# Gaussian Process Laboratory

## Documentation for package ‘kergp’ version 0.5.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A C G H I K M N O P Q S T V W

kergp-package | Gaussian Process Laboratory

## -- A --

as.list-method | Coerce a 'covTP' Object into a List
as.list-method | Class '"covComp"'

## -- C --

checkGrad | Check the Gradient Provided in a 'covMan' Object
checkPar | Check Length and Names of a Vector of Values for Parameters or Bounds
checkX | Generic function: Check the Compatibility of a Design Matrix with a Given Covariance Object
checkX-method | Check the Compatibility of a Design with a Given Covariance Object
checkX-method | Virtual Class '"covAll"'
checkX-method | Class '"covComp"'
checkX-method | Class '"covOrd"'
checkX-method | Class '"covQual"'
coef,methods | Extract Coefficients of a Covariance Kernel Object as Vector, List or Matrix
coef-method | Extract Coefficients of a Covariance Kernel Object as Vector, List or Matrix
coef-method | Class '"covANOVA"'
coef-method | Class '"covComp"'
coef-method | Class '"covOrd"'
coef-method | Class '"covQual"'
coef-method | Class '"covRadial"'
coef-method | Class '"covTP"'
coef<- | Generic Function: Replacement of Coefficient Values
coef<--method | Class '"covANOVA"'
coef<--method | Class '"covComp"'
coef<--method | Class '"covMan"'
coef<--method | Class '"covOrd"'
coef<--method | Class '"covQual"'
coef<--method | Class '"covRadial"'
coef<--method | Class '"covTP"'
coef<--method | Class '"covTS"'
coefLower | Extract or Set Lower/Upper Bounds on Coefficients
coefLower-method | Class '"covANOVA"'
coefLower-method | Class '"covComp"'
coefLower-method | Class '"covMan"'
coefLower-method | Class '"covOrd"'
coefLower-method | Class '"covQual"'
coefLower-method | Class '"covRadial"'
coefLower-method | Class '"covTP"'
coefLower-method | Class '"covTS"'
coefLower<- | Extract or Set Lower/Upper Bounds on Coefficients
coefLower<--method | Class '"covANOVA"'
coefLower<--method | Class '"covMan"'
coefLower<--method | Class '"covOrd"'
coefLower<--method | Class '"covQual"'
coefLower<--method | Class '"covRadial"'
coefLower<--method | Class '"covTP"'
coefLower<--method | Class '"covTS"'
coefUpper | Extract or Set Lower/Upper Bounds on Coefficients
coefUpper-method | Class '"covANOVA"'
coefUpper-method | Class '"covComp"'
coefUpper-method | Class '"covMan"'
coefUpper-method | Class '"covOrd"'
coefUpper-method | Class '"covQual"'
coefUpper-method | Class '"covRadial"'
coefUpper-method | Class '"covTP"'
coefUpper-method | Class '"covTS"'
coefUpper<- | Extract or Set Lower/Upper Bounds on Coefficients
coefUpper<--method | Class '"covANOVA"'
coefUpper<--method | Class '"covMan"'
coefUpper<--method | Class '"covOrd"'
coefUpper<--method | Class '"covQual"'
coefUpper<--method | Class '"covRadial"'
coefUpper<--method | Class '"covTP"'
coefUpper<--method | Class '"covTS"'
coerce-method | Class '"covMan"'
coerce-method | Class '"covOrd"'
coerce-method | Class '"covQual"'
contr.helmod | Modified Helmert Contrast Matrix
corLevCompSymm | Correlation Matrix for the Compound Symmetry Structure
corLevDiag | Correlation or Covariance Matrix for a Diagonal Structure
corLevLowRank | Correlation Matrix for a Low-Rank Structure
corLevSymm | Correlation Matrix for a General Symmetric Correlation Structure
covAll-class | Virtual Class '"covAll"'
covANOVA | Creator for the Class '"covANOVA"'
covANOVA-class | Class '"covANOVA"'
covComp | Creator for the Class '"covComp"' for Composite Covariance Kernels
covComp-class | Class '"covComp"'
covMan | Creator Function for 'covMan' Objects
covMan-class | Class '"covMan"'
covMat | Generic Function: Covariance or Cross-Covariance Matrix Between two Sets of Locations
covMat-method | Class '"covANOVA"'
covMat-method | Class '"covComp"'
covMat-method | Covariance Matrix for a Covariance Kernel Object
covMat-method | Class '"covOrd"'
covMat-method | Class '"covQual"'
covMat-method | Class '"covRadial"'
covMat-method | Class '"covTP"'
covOrd | Warping-Based Covariance for an Ordinal Input
covOrd-class | Class '"covOrd"'
covQual-class | Class '"covQual"'
covQualNested | Nested Qualitative Covariance
covQualNested-class | Class '"covQualNested"'
covRadial | Creator for the Class '"covRadial"'
covRadial-class | Class '"covRadial"'
covTP | Creator for the Class '"covTP"'
covTP-class | Class '"covTP"'
covTS | Creator Function for 'covTS' Objects
covTS-class | Class '"covTS"'

## -- G --

gls | Generic Function: Generalized Least Squares Estimation with a Given Covariance Kernel
gls-method | Generalized Least Squares Estimation with a Given Covariance Kernel
gls-methods | Generalized Least Squares Estimation with a Given Covariance Kernel
gp | Gaussian Process Model

## -- H --

hasGrad | Generic Function: Extract slot hasGrad of a Covariance Kernel
hasGrad-method | Generic Function: Extract slot hasGrad of a Covariance Kernel

## -- I --

influence.gp | Diagnostics for a Gaussian Process Model, Based on Leave-One-Out
inputNames | Generic Function: Names of the Inputs of a Covariance Kernel
inputNames-method | Generic Function: Names of the Inputs of a Covariance Kernel
inputNames<- | Generic Function: Names of the Inputs of a Covariance Kernel
inputNames<--method | Class '"covComp"'
inputNames<--method | Generic Function: Names of the Inputs of a Covariance Kernel

## -- K --

k1Exp | Predefined covMan Objects for 1D Kernels
k1Fun1Cos | One-Dimensional Classical Covariance Kernel Functions
k1Fun1Exp | One-Dimensional Classical Covariance Kernel Functions
k1Fun1Gauss | One-Dimensional Classical Covariance Kernel Functions
k1Fun1Matern3_2 | One-Dimensional Classical Covariance Kernel Functions
k1Fun1Matern5_2 | One-Dimensional Classical Covariance Kernel Functions
k1Fun1PowExp | One-Dimensional Classical Covariance Kernel Functions
k1FunExp | One-Dimensional Classical Covariance Kernel Functions
k1FunGauss | One-Dimensional Classical Covariance Kernel Functions
k1FunMatern3_2 | One-Dimensional Classical Covariance Kernel Functions
k1FunMatern5_2 | One-Dimensional Classical Covariance Kernel Functions
k1FunPowExp | One-Dimensional Classical Covariance Kernel Functions
k1Gauss | Predefined covMan Objects for 1D Kernels
k1Matern3_2 | Predefined covMan Objects for 1D Kernels
k1Matern5_2 | Predefined covMan Objects for 1D Kernels
k1PowExp | Predefined covMan Objects for 1D Kernels
kergp | Gaussian Process Laboratory
kernelName | Name of the One-Dimensional Kernel in a Composite Kernel Object
kernelName-method | Class '"covTS"'
kExp | Matérn Kernels
kGauss | Gauss (Squared-Exponential) Kernel
kMatern | Matérn Kernels
kSE | Gauss (Squared-Exponential) Kernel

## -- M --

mle | Generic Function: Maximum Likelihood Estimation of a Gaussian Process Model
mle-method | Maximum Likelihood Estimation of Gaussian Process Model Parameters
mle-methods | Maximum Likelihood Estimation of Gaussian Process Model Parameters

## -- N --

npar | Generic function: Number of Free Parameters in a Covariance Kernel
npar-method | Class '"covANOVA"'
npar-method | Class '"covOrd"'
npar-method | Class '"covQual"'
npar-method | Class '"covRadial"'
npar-method | Class '"covTP"'
npar-method | Number of Parameters for a Covariance Kernel Object

## -- O --

optimMethods | Optimization Methods (or Algorithms) for the 'mle' Method

## -- P --

parMap | Generic Function: Map the Parameters of a Composite Covariance Kernel
parMap-method | Map the Parameters of a Structure on the Inputs and Kernel Parameters
parNamesSymm | Vector of Names for the General 'Symm' Parameterisation
parseCovFormula | Parse a Formula or Expression Describing a Composite Covariance Kernel
plot | Plot for a qualitative input
plot-method | Plot for a qualitative input
plot.covQual | Plot for a qualitative input
plot.gp | Diagnostic Plot for the Validation of a 'gp' Object
plot.simulate.gp | Plot Simulations from a 'gp' Object
predict.gp | Prediction Method for the '"gp"' S3 Class
prinKrige | Principal Kriging Functions

## -- Q --

q1CompSymm | Qualitative Correlation or Covariance Kernel with one Input and Compound Symmetric Correlation
q1Diag | Qualitative Correlation or Covariance Kernel with one Input and Diagonal Structure
q1LowRank | Qualitative Correlation or Covariance Kernel with one Input and Low-Rank Correlation
q1Symm | Qualitative Correlation or Covariance Kernel with one Input and General Symmetric Correlation

## -- S --

scores | Generic Function: Scores for a Covariance Kernel Object
scores-method | Class '"covANOVA"'
scores-method | Class '"covComp"'
scores-method | Class '"covMan"'
scores-method | Class '"covOrd"'
scores-method | Class '"covQual"'
scores-method | Class '"covRadial"'
scores-method | Class '"covTP"'
scores-method | Class '"covTS"'
shapeSlot | Extracts the Slots of a Structure
show-method | Class '"covANOVA"'
show-method | Class '"covComp"'
show-method | Class '"covMan"'
show-method | Class '"covOrd"'
show-method | Class '"covQual"'
show-method | Class '"covRadial"'
show-method | Class '"covTP"'
show-method | Class '"covTS"'
simulate-method | Class '"covOrd"'
simulate-method | Class '"covQual"'
simulate-method | Simulation of a 'covAll' Object
simulate.gp | Simulation of Paths from a 'gp' Object
simulPar | Generic function: Draw Random Values for the Parameters of a Covariance Kernel
simulPar-method | Draw Random Values for the Parameters of a Covariance Kernel
symIndices | Vector of Indices Useful for Symmetric or Anti-Symmetric Matrices.

## -- T --

translude | Make Translucent colors

## -- V --

varVec | Generic Function: Variance of Gaussian Process at Specific Locations
varVec-method | Class '"covANOVA"'
varVec-method | Class '"covComp"'
varVec-method | Class '"covOrd"'
varVec-method | Class '"covQual"'
varVec-method | Class '"covRadial"'
varVec-method | Class '"covTP"'
varVec-method | Covariance Matrix for a Covariance Kernel Object

## -- W --

warpFun | Warpings for Ordinal Inputs
warpNorm | Warpings for Ordinal Inputs
warpPower | Warpings for Ordinal Inputs
warpSpline1 | Warpings for Ordinal Inputs
warpSpline2 | Warpings for Ordinal Inputs
warpUnorm | Warpings for Ordinal Inputs