Nothing
havePackages = c(
'INLA' = requireNamespace('INLA', quietly=TRUE)
)
if(requireNamespace("INLA", quietly=TRUE) ) {
INLA::inla.setOption(num.threads=2)
# not all versions of INLA support blas.num.threads
try(INLA::inla.setOption(blas.num.threads=2), silent=TRUE)
}
print(havePackages)
# as in example
require('geostatsp')
myPoints = vect(cbind(rbeta(100,2,2), rbeta(100,3,4)))
mycov = rast(matrix(rbinom(100, 1, 0.5), 10, 10), extent=ext(0, 1, 0, 1))
names(mycov)="x1"
res = lgcp(
formula=~factor(x1),
data=myPoints,
grid=20,
covariates=mycov,
prior=list(sd=0.1, range=c(0.4)),
)
if(length(res$parameters)) {
knitr::kable(res$parameters$summary, digits=3)
plot(res$raster[["predict.exp"]])
plot(myPoints,add=TRUE,col="#0000FF30",cex=0.5)
}
# intercept only
res = lgcp(
data=myPoints,
grid=20,
covariates=mycov,
formula=~1,
priorCI=list(sd=c(0.9, 1.1), range=c(0.4, 0.41))
)
if(length(res$parameters)) {
knitr::kable(res$parameters$summary, digits=3)
plot(res$raster[["predict.exp"]])
plot(myPoints,add=TRUE,col="#0000FF30",cex=0.5)
}
# some missing values
mycov2 = deepcopy(mycov)
temp = values(mycov2)
temp[1:4] = NA
values(mycov2) = temp
if(all(havePackages)) {
res = lgcp(data=myPoints, grid=20, covariates=mycov2,
formula=~factor(x1),
priorCI=list(sd=c(0.9, 1.1), range=c(0.4, 0.41))
)
if(length(res$parameters)) {
plot(res$raster[["predict.exp"]])
plot(myPoints,add=TRUE,col="#0000FF30",cex=0.5)
}
}
data('murder')
murder = unwrap(murder)
data('torontoPop')
torontoPdens = unwrap(torontoPdens)
torontoIncome = unwrap(torontoIncome)
torontoBorder = unwrap(torontoBorder)
highDens = torontoPdens > 100
myCov = list(
pop=torontoPdens,
highDens = highDens,
inc = log(torontoIncome)
)
formula = ~ inc*highDens + offset(pop, log=TRUE)
resL=lgcp(formula, data=murder,
grid=squareRaster(murder, 30),
covariates=myCov, verbose=TRUE,
border=torontoBorder)
resO = lgcp( ~ inc + pop,
data=murder,
grid=squareRaster(murder, 30),
covariates=list(inc=myCov$inc, pop=log(myCov$pop)),
border=torontoBorder)
if(length(resL$parameters)) {
rbind(resL$param$summary, resO$param$summary)
}
# check spdfToBrock
if(requireNamespace('diseasemapping', quietly=TRUE)){
require('diseasemapping')
data('kentucky')
kentucky = unwrap(kentucky)
popList = list(
'2002' = kentucky[,c('M.50', 'M.55', 'M.60')],
'2005' = kentucky[,c('F.50', 'F.55', 'F.60')]
)
for(D in names(popList))
names(popList[[D]]) = paste('expected_', seq(as.numeric(D)-1, len=3), sep='')
popBrick = spdfToBrick(
x=popList,
template=squareRaster(kentucky, 10),
logSumExpected=FALSE
)
sum(popList[['2002']]$expected_2001, na.rm=TRUE)
sum(values(popBrick[['expected_2001']]), na.rm=TRUE)*prod(res(popBrick))
popBrick2 = spdfToBrick(
x=popList,
template=squareRaster(kentucky, 10),
logSumExpected=TRUE
)
sum(unlist(lapply(popList, function(qq) apply(values(qq), 2, sum, na.rm=TRUE))))
sum(exp(values(popBrick2)), na.rm=TRUE)*prod(res(popBrick2))
}
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