Package: lgcp 2.0

lgcp: Log-Gaussian Cox Process

Spatial and spatio-temporal modelling of point patterns using the log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal, multivariate and aggregated point processes using Markov chain Monte Carlo. See Benjamin M. Taylor, Tilman M. Davies, Barry S. Rowlingson, Peter J. Diggle (2015) <doi:10.18637/jss.v063.i07>.

Authors:Benjamin M. Taylor, Tilman M. Davies, Barry S. Rowlingson, Peter J. Diggle. Additional code contributions from Edzer Pebesma, Dominic Schumacher.

lgcp_2.0.tar.gz
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lgcp.pdf |lgcp.html✨
lgcp/json (API)
NEWS

# Install 'lgcp' in R:

install.packages('lgcp', repos = c('https://bentaylor1.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

wpopdata - Population of Welsh counties
wtowncoords - Welsh town details: location
wtowns - Welsh town details: population

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.47 score 27 scripts 1.1k downloads 2 mentions 212 exports 39 dependencies

Last updated 1 years agofrom:f81be09701. Checks:OK: 3 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 01 2024
R-4.5-win	NOTE	Nov 01 2024
R-4.5-linux	NOTE	Nov 01 2024
R-4.4-win	NOTE	Nov 01 2024
R-4.4-mac	NOTE	Nov 01 2024
R-4.3-win	OK	Nov 01 2024
R-4.3-mac	OK	Nov 01 2024

Exports:add.list addTemporalCovariates aggCovInfo aggregateCovariateInfo aggregateformulaList andrieuthomsh as.fromXYZ as.owinlist as.SpatialGridDataFrame as.SpatialPixelsDataFrame as.stppp assigninterp autocorr autocorrMultitype BetaParameters betavals blockcircbase blockcircbaseFunction checkObsWin chooseCellwidth circulant clearinterp computeGradtruncSpatial computeGradtruncSpatioTemporal condProbs constanth constantInTime cov.interp.fft CovarianceFct covEffects CovFunction CovParameters Cvb discreteWindow dump2dir eigenfrombase etavals EvaluatePrior exceedProbs exceedProbsAggregated expectation exponentialCovFct extendspatialAtRisk extract fftgrid fftinterpolate fftmultiply formulaList GAfinalise GAinitialise GammafromY GAreturnvalue GAupdate GaussianPrior gDisjoint_wg genFFTgrid getCellCounts getCounts getCovParameters getinterp getlgcpPredictSpatialINLA getLHSformulaList getpolyol getRotation getup getZmat getZmats GFfinalise GFinitialise GFreturnvalue GFupdate ginhomAverage gIntersects_pg gOverlay GPdrv GPdrv2 GPdrv2_Multitype GPlist2array GPrealisation grid2spdf grid2spix grid2spoly grid2spts gridav gridfun gridInWindow gTouches_wg guessinterp hasNext hvals identifygrid initialiseAMCMC integerise intens interptypes inversebase is.burnin is.pow2 is.retain is.SPD iteration KinhomAverage lambdaEst lgcpbayes lgcpForecast lgcpgrid lgcpInits lgcppars lgcpPredict lgcpPredictAggregated lgcpPredictAggregateSpatialPlusPars lgcpPredictMultitypeSpatialPlusPars lgcpPredictSpatial lgcpPredictSpatialINLA lgcpPredictSpatialPlusPars lgcpPredictSpatioTemporalPlusPars lgcpPrior lgcpSim lgcpSimMultitypeSpatialCovariates lgcpSimSpatial lgcpSimSpatialCovariates lgcpvignette loc2poly LogGaussianPrior loop.mcmc ltar MALAlgcp MALAlgcpAggregateSpatial.PlusPars MALAlgcpMultitypeSpatial.PlusPars MALAlgcpSpatial MALAlgcpSpatial.PlusPars MALAlgcpSpatioTemporal.PlusPars matchcovariance maternCovFct15 maternCovFct25 mcmcLoop mcmcpars mcmcProgressNone mcmcProgressPrint mcmcProgressTextBar mcmcProgressTk mcmctrace meanfield MonteCarloAverage mstppp muEst multiply.list neattable neigh2D nextStep nullAverage nullFunction numCases osppp2latlon osppp2merc paramprec paramprecbase parautocorr parsummary plotExceed plotit postcov priorpost PriorSpec RandomFieldsCovFct resetLoop rgauss roteffgain rotmat rr samplePosterior segProbs seintens selectObsWindow serr setoutput setTxtProgressBar2 showGrid smultiply.list sparsebase spatialAtRisk spatialIntensities spatialparsEst SpatialPolygonsDataFrame.stapp SpikedExponentialCovFct stapp stGPrealisation stppp target.and.grad.AggregateSpatialPlusPars target.and.grad.MultitypespatialPlusPars target.and.grad.spatial target.and.grad.spatialPlusPars target.and.grad.spatiotemporal target.and.grad.SpatioTemporalPlusPars temporalAtRisk tempRaster textsummary thetaEst toral.cov.mat touchingowin traceplots transblack transblue transgreen transred txtProgressBar2 updateAMCMC varfield xvals YfromGamma yvals zvals

Dependencies:abind class classInt DBI deldir dotCall64 e1071 fields goftest iterators KernSmooth lattice magrittr maps MASS Matrix ncdf4 nlme polyclip proxy raster Rcpp rpanel s2 sf sp spam spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils tensor terra units viridisLite wk

lgcp

Rendered fromlgcp.Rnwusingutils::Sweaveon Nov 01 2024.

Last update: 2015-02-04
Started: 2014-01-07

Help page	Topics
lgcp	lgcp-package lgcp
.onAttach function	.onAttach
add.list function	add.list
addTemporalCovariates function	addTemporalCovariates
affine.fromFunction function	affine.fromFunction
affine.fromSPDF function	affine.fromSPDF
affine.fromXYZ function	affine.fromXYZ
affine.SpatialPolygonsDataFrame function	affine.SpatialPolygonsDataFrame
affine.stppp function	affine.stppp
aggCovInfo function	aggCovInfo
aggCovInfo.ArealWeightedMean function	aggCovInfo.ArealWeightedMean
aggCovInfo.ArealWeightedSum function	aggCovInfo.ArealWeightedSum
aggCovInfo.Majority function	aggCovInfo.Majority
aggregateCovariateInfo function	aggregateCovariateInfo
aggregateformulaList function	aggregateformulaList
andrieuthomsh function	andrieuthomsh
as.array.lgcpgrid function	as.array.lgcpgrid
as.fromXYZ function	as.fromXYZ
as.fromXYZ.fromFunction function	as.fromXYZ.fromFunction
as.im.fromFunction function	as.im.fromFunction
as.im.fromSPDF function	as.im.fromSPDF
as.im.fromXYZ function	as.im.fromXYZ
as.list.lgcpgrid function	as.list.lgcpgrid
as.owin.stapp function	as.owin.stapp
as.owinlist function	as.owinlist
as.owinlist.SpatialPolygonsDataFrame function	as.owinlist.SpatialPolygonsDataFrame
as.owinlist.stapp function	as.owinlist.stapp
as.ppp.mstppp function	as.ppp.mstppp
as.ppp.stppp function	as.ppp.stppp
as.SpatialGridDataFrame function	as.SpatialGridDataFrame
as.SpatialGridDataFrame.fromXYZ function	as.SpatialGridDataFrame.fromXYZ
as.SpatialPixelsDataFrame function	as.SpatialPixelsDataFrame
as.SpatialPixelsDataFrame.lgcpgrid function	as.SpatialPixelsDataFrame.lgcpgrid
as.stppp function	as.stppp
as.stppp.stapp function	as.stppp.stapp
assigninterp function	assigninterp
at function	at
autocorr function	autocorr
autocorrMultitype function	autocorrMultitype
BetaParameters function	BetaParameters
betavals function	betavals
blockcircbase function	blockcircbase
blockcircbaseFunction function	blockcircbaseFunction
bt.scalar function	bt.scalar
checkObsWin function	checkObsWin
chooseCellwidth function	chooseCellwidth
circulant function	circulant
circulant.matrix function	circulant.matrix
circulant.numeric function	circulant.numeric
clearinterp function	clearinterp
computeGradtruncSpatial function	computeGradtruncSpatial
computeGradtruncSpatioTemporal function	computeGradtruncSpatioTemporal
condProbs function	condProbs
constanth function	constanth
constantInTime function	constantInTime
constantInTime.numeric function	constantInTime.numeric
constantInTime.stppp function	constantInTime.stppp
cov.interp.fft function	cov.interp.fft
CovarianceFct function	CovarianceFct
covEffects function	covEffects
CovFunction function	CovFunction
CovFunction.function function	CovFunction.function
CovParameters function	CovParameters
Cvb function	Cvb
d.func function	d.func
density.stppp function	density.stppp
discreteWindow function	discreteWindow
discreteWindow.lgcpPredict function	discreteWindow.lgcpPredict
dump2dir function	dump2dir
eigenfrombase function	eigenfrombase
etavals function	etavals
EvaluatePrior function	EvaluatePrior
exceedProbs function	exceedProbs
exceedProbsAggregated function	exceedProbsAggregated
expectation function	expectation
expectation.lgcpPredict function	expectation.lgcpPredict
expectation.lgcpPredictSpatialOnlyPlusParameters function	expectation.lgcpPredictSpatialOnlyPlusParameters
exponentialCovFct function	exponentialCovFct
extendspatialAtRisk function	extendspatialAtRisk
extract function	extract
extract.lgcpPredict function	extract.lgcpPredict
Extract.mstppp function	"[.mstppp" Extract.mstppp [.mstppp
Extract.stppp function	"[.stppp" Extract.stppp [.stppp
fftgrid function	fftgrid
fftinterpolate function	fftinterpolate
fftinterpolate.fromFunction function	fftinterpolate.fromFunction
fftinterpolate.fromSPDF function	fftinterpolate.fromSPDF
interpolate.fromXYZ function	fftinterpolate.fromXYZ
fftmultiply function	fftmultiply
formulaList function	formulaList
GAfinalise function	GAfinalise
GAfinalise.MonteCarloAverage function	GAfinalise.MonteCarloAverage
GAfinalise.nullAverage function	GAfinalise.nullAverage
GAinitialise function	GAinitialise
GAinitialise.MonteCarloAverage function	GAinitialise.MonteCarloAverage
GAinitialise.nullAverage function	GAinitialise.nullAverage
GammafromY function	GammafromY
GAreturnvalue function	GAreturnvalue
GAreturnvalue.MonteCarloAverage function	GAreturnvalue.MonteCarloAverage
GAreturnvalue.nullAverage function##'	GAreturnvalue.nullAverage
GAupdate function	GAupdate
GAupdate.MonteCarloAverage function	GAupdate.MonteCarloAverage
GAupdate.nullAverage function	GAupdate.nullAverage
GaussianPrior function	GaussianPrior
gDisjoint_wg function	gDisjoint_wg
genFFTgrid function	genFFTgrid
getCellCounts function	getCellCounts
getCounts function	getCounts
getCovParameters function	getCovParameters
getCovParameters.GPrealisation function	getCovParameters.GPrealisation
getCovParameters.list function	getCovParameters.list
getinterp function	getinterp
getlgcpPredictSpatialINLA function	getlgcpPredictSpatialINLA
getLHSformulaList function	getLHSformulaList
getpolyol function	getpolyol
getRotation function	getRotation
getRotation.default function	getRotation.default
getRotation.stppp function	getRotation.stppp
getup function	getup
getZmat function	getZmat
getZmats function	getZmats
GFfinalise function	GFfinalise
GFfinalise.dump2dir function	GFfinalise.dump2dir
GFfinalise.nullFunction function	GFfinalise.nullFunction
GFinitialise function	GFinitialise
GFinitialise.dump2dir function	GFinitialise.dump2dir
GFinitialise.nullFunction function	GFinitialise.nullFunction
GFreturnvalue function	GFreturnvalue
GFreturnvalue.dump2dir function	GFreturnvalue.dump2dir
GFreturnvalue.nullFunction function	GFreturnvalue.nullFunction
GFupdate function	GFupdate
GFupdate.dump2dir function	GFupdate.dump2dir
GFupdate.nullFunction function	GFupdate.nullFunction
ginhomAverage function	ginhomAverage
gIntersects_pg function	gIntersects_pg
gOverlay function	gOverlay
GPdrv function	GPdrv
GPdrv2 function	GPdrv2
GPdrv2_Multitype function	GPdrv2_Multitype
GPlist2array function	GPlist2array
GPrealisation function	GPrealisation
grid2spdf function	grid2spdf
grid2spix function	grid2spix
grid2spoly function	grid2spoly
grid2spts function	grid2spts
gridav function	gridav
gridav.lgcpPredict function	gridav.lgcpPredict
gridfun function	gridfun
gridfun.lgcpPredict function	gridfun.lgcpPredict
gridInWindow function	gridInWindow
gTouches_wg function	gTouches_wg
gu function	gu
guessinterp function	guessinterp
generic hasNext method	hasNext
hasNext.iter function	hasNext.iter
hvals function	hvals
hvals.lgcpPredict function	hvals.lgcpPredict
identify.lgcpPredict function	identify.lgcpPredict
identifygrid function	identifygrid
image.lgcpgrid function	image.lgcpgrid
initialiseAMCMC function	initialiseAMCMC
initaliseAMCMC.andrieuthomsh function	initialiseAMCMC.andrieuthomsh
initaliseAMCMC.constanth function	initialiseAMCMC.constanth
integerise function	integerise
integerise.mstppp function	integerise.mstppp
integerise.stppp function	integerise.stppp
intens function	intens
intens.lgcpPredict function	intens.lgcpPredict
intens.lgcpSimMultitypeSpatialPlusParameters function	intens.lgcpSimMultitypeSpatialPlusParameters
intens.lgcpSimSpatialPlusParameters function	intens.lgcpSimSpatialPlusParameters
interptypes function	interptypes
inversebase function	inversebase
is this a burn-in iteration?	is.burnin
is.pow2 function	is.pow2
do we retain this iteration?	is.retain
is.SPD function	is.SPD
iteration number	iteration
KinhomAverage function	KinhomAverage
lambdaEst function	lambdaEst
lambdaEst.ppp function	lambdaEst.ppp
lambdaEst.stppp function	lambdaEst.stppp
lgcpbayes function	lgcpbayes
lgcpForecast function	lgcpForecast
lgcpgrid function	lgcpgrid
lgcpgrid.array function	lgcpgrid.array
lgcpgrid.list function	lgcpgrid.list
lgcpgrid.matrix function	lgcpgrid.matrix
lgcpInits function	lgcpInits
lgcppars function	lgcppars
lgcpPredict function	lgcpPredict
lgcpPredictAggregated function	lgcpPredictAggregated
lgcpPredictAggregateSpatialPlusPars function	lgcpPredictAggregateSpatialPlusPars
lgcpPredictMultitypeSpatialPlusPars function	lgcpPredictMultitypeSpatialPlusPars
lgcpPredictSpatial function	lgcpPredictSpatial
lgcpPredictSpatialINLA function	lgcpPredictSpatialINLA
lgcpPredictSpatialPlusPars function	lgcpPredictSpatialPlusPars
lgcpPredictSpatioTemporalPlusPars function	lgcpPredictSpatioTemporalPlusPars
lgcpPrior function	lgcpPrior
lgcpSim function	lgcpSim
lgcpSimMultitypeSpatialCovariates function	lgcpSimMultitypeSpatialCovariates
lgcpSimSpatial function	lgcpSimSpatial
lgcpSimSpatialCovariates function	lgcpSimSpatialCovariates
lgcpvignette function	lgcpvignette
loc2poly function	loc2poly
LogGaussianPrior function	LogGaussianPrior
loop over an iterator	loop.mcmc
ltar function	ltar
MALAlgcp function	MALAlgcp
MALAlgcpAggregateSpatial.PlusPars function	MALAlgcpAggregateSpatial.PlusPars
MALAlgcpMultitypeSpatial.PlusPars function	MALAlgcpMultitypeSpatial.PlusPars
MALAlgcpSpatial function	MALAlgcpSpatial
MALAlgcpSpatial.PlusPars function	MALAlgcpSpatial.PlusPars
MALAlgcpSpatioTemporal.PlusPars function	MALAlgcpSpatioTemporal.PlusPars
matchcovariance function	matchcovariance
maternCovFct15 function	maternCovFct15
maternCovFct25 function	maternCovFct25
iterator for MCMC loops	mcmcLoop
mcmcpars function	mcmcpars
null progress monitor	mcmcProgressNone
printing progress monitor	mcmcProgressPrint
text bar progress monitor	mcmcProgressTextBar
graphical progress monitor	mcmcProgressTk
mcmctrace function	mcmctrace
mcmctrace.lgcpPredict function	mcmctrace.lgcpPredict
meanfield function	meanfield
meanfield.lgcpPredict function	meanfield.lgcpPredict
meanfield.lgcpPredictINLA function	meanfield.lgcpPredictINLA
MonteCarloAverage function	MonteCarloAverage
mstppp function	mstppp
mstppp.list function	mstppp.list
mstppp.ppp function	mstppp.ppp
mstppp.stppp function	mstppp.stppp
muEst function	muEst
multiply.list function	multiply.list
neattable function	neattable
neigh2D function	neigh2D
next step of an MCMC chain	nextStep
nullAverage function	nullAverage
nullFunction function	nullFunction
numCases function	numCases
osppp2latlon function	osppp2latlon
osppp2merc function	osppp2merc
paramprec function	paramprec
paramprecbase function	paramprecbase
parautocorr function	parautocorr
parsummary function	parsummary
plot.fromSPDF function	plot.fromSPDF
plot.fromXYZ function	plot.fromXYZ
plot.lgcpAutocorr function	plot.lgcpAutocorr
plot.lgcpgrid function	plot.lgcpgrid
plot.lgcpPredict function	plot.lgcpPredict
plot.lgcpQuantiles function	plot.lgcpQuantiles
plot.lgcpZmat function	plot.lgcpZmat
plot.mcmcdiag function	plot.mcmcdiag
plot.mstppp function	plot.mstppp
plot.stppp function	plot.stppp
plot.temporalAtRisk function	plot.temporalAtRisk
plotExceed function	plotExceed
plotExceed.array function	plotExceed.array
plotExceed.lgcpPredict function	plotExceed.lgcpPredict
plotit function	plotit
postcov function	postcov
postcov.lgcpPredictAggregateSpatialPlusParameters function	postcov.lgcpPredictAggregateSpatialPlusParameters
postcov.lgcpPredictMultitypeSpatialPlusParameters function	postcov.lgcpPredictMultitypeSpatialPlusParameters
postcov.lgcpPredictSpatialOnlyPlusParameters function	postcov.lgcpPredictSpatialOnlyPlusParameters
postcov.lgcpPredictSpatioTemporalPlusParameters function	postcov.lgcpPredictSpatioTemporalPlusParameters
print.dump2dir function	print.dump2dir
print.fromFunction function	print.fromFunction
print.fromSPDF function	print.fromSPDF
print.fromXYZ function	print.fromXYZ
print.gridaverage function	print.gridaverage
print.lgcpgrid function	print.lgcpgrid
print.lgcpPredict function	print.lgcpPredict
print.mcmc function	print.mcmc
print.mstppp function	print.mstppp
print.stapp function	print.stapp
print.stppp function	print.stppp
print.temporalAtRisk function	print.temporalAtRisk
priorpost function	priorpost
PriorSpec function	PriorSpec
PriorSpec.list function	PriorSpec.list
quantile.lgcpgrid function	quantile.lgcpgrid
quantile.lgcpPredict function	quantile.lgcpPredict
RandomFieldsCovFct function	RandomFieldsCovFct
raster.lgcpgrid function	raster.lgcpgrid
rescale.mstppp function	rescale.mstppp
rescale.stppp function	rescale.stppp
reset iterator	resetLoop
rgauss function	rgauss
roteffgain function	roteffgain
rotmat function	rotmat
rr function	rr
rr.lgcpPredict function	rr.lgcpPredict
samplePosterior function	samplePosterior
segProbs function	segProbs
seintens function	seintens
seintens.lgcpPredict function	seintens.lgcpPredict
selectObsWindow function	selectObsWindow
selectObsWindow.default function	selectObsWindow.default
selectObsWindow.stppp function	selectObsWindow.stppp
serr function	serr
serr.lgcpPredict function	serr.lgcpPredict
setoutput function	setoutput
set the progress bar	setTxtProgressBar2
showGrid function	showGrid
showGrid.default function	showGrid.default
showGrid.lgcpPredict function	showGrid.lgcpPredict
showGrid.stppp function	showGrid.stppp
smultiply.list function	smultiply.list
sparsebase function	sparsebase
spatialAtRisk function	spatialAtRisk
spatialAtRisk.bivden function	spatialAtRisk.bivden
spatialAtRisk.default function	spatialAtRisk.default
spatialAtRisk.fromXYZ function	spatialAtRisk.fromXYZ
spatialAtRisk.function function	spatialAtRisk.function
spatialAtRisk.im function	spatialAtRisk.im
spatialAtRisk.lgcpgrid function	spatialAtRisk.lgcpgrid
spatialAtRisk.SpatialGridDataFrame function	spatialAtRisk.SpatialGridDataFrame
spatialAtRisk.SpatialPolygonsDataFrame function	spatialAtRisk.SpatialPolygonsDataFrame
spatialIntensities function	spatialIntensities
spatialIntensities.fromSPDF function	spatialIntensities.fromSPDF
spatialIntensities.fromXYZ function	spatialIntensities.fromXYZ
spatialparsEst function	spatialparsEst
SpatialPolygonsDataFrame.stapp function	SpatialPolygonsDataFrame.stapp
SpikedExponentialCovFct function	SpikedExponentialCovFct
stapp function	stapp
stapp.list function	stapp.list
stapp.SpatialPolygonsDataFrame function	stapp.SpatialPolygonsDataFrame
stGPrealisation function	stGPrealisation
stppp function	stppp
stppp.list function	stppp.list
stppp.ppp function	stppp.ppp
summary.lgcpgrid function	summary.lgcpgrid
summary.mcmc function	summary.mcmc
target.and.grad.AggregateSpatialPlusPars function	target.and.grad.AggregateSpatialPlusPars
target.and.grad.MultitypespatialPlusPars function	target.and.grad.MultitypespatialPlusPars
target.and.grad.spatial function	target.and.grad.spatial
target.and.grad.spatialPlusPars function	target.and.grad.spatialPlusPars
target.and.grad.spatiotemporal function	target.and.grad.spatiotemporal
target.and.grad.SpatioTemporalPlusPars function	target.and.grad.SpatioTemporalPlusPars
temporalAtRisk function	temporalAtRisk
temporalAtRisk.function function	temporalAtRisk.function
temporalAtRisk.numeric function	temporalAtRisk.numeric
tempRaster function	tempRaster
textsummary function	textsummary
thetaEst function	thetaEst
toral.cov.mat function	toral.cov.mat
touchingowin function	touchingowin
traceplots function	traceplots
transblack function	transblack
transblue function	transblue
transgreen function	transgreen
transred function	transred
A text progress bar with label	txtProgressBar2
updateAMCMC function	updateAMCMC
updateAMCMC.andrieuthomsh function	updateAMCMC.andrieuthomsh
updateAMCMC.constanth function	updateAMCMC.constanth
varfield function	varfield
varfield.lgcpPredict function	varfield.lgcpPredict
varfield.lgcpPredictINLA function	varfield.lgcpPredictINLA
window.lgcpPredict function	window.lgcpPredict
Population of Welsh counties	wpopdata
Welsh town details: location	wtowncoords
Welsh town details: population	wtowns
xvals function	xvals
xvals.default function	xvals.default
xvals.fromXYZ function	xvals.fromXYZ
xvals.lgcpPredict function	xvals.lgcpPredict
xvals.SpatialGridDataFrame function	xvals.SpatialGridDataFrame
YfromGamma function	YfromGamma
yvals function	yvals
yvals.default function	yvals.default
yvals.fromXYZ function	yvals.fromXYZ
yvals.lgcpPredict function	yvals.lgcpPredict
yvals.SpatialGridDataFrame function	yvals.SpatialGridDataFrame
zvals function	zvals
zvals.default function	zvals.default
zvals.fromXYZ function	zvals.fromXYZ
zvals.SpatialGridDataFrame function	zvals.SpatialGridDataFrame

Package: lgcp 2.0

lgcp: Log-Gaussian Cox Process

lgcp

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