#
source("acheck.R")

try(library(compositions,lib.loc="compositions.Rcheck"))
options(error=dump.frames)
options(warn=2)
try(library(compositions))
data(juraset)

X <- with(juraset,cbind(X,Y))
comp <- acomp(juraset,c("Cd","Cu","Pb","Co","Cr"))


lrv <- logratioVariogram(comp,X,maxdist=1,nbins=10)

plot(lrv)




fff <- CompLinModCoReg(~nugget()+sph(0.5)+exp(0.7),comp)
#fff <- CompLinModCoReg(~nugget()+sph(0.5),comp)
fit <- vgmFit2lrv(lrv,fff,iterlim=1000,print.level=0)
fit
fff(1:3)
plot(lrv,lrvg=vgram2lrvgram(fit$vg))

x <- (0:60/60)*6
y <- (0:40/40)*6
Xnew <- cbind(rep(x,length(y)),rep(y,each=length(x)))


# Grid example
erg <- compOKriging(comp,X,Xnew,fit$vg,err=FALSE)
image(x,y,structure(balance(erg$Z,~Cd/Cu),dim=c(length(x),length(y))))
par(mar=c(0,0,1,0))
pairwisePlot(erg$Z,panel=function(a,b,xlab,ylab) {image(x,y,
                     structure(log(a/b),dim=c(length(x),length(y))),main=paste("log(",xlab,"/",ylab,")",sep=""));points(X,pch=".")})

#erg <- compOKriging(comp,X,Xnew,fit$vg,err=TRUE)


# Checking 
ergR <- compOKriging(comp,X,X+1E-7,fit$vg,err=FALSE)
ergR <- compOKriging(comp,X,X,fit$vg,err=FALSE)
pairwisePlot(ilr(comp),ilr(ergR$Z))

ergR <- compOKriging(comp,X,X[rev(1:31),],fit$vg,err=FALSE)
pairwisePlot(ilr(comp)[rev(1:31),],ilr(ergR$Z))

plot(ergR$Z-comp) 
plot(ergR$Z)
plot(comp)
#

                                        # Small example
X <- rbind(c(0,1),c(1,0),c(1,1),c(0,0))
Z <- acomp(rbind(c(2,1,1),c(1,2,1),c(1,1,2),c(1,1,1)))
Xnew <- rbind(c(0,1),c(0.5,0.5))

vg <- CompLinModCoReg(~nugget()+sph(3),Z)
vg
(ergR <- compOKriging(Z,X,X,vg,err=FALSE))

## Explicit vgmodel
vgmodel <- function(h,nugget=0.2*parameterPosDefMat(diag(5)),sill=0.6*parameterPosDefMat(diag(5)),range1=1) {
  (h>0) %o% parametricPosdefMat(nugget)+ vgram.sph(h,range=range1)%o%parametricPosdefMat(sill)
}
plot(lrv,lrvg=vgram2lrvgram(vgmodel))

fit <- vgmFit(lrv,vgmodel)
fit <- vgmFit(lrv,vgmodel,mode="ls")
fit
vgmGof(emp=lrv,vg=vgmodel,mode="ls")
vgmGof(emp=lrv,vg=vgmodel,mode="log")
lrv$h
lrv$vg
vgmGof(emp=lrv,vg=fit$vg,mode="ls")
vgmGof(emp=lrv,vg=fit$vg,mode="log")

plot(lrv,lrvg=vgram2lrvgram(fit$vg))