laGP (version 1.5-5)

discrep.est: Estimate Discrepancy in Calibration Model


Estimates the Gaussian process discrepancy/bias and/or noise term in a modularized calibration of a computer model (emulator) to field data, and returns the log likelihood or posterior probability


discrep.est(X, Y, Yhat, d, g, bias = TRUE, clean = TRUE)



a matrix or data.frame containing a design matrix of input locations for field data sites. Any columns of X without at least three unique input settings are dropped in a pre-processing step


a vector of values with length(Y) = ncol(X) containing the response from field data observations at X. A Y-vector with length(Y) = k*ncol(X), for positive integer k, can be supplied in which case the multiple code Y-values will be treated as replicates at the X-values


a vector with length(Yhat) = length(Y) containing predictions at X from an emulator of a computer simulation


a prior or initial setting for the (single/isotropic) lengthscale parameter in a Gaussian correlation function; a (default) NULL value triggers a sensible regularization (prior) and initial setting to be generated via darg; a scalar specifies an initial value, causing darg to only generate the prior; otherwise, a list or partial list matching the output of darg can be used to specify a custom prior. In the case of a partial list, the only the missing entries will be generated. Note that a default/generated list specifies MLE/MAP inference for this parameter. When specifying initial values, a vector of length nrow(XX) can be provided, giving a different initial value for each predictive location.


a prior or initial setting for the nugget parameter; a NULL value causes a sensible regularization (prior) and initial setting to be generated via garg; a scalar (default g = 1/1000) specifies an initial value, causing garg to only generate the prior; otherwise, a list or partial list matching the output of garg can be used to specify a custom prior. In the case of a partial list, only the missing entries will be generated. Note that a default/generated list specifies no inference for this parameter; i.e., it is fixed at its starting value, which may be appropriate for emulating deterministic computer code output


a scalar logical indicating if a (isotropic) GP discrepancy should be estimated (TRUE) or a Gaussian noise term only (FALSE)


a scalar logical indicating if the C-side GP object should be freed before returning.


The output object is comprised of the output of jmleGP, applied to a GP object built with responses Y - Yhat. That object is augmented with a log likelihood, in $ll, and with a GP index $gpi when clean=FALSE. When bias = FALSE the output object retains the same form as above, except with dummy zero-values since calling jmleGP is not required


Estimates an isotropic Gaussian correlation Gaussian process (GP) discrepancy term for the difference between a computer model output (Yhat) and field data observations (Y) at locations X. The computer model predictions would typically come from a GP emulation from simulation data, possibly via aGP if the computer experiment is large.

This function is used primarily as a subroutine by fcalib which defines an objective function for optimization in order to solve the calibration problem via the method described by Gramacy, et al. (2015), designed for large computer experiments. However, once calibration is performed this function can be useful for making comparisons to other methods. Examples are provided in the fcalib documentation.

When bias=FALSE no discrepancy is estimated; only a zero-mean Gaussian error distribution is assumed


R.B. Gramacy (2016). laGP: Large-Scale Spatial Modeling via Local Approximate Gaussian Processes in R., Journal of Statistical Software, 72(1), 1-46; or see vignette("laGP")

R.B. Gramacy, D. Bingham, JP. Holloway, M.J. Grosskopf, C.C. Kuranz, E. Rutter, M. Trantham, P.R. Drake (2015). Calibrating a large computer experiment simulating radiative shock hydrodynamics. Annals of Applied Statistics, 9(3) 1141-1168; preprint on arXiv:1410.3293

F. Liu, M. Bayarri and J. Berger (2009). Modularization in Bayesian analysis, with emphasis on analysis of computer models. Bayesian Analysis, 4(1) 119-150.

See Also

vignette("laGP"), jmleGP, newGP, aGP.seq, fcalib


## the example here combines aGP.seq and discrep.est functions; 
## it is comprised of snippets from demo("calib"), which contains
## code from the Calibration Section of vignette("laGP")

## Here we generate calibration data using a true calibration
## parameter, u, and then evaluate log posterior probabilities
## and out-of-sample RMSEs for that u value;  the fcalib 
## documentation repeats this with a single call to fcalib rather 
## than first aGP.seq and then discrep.est

## begin data-generation code identical to aGP.seq, discrep.est, fcalib
## example sections and demo("calib")

## M: computer model test functon used in Goh et al, 2013 (Technometrics)
## an elaboration of one from Bastos and O'Hagan, 2009 (Technometrics) 
M <- function(x,u) 
    x <- as.matrix(x)
    u <- as.matrix(u)
    out <- (1-exp(-1/(2*x[,2]))) 
    out <- out * (1000*u[,1]*x[,1]^3+1900*x[,1]^2+2092*x[,1]+60) 
    out <- out / (100*u[,2]*x[,1]^3+500*x[,1]^2+4*x[,1]+20)  
## bias: discrepancy function from Goh et al, 2013 
bias <- function(x) 
    out<- 2*(10*x[,1]^2+4*x[,2]^2) / (50*x[,1]*x[,2]+10)

## beta.prior: marginal beta prior for u, 
## defaults to a mode at 1/2 in hypercube
beta.prior <- function(u, a=2, b=2, log=TRUE)
  if(length(a) == 1) a <- rep(a, length(u))
  else if(length(a) != length(u)) stop("length(a) must be 1 or length(u)")
  if(length(b) == 1) b <- rep(b, length(u))
  else if(length(b) != length(u)) stop("length(b) must be 1 or length(u)")
  if(log) return(sum(dbeta(u, a, b, log=TRUE)))
  else return(prod(dbeta(u, a, b, log=FALSE)))

## tgp for LHS sampling
rect <- matrix(rep(0:1, 4), ncol=2, byrow=2)

## training and testing inputs
ny <- 50; nny <- 1000  
X <- lhs(ny, rect[1:2,])    ## computer model train
XX <- lhs(nny, rect[1:2,],) ## test

## true (but unknown) setting of the calibration parameter
## for the computer model
u <- c(0.2, 0.1)
Zu <- M(X, matrix(u, nrow=1)) 
ZZu <- M(XX, matrix(u, nrow=1)) 

## field data response, biased and replicated
sd <- 0.5
## Y <- computer output + bias + noise
reps <- 2 ## example from paper uses reps <- 10
Y <- rep(Zu,reps) + rep(bias(X),reps) + rnorm(reps*length(Zu), sd=sd) 
YYtrue <- ZZu + bias(XX) 
## variations: remove the bias or change 2 to 1 to remove replicates

## computer model design
nz <- 10000
XT <- lhs(nz, rect)
nth <- 1 ## number of threads to use in emulation, demo uses 8

## augment with physical model design points 
## with various u settings
XT2 <- matrix(NA, nrow=10*ny, ncol=4)
for(i in 1:10) {
  I <- ((i-1)*ny+1):(ny*i)
  XT2[I,1:2] <- X
XT2[,3:4] <- lhs(10*ny, rect[3:4,])
XT <- rbind(XT, XT2)

## evaluate the computer model
Z <- M(XT[,1:2], XT[,3:4])

## flag indicating if estimating bias/discrepancy or not
bias.est <- TRUE
## two passes of ALC with MLE calculations for aGP.seq
methods <- rep("alcray", 2) ## demo uses rep("alc", 2)

## set up priors
da <- d <- darg(NULL, XT)
g <- garg(list(mle=TRUE), Y) 

## end identical data generation code

## now calculate log posterior and do out-of-sample RMSE calculation
## for true calibration parameter value (u).  You could repeat
## this for an estimate value from demo("calib"), for example
## u.hat <- c(0.8236673, 0.1406989)

## first log posterior

## emulate at field-data locations Xu
Xu <- cbind(X, matrix(rep(u, ny), ncol=2, byrow=TRUE))
ehat.u <- aGP.seq(XT, Z, Xu, da, methods, ncalib=2, omp.threads=nth, verb=0)

## estimate discrepancy from the residual
cmle.u <- discrep.est(X, Y, ehat.u$mean, d, g, bias.est, FALSE)
cmle.u$ll <- cmle.u$ll + beta.prior(u)
## compare to same calculation with u.hat above

## now RMSE
# }
## predictive design with true calibration parameter
XXu <- cbind(XX, matrix(rep(u, nny), ncol=2, byrow=TRUE))

## emulate at predictive design
ehat.oos.u <- aGP.seq(XT, Z, XXu, da, methods, ncalib=2, 
  omp.threads=nth, verb=0)

## predict via discrepency
YYm.pred.u <- predGP(cmle.u$gp, XX)

## add in emulation
YY.pred.u <- YYm.pred.u$mean + ehat.oos.u$mean

## calculate RMSE
rmse.u <- sqrt(mean((YY.pred.u - YYtrue)^2))
## compare to same calculation with u.hat above

## clean up
# }