# LatticeKrig
# Copyright 2004-2011, Institute for Mathematics Applied Geosciences
# University Corporation for Atmospheric Research
# Licensed under the GPL -- www.gpl.org/licenses/gpl.html

suppressMessages(library(LatticeKrig))
options(echo = FALSE)
test.for.zero.flag <- 1

# small test dataset
data(ozone2)
x <- ozone2$lon.lat
y <- ozone2$y[16, ]
good <- !is.na(y)
x <- x[good, ]
y <- y[good]
x <- x[1:10, ]
y <- y[1:10]

a.wght <- 5
lambda <- 0.25
# in both calls iseed is set the same so we can compare 
# Monte Carlo estimates of effective degrees of freedom
obj1 <- LKrig(x, y, NC = 5, nlevel = 1, alpha = 1, lambda = lambda, a.wght = 5, 
	NtrA = 5, iseed = 122, NC.buffer = 1, return.cholesky = TRUE)
obj2 <- mKrig(x, y, lambda = lambda, m = 2, cov.function = "LKrig.cov", 
	cov.args = list(LKinfo = obj1$LKinfo), NtrA = 5, iseed = 122)
obj3 <- Krig(x, y, lambda = lambda,  m = 2, cov.function = "LKrig.cov", 
	cov.args = list(LKinfo = obj1$LKinfo))
test.for.zero(obj1$fitted.values, obj2$fitted.values, tag = "comparing predicted values LKrig and mKrig")

# as interim for avoiding bug in fields 8.15 compute eff.df directly
#
NtrA<- 5
set.seed( 122)
Ey <- matrix(rnorm(obj2$np * NtrA), nrow = obj2$np, 
             ncol = NtrA)
trA.info <- colSums(Ey * (predict.mKrig(obj2, ynew = Ey,
                                        collapseFixedEffect=FALSE)))
trA.est <- mean(trA.info)
test.for.zero(obj1$eff.df, trA.est, 
              tag = "comparing Monte Carlo based effective degrees of freedom")
######## WARNING: Use this code once fields 8.16 is on CRAN
########test.for.zero(obj1$eff.df, obj2$eff.df, 
########              tag = "comparing effective degrees of freedom from MC trace (same seed) LKrig and mKrig")
test.for.zero(obj1$fitted.values, obj3$fitted.values, tag = "comparing predicted values LKrig and Krig")

test3.se <- predictSE.Krig(obj3, x[2:3, ])
test2.se <- predictSE.mKrig(obj2, x[2:3, ])
test1.se <- predictSE.LKrig(obj1, x[2:3, ])
test.for.zero(test1.se, test2.se, tag = "comparing SE values LKrig and mKrig equal weights")
test.for.zero(test1.se, test3.se, tag = "comparing SE values LKrig and Krig equal weights")

###########################
##### weighted case
###########################
set.seed(123)
weights <- runif(10)
obj1 <- LKrig(x, y, NC = 16, nlevel = 1, alpha = 1, lambda = lambda, a.wght = 5, 
	NtrA = 5, iseed = 122, return.cholesky = TRUE, weights = weights)
obj2 <- mKrig(x, y, lambda = lambda, m = 2, cov.function = "LKrig.cov", 
	cov.args = list(LKinfo = obj1$LKinfo), NtrA = 5, iseed = 122, weights = weights)
obj0 <- Krig(x, y, lambda = lambda, m = 2, cov.function = "LKrig.cov", 
	cov.args = list(LKinfo = obj1$LKinfo), weights = weights)
test0.se <- predictSE.Krig( obj0, x[1:3, ])
test1.se <- predictSE.LKrig(obj1, x[1:3, ])
test2.se <- predictSE.mKrig(obj2, x[1:3, ])
test.for.zero(test0.se, test2.se, tag = "sanity for SE Krig and mKrig unequal weights")
test.for.zero(test1.se, test2.se, tag = " SE LKrig and mKrig unequal weights")
###########################
######## covariates
##########################
set.seed(122)
nX <- nrow(x)
Z <- matrix(runif(nX * 2), ncol = 2, nrow = nX)
obj1 <- LKrig(x, y, NC = 16, nlevel = 1, alpha = 1, lambda = lambda, a.wght = 5, 
	NtrA = 5, iseed = 122, return.cholesky = TRUE, weights = weights, 
	Z = Z)
obj0 <- Krig(x, y, lambda = lambda, m = 2, cov.function = "LKrig.cov", 
	cov.args = list(LKinfo = obj1$LKinfo), weights = weights, Z = Z)
test0 <- predictSE(obj0, drop.Z = FALSE, Z = Z)
test1 <- predictSE(obj1, Z = Z)
test.for.zero(test0, test1, tag = "check on SE values with drop.Z=FALSE")


cat("All done with SE tests", fil = TRUE)
options(echo = TRUE)