Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
echo = TRUE, results = 'hold', warning=F, cache=F,
#dev = 'pdf',
message=F,
fig.width=5, fig.height=5,
tidy.opts=list(width.cutoff=75), tidy=FALSE
)
old <- options(scipen = 1, digits = 4)
## ----setup--------------------------------------------------------------------
library(GPFDA)
require(MASS)
# packages required for visualisation:
require(interp)
require(fields)
## -----------------------------------------------------------------------------
set.seed(123)
nrep <- 10
n1 <- 30
n2 <- 30
n <- n1*n2
input1 <- seq(0,1,len=n1)
input2 <- seq(0,1,len=n2)
input <- as.matrix(expand.grid(input1=input1, input2=input2))
hp <- list('matern.v'=log(2),'matern.w'=c(log(20), log(25)),'vv'=log(0.2))
nu <- 1.5
Sigma <- cov.matern(hyper = hp, input = input, nu = nu) + diag(exp(hp$vv), n)
Y <- t(mvrnorm(n=nrep, mu=rep(0,n), Sigma=Sigma))
## -----------------------------------------------------------------------------
idx <- expand.grid(1:n1, 1:n2)
n1test <- floor(n1*0.8)
n2test <- floor(n2*0.8)
idx1 <- sort(sample(1:n1, n1test))
idx2 <- sort(sample(1:n2, n2test))
whichTest <- idx[,1]%in%idx1 & idx[,2]%in%idx2
inputTest <- input[whichTest, ]
Ytest <- Y[whichTest, ]
inputTrain <- input[!whichTest, ]
Ytrain <- Y[!whichTest, ]
## -----------------------------------------------------------------------------
fit <- gpr(input=inputTrain, response=Ytrain, Cov='matern', trace=4, useGradient=T,
iter.max=50, nu=nu, nInitCandidates=50)
## -----------------------------------------------------------------------------
sapply(fit$hyper, exp)
## -----------------------------------------------------------------------------
pred <- gprPredict(train=fit, inputNew=inputTest, noiseFreePred=T)
## ---- fig.width=6, fig.height=5-----------------------------------------------
zlim <- range(c(pred$pred.mean, Ytest))
plotImage(response = Ytest, input = inputTest, realisation = 1,
n1 = n1test, n2 = n2test,
zlim = zlim, main = "observed")
plotImage(response = pred$pred.mean, input = inputTest, realisation = 1,
n1 = n1test, n2 = n2test,
zlim = zlim, main = "prediction")
## ---- include = FALSE---------------------------------------------------------
options(old)
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