phi.fun.toy

0th

Percentile

Functions to create or change hyperparameters

Function to create (phi.fun.toy) or modify (phi.change) toy hyperparameters \(\phi\) in a form suitable for passing to the other functions in the library.

The user should never make \(\phi\) by hand; always use one of these functions

Keywords
array
Usage
phi.fun.toy(rho, lambda, psi1, psi1.apriori, psi2, psi2.apriori,
  theta.apriori)
phi.change(phi.fun, old.phi = NULL, rho = NULL, lambda = NULL,
          psi1 = NULL, psi1.apriori=NULL,  psi1.apriori.mean=NULL,
          psi1.apriori.sigma=NULL, psi2 = NULL, psi2.apriori=NULL,
          psi2.apriori.mean=NULL,  psi2.apriori.sigma=NULL,
          theta.apriori=NULL, theta.apriori.mean=NULL,
          theta.apriori.sigma=NULL)
Arguments
phi.fun

In phi.change(), the name of the function that creates the hyperparameters. Use phi.fun.toy() for the toy dataset

old.phi

In function phi.change(), the hyperparameter object \(\phi\) to be modified

rho

Correlation hyperparameter appearing in main equation

lambda

Noise hyperparameter

psi1

Roughness lengths hyperparameter for design matrix D1. Internal function pdm.maker.psi1() takes psi1 as an argument and returns omega_x, omega_t and sigma1squared.

Recall that \(\Omega_x\) and \(Omega_t\) are arbitrary functions of \(\psi_1\). In this case, the values are omega_x=psi1[1:2], omega_t=psi1[3:4] and sigma1squared=psi1[6]

psi1.apriori

A priori PDF for \(\psi_1\). In the form of a two element list with first element (mean) the mean and second element (sigma) the covariance matrix; distribution of the logarithms is assumed to be multivariate normal. In the toy example, the mean is a vector of length six (the first five are \(\psi_1\) and the sixth is for \(\sigma_1^2\)), and the variance is the corresponding six-by-six matrix. Use function prob.psi1() to calculate the apriori probability density for a particular value of \(\psi_1\)

psi1.apriori.mean

In function phi.change.toy(), use this argument to change just the mean of psi1 (and leave the value of sigma unchanged)

psi1.apriori.sigma

In function phi.change.toy(), use this argument to change just the variance matrix of psi1

psi2

Roughness lengths hyperparameter for D2.

Internal function pdm.maker.psi2() takes psi2 as an argument and returns omegastar_x and sigma2squared. In phi.fun.toy(), the values are omegastar_x=psi2[1:2] and sigma2squared=psi2[3].

NB: function stage2() optimizes more than just psi2. It simultaneously optimizes psi2 and lambda and rho

psi2.apriori

A priori PDF for \(\psi_2\) and hyperparameters \(\rho\) and \(\lambda\) (in that order).

As for psi1.apriori, this is in the form of a list with the first element (mean) the mean and second element (sigma) the covariance matrix; the logs are multivariate normal. In the toy example, the mean is a vector of length five. The first and second elements of the mean are the apriori mean of \(\rho\) and \(\lambda\) respectively; the third and fourth elements are the apriori mean of \(\psi_2\) (that is, x and y respectively); and the fifth is the mean of \(\sigma_2^2\).

The second element of phi.toy$psi2.apriori, sigma, is the corresponding four-by-four variance matrix. Use function prob.psi2() to calculate the apriori probability density of a particular value of \(\psi_2\)

psi2.apriori.mean

In phi.change.toy(), use to change just the mean of psi2

psi2.apriori.sigma

In phi.change.toy(), use to change just the variance matrix of psi2

theta.apriori

Apriori PDF for \(\theta\). As above, in the form of a list with elements for the mean and covariance. The distribution is multivariate normal (NB: The distribution is multivariate normal and NOT lognormal! To be explicit: \(\log(\theta)\) is lognormally distributed). Use function prob.theta() to calculate the apriori probability density of a particular value of \(\theta\)

theta.apriori.mean

In phi.change.toy(), use to change just the mean of theta

theta.apriori.sigma

In phi.change.toy(), use to change just the variance matrix of theta

Details

Note that this toy function contains within itself pdm.maker.toy() which extracts omega_x and omega_t and sigma1squared from psi1. This will need to be changed for real-world applications.

Earlier versions of the package had pdm.maker.toy() defined separately.

Value

Returns a list of several elements:

rho

Correlation hyperparameter

lambda

Noise hyperparameter

psi1

Roughness lengths hyperparameter for D1

psi1.apriori

Apriori mean and variance matrix for psi1

psi2

Roughness lengths hyperparameter for D2

psi2.apriori

Apriori mean and variance matrix for psi2

theta.apriori

Apriori mean and variance matrix for the parameters

omega_x

Positive definite matrix for the lat/long part of D1, whose diagonal is psi1[1:2]

omega_t

Positive definite matrix for the code parameters theta, whose diagonal is psi1[3:5]

omegastar_x

Positive definite matrix for use in equation 13 of the supplement; represents distances between rows of D2

sigma1squared

variance

sigma2squared

variance

omega_x.upper

Upper triangular Cholesky decomposition for omega_x

omega_x.lower

Lower triangular Cholesky decomposition for omega_x

omega_t.upper

Upper triangular Cholesky decomposition for omega_t

omega_t.lower

Lower triangular Cholesky decomposition for omega_t

a

Precalculated matrix for use in Edash.theta(...,fast.but.opaque=TRUE)

b

Precalculated matrix for use in Edash.theta(...,fast.but.opaque=TRUE)

c

Precalculated scalar for use in ht.fun(...,fast.but.opaque=TRUE)

A

Precalculated scalarfor use in tt.fun()

A.upper

Upper triangular Cholesky decomposition for A

A.lower

Lower triangular Cholesky decomposition for A

References

  • M. C. Kennedy and A. O'Hagan 2001. Bayesian calibration of computer models. Journal of the Royal Statistical Society B, 63(3) pp425-464

  • M. C. Kennedy and A. O'Hagan 2001. Supplementary details on Bayesian calibration of computer models, Internal report, University of Sheffield. Available at http://www.tonyohagan.co.uk/academic/ps/calsup.ps

  • R. K. S. Hankin 2005. Introducing BACCO, an R bundle for Bayesian analysis of computer code output, Journal of Statistical Software, 14(16)

See Also

toys, H1.toy

Aliases
  • phi.fun.toy
  • phi.change
Examples
# NOT RUN {
phi.fun.toy(100,101,1:6,list(mean=rep(1,6),sigma=1+diag(6)),50:55,
list(mean=rep(0,4),sigma=0.1+diag(4)),
list(mean=0.1+(1:3),sigma=2.1+diag(3)))

phi.fun.toy(rho=1, lambda=1,
    psi1 = structure(c(1.1, 1.2, 1.3, 1.4, 1.5, 0.7),
            .Names = c("x", "y", "A","B", "C","s1sq")),
    psi1.apriori  = list(
             mean=rep(0,6), sigma=0.4+diag(6)),
             psi2=structure(c(2.1, 2.2), .Names = c("x","y")),
             psi2.apriori  = list(mean=rep(0,5),sigma=0.2+diag(5)),
             theta.apriori = list(mean=0.1+(1:3),sigma=2.1+diag(3))
)

data(toys)
phi.change(phi.fun=phi.fun.toy, old.phi = phi.toy, rho = 100)
phi.change(phi.fun=phi.fun.toy, old.phi = phi.toy,
     theta.apriori.sigma = 4*diag(3))

identical(phi.toy, phi.change(phi.fun=phi.fun.toy, old.phi=phi.toy))
# }
Documentation reproduced from package calibrator, version 1.2-8, License: GPL-2

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