interptypes | interptypes function
inversebase | inversebase function
is.burnin | is this a burn-in iteration?
is.pow2 | is.pow2 function
is.retain | do we retain this iteration?
is.SPD | is.SPD function
iteration | iteration number

## -- K --

KinhomAverage | KinhomAverage function

## -- L --

lambdaEst | lambdaEst function
lambdaEst.ppp | lambdaEst.ppp function
lambdaEst.stppp | lambdaEst.stppp function
lgcp | lgcp
lgcpbayes | lgcpbayes function
lgcpForecast | lgcpForecast function
lgcpgrid | lgcpgrid function
lgcpgrid.array | lgcpgrid.array function
lgcpgrid.list | lgcpgrid.list function
lgcpgrid.matrix | lgcpgrid.matrix function
lgcpInits | lgcpInits function
lgcppars | lgcppars function
lgcpPredict | lgcpPredict function
lgcpPredictAggregated | lgcpPredictAggregated function
lgcpPredictAggregateSpatialPlusPars | lgcpPredictAggregateSpatialPlusPars function
lgcpPredictMultitypeSpatialPlusPars | lgcpPredictMultitypeSpatialPlusPars function
lgcpPredictSpatial | lgcpPredictSpatial function
lgcpPredictSpatialINLA | lgcpPredictSpatialINLA function
lgcpPredictSpatialPlusPars | lgcpPredictSpatialPlusPars function
lgcpPredictSpatioTemporalPlusPars | lgcpPredictSpatioTemporalPlusPars function
lgcpPrior | lgcpPrior function
lgcpSim | lgcpSim function
lgcpSimMultitypeSpatialCovariates | lgcpSimMultitypeSpatialCovariates function
lgcpSimSpatial | lgcpSimSpatial function
lgcpSimSpatialCovariates | lgcpSimSpatialCovariates function
lgcpvignette | lgcpvignette function
loc2poly | loc2poly function
LogGaussianPrior | LogGaussianPrior function
loop.mcmc | loop over an iterator
ltar | ltar function

## -- M --

MALAlgcp | MALAlgcp function
MALAlgcpAggregateSpatial.PlusPars | MALAlgcpAggregateSpatial.PlusPars function
MALAlgcpMultitypeSpatial.PlusPars | MALAlgcpMultitypeSpatial.PlusPars function
MALAlgcpSpatial | MALAlgcpSpatial function
MALAlgcpSpatial.PlusPars | MALAlgcpSpatial.PlusPars function
MALAlgcpSpatioTemporal.PlusPars | MALAlgcpSpatioTemporal.PlusPars function
matchcovariance | matchcovariance function
maternCovFct15 | maternCovFct15 function
maternCovFct25 | maternCovFct25 function
mcmcLoop | iterator for MCMC loops
mcmcpars | mcmcpars function
mcmcProgressNone | null progress monitor
mcmcProgressPrint | printing progress monitor
mcmcProgressTextBar | text bar progress monitor
mcmcProgressTk | graphical progress monitor
mcmctrace | mcmctrace function
mcmctrace.lgcpPredict | mcmctrace.lgcpPredict function
meanfield | meanfield function
meanfield.lgcpPredict | meanfield.lgcpPredict function
meanfield.lgcpPredictINLA | meanfield.lgcpPredictINLA function
MonteCarloAverage | MonteCarloAverage function
mstppp | mstppp function
mstppp.list | mstppp.list function
mstppp.ppp | mstppp.ppp function
mstppp.stppp | mstppp.stppp function
muEst | muEst function
multiply.list | multiply.list function

## -- N --

neattable | neattable function
neigh2D | neigh2D function
nextStep | next step of an MCMC chain
nullAverage | nullAverage function
nullFunction | nullFunction function
numCases | numCases function

## -- O --

osppp2latlon | osppp2latlon function
osppp2merc | osppp2merc function

## -- P --

paramprec | paramprec function
paramprecbase | paramprecbase function
parautocorr | parautocorr function
parsummary | parsummary function
plot.fromSPDF | plot.fromSPDF function
plot.fromXYZ | plot.fromXYZ function
plot.lgcpAutocorr | plot.lgcpAutocorr function
plot.lgcpgrid | plot.lgcpgrid function
plot.lgcpPredict | plot.lgcpPredict function
plot.lgcpQuantiles | plot.lgcpQuantiles function
plot.lgcpZmat | plot.lgcpZmat function
plot.mcmcdiag | plot.mcmcdiag function
plot.mstppp | plot.mstppp function
plot.stppp | plot.stppp function
plot.temporalAtRisk | plot.temporalAtRisk function
plotExceed | plotExceed function
plotExceed.array | plotExceed.array function
plotExceed.lgcpPredict | plotExceed.lgcpPredict function
plotit | plotit function
postcov | postcov function
postcov.lgcpPredictAggregateSpatialPlusParameters | postcov.lgcpPredictAggregateSpatialPlusParameters function
postcov.lgcpPredictMultitypeSpatialPlusParameters | postcov.lgcpPredictMultitypeSpatialPlusParameters function
postcov.lgcpPredictSpatialOnlyPlusParameters | postcov.lgcpPredictSpatialOnlyPlusParameters function
postcov.lgcpPredictSpatioTemporalPlusParameters | postcov.lgcpPredictSpatioTemporalPlusParameters function
print.dump2dir | print.dump2dir function
print.fromFunction | print.fromFunction function
print.fromSPDF | print.fromSPDF function
print.fromXYZ | print.fromXYZ function
print.gridaverage | print.gridaverage function
print.lgcpgrid | print.lgcpgrid function
print.lgcpPredict | print.lgcpPredict function
print.mcmc | print.mcmc function
print.mstppp | print.mstppp function
print.stapp | print.stapp function
print.stppp | print.stppp function
print.temporalAtRisk | print.temporalAtRisk function
priorpost | priorpost function
PriorSpec | PriorSpec function
PriorSpec.list | PriorSpec.list function

## -- Q --

quantile.lgcpgrid | quantile.lgcpgrid function
quantile.lgcpPredict | quantile.lgcpPredict function

## -- R --

RandomFieldsCovFct | RandomFieldsCovFct function
raster.lgcpgrid | raster.lgcpgrid function
rescale.mstppp | rescale.mstppp function
rescale.stppp | rescale.stppp function
resetLoop | reset iterator
rgauss | rgauss function
roteffgain | roteffgain function
rotmat | rotmat function
rr | rr function
rr.lgcpPredict | rr.lgcpPredict function

## -- S --

samplePosterior | samplePosterior function
segProbs | segProbs function
seintens | seintens function
seintens.lgcpPredict | seintens.lgcpPredict function
selectObsWindow | selectObsWindow function
selectObsWindow.default | selectObsWindow.default function
selectObsWindow.stppp | selectObsWindow.stppp function
serr | serr function
serr.lgcpPredict | serr.lgcpPredict function
setoutput | setoutput function
setTxtProgressBar2 | set the progress bar
showGrid | showGrid function
showGrid.default | showGrid.default function
showGrid.lgcpPredict | showGrid.lgcpPredict function
showGrid.stppp | showGrid.stppp function
smultiply.list | smultiply.list function
sparsebase | sparsebase function
spatialAtRisk | spatialAtRisk function
spatialAtRisk.bivden | spatialAtRisk.bivden function
spatialAtRisk.default | spatialAtRisk.default function
spatialAtRisk.fromXYZ | spatialAtRisk.fromXYZ function
spatialAtRisk.function | spatialAtRisk.function function
spatialAtRisk.im | spatialAtRisk.im function
spatialAtRisk.lgcpgrid | spatialAtRisk.lgcpgrid function
spatialAtRisk.SpatialGridDataFrame | spatialAtRisk.SpatialGridDataFrame function
spatialAtRisk.SpatialPolygonsDataFrame | spatialAtRisk.SpatialPolygonsDataFrame function
spatialIntensities | spatialIntensities function
spatialIntensities.fromSPDF | spatialIntensities.fromSPDF function
spatialIntensities.fromXYZ | spatialIntensities.fromXYZ function
spatialparsEst | spatialparsEst function
SpatialPolygonsDataFrame.stapp | SpatialPolygonsDataFrame.stapp function
SpikedExponentialCovFct | SpikedExponentialCovFct function
stapp | stapp function
stapp.list | stapp.list function
stapp.SpatialPolygonsDataFrame | stapp.SpatialPolygonsDataFrame function
stGPrealisation | stGPrealisation function
stppp | stppp function
stppp.list | stppp.list function
stppp.ppp | stppp.ppp function
summary.lgcpgrid | summary.lgcpgrid function
summary.mcmc | summary.mcmc function

## -- T --

target.and.grad.AggregateSpatialPlusPars | target.and.grad.AggregateSpatialPlusPars function
target.and.grad.MultitypespatialPlusPars | target.and.grad.MultitypespatialPlusPars function
target.and.grad.spatial | target.and.grad.spatial function
target.and.grad.spatialPlusPars | target.and.grad.spatialPlusPars function
target.and.grad.spatiotemporal | target.and.grad.spatiotemporal function
target.and.grad.SpatioTemporalPlusPars | target.and.grad.SpatioTemporalPlusPars function
temporalAtRisk | temporalAtRisk function
temporalAtRisk.function | temporalAtRisk.function function
temporalAtRisk.numeric | temporalAtRisk.numeric function
tempRaster | tempRaster function
textsummary | textsummary function
thetaEst | thetaEst function
toral.cov.mat | toral.cov.mat function
touchingowin | touchingowin function
traceplots | traceplots function
transblack | transblack function
transblue | transblue function
transgreen | transgreen function
transred | transred function
txtProgressBar2 | A text progress bar with label

## -- U --

updateAMCMC | updateAMCMC function
updateAMCMC.andrieuthomsh | updateAMCMC.andrieuthomsh function
updateAMCMC.constanth | updateAMCMC.constanth function

## -- V --

varfield | varfield function
varfield.lgcpPredict | varfield.lgcpPredict function
varfield.lgcpPredictINLA | varfield.lgcpPredictINLA function

## -- W --

window.lgcpPredict | window.lgcpPredict function
wpopdata | Population of Welsh counties
wtowncoords | Welsh town details: location
wtowns | Welsh town details: population

## -- X --

xvals | xvals function
xvals.default | xvals.default function
xvals.fromXYZ | xvals.fromXYZ function
xvals.lgcpPredict | xvals.lgcpPredict function
xvals.SpatialGridDataFrame | xvals.SpatialGridDataFrame function

## -- Y --

YfromGamma | YfromGamma function
yvals | yvals function
yvals.default | yvals.default function
yvals.fromXYZ | yvals.fromXYZ function
yvals.lgcpPredict | yvals.lgcpPredict function
yvals.SpatialGridDataFrame | yvals.SpatialGridDataFrame function

## -- Z --

zvals | zvals function
zvals.default | zvals.default function
zvals.fromXYZ | zvals.fromXYZ function
zvals.SpatialGridDataFrame | zvals.SpatialGridDataFrame function

## -- misc --

"[.mstppp" | Extract.mstppp function
"[.stppp" | Extract.stppp function
.onAttach | .onAttach function
[.mstppp | Extract.mstppp function
[.stppp | Extract.stppp function