bass: Bayesian Adaptive Spline Surfaces (BASS)

In BASS: Bayesian Adaptive Spline Surfaces

Bayesian Adaptive Spline Surfaces (BASS)

Description

Fits a BASS model using RJMCMC. Optionally uses parallel tempering to improve mixing. Can be used with scalar or functional response. Also can use categorical inputs.

Usage

bass(
  xx,
  y,
  maxInt = 3,
  maxInt.func = 3,
  maxInt.cat = 3,
  xx.func = NULL,
  degree = 1,
  maxBasis = 1000,
  npart = NULL,
  npart.func = NULL,
  nmcmc = 10000,
  nburn = 9000,
  thin = 1,
  g1 = 0,
  g2 = 0,
  s2.lower = 0,
  h1 = 10,
  h2 = 10,
  a.tau = 0.5,
  b.tau = NULL,
  w1 = 5,
  w2 = 5,
  beta.prior = "g",
  temp.ladder = NULL,
  start.temper = NULL,
  curr.list = NULL,
  save.yhat = TRUE,
  small = FALSE,
  verbose = TRUE,
  ret.str = F
)

Arguments

xx	a data frame or matrix of predictors. Categorical predictors should be included as factors.
y	a response vector (scalar response) or matrix (functional response). Note: If sum(y^2) is large (i.e. 1e10), please center/rescale (and rescale g1 and g2 if necessary).
maxInt	integer for maximum degree of interaction in spline basis functions. Defaults to the number of predictors, which could result in overfitting.
maxInt.func	(functional response only) integer for maximum degree of interaction in spline basis functions describing the functional response.
maxInt.cat	(categorical input only) integer for maximum degree of interaction of categorical inputs.
xx.func	a vector, matrix or data frame of functional variables.
degree	degree of splines. Stability should be examined for anything other than 1.
maxBasis	maximum number of basis functions. This should probably only be altered if you run out of memory.
npart	minimum number of non-zero points in a basis function. If the response is functional, this refers only to the portion of the basis function coming from the non-functional predictors. Defaults to 20 or 0.1 times the number of observations, whichever is smaller.
npart.func	same as npart, but for functional portion of basis function.
nmcmc	number of RJMCMC iterations.
nburn	number of the nmcmc iterations to disregard.
thin	keep every thin samples
g1	shape for IG prior on \sigma^2.
g2	scale for IG prior on \sigma^2.
s2.lower	lower bound for s2. Turns IG prior for s2 into a truncated IG.
h1	shape for gamma prior on \lambda.
h2	rate for gamma prior on \lambda. This is the primary way to control overfitting. A large value of h2 favors fewer basis functions.
a.tau	shape for gamma prior on \tau.
b.tau	rate for gamma prior on \tau. Defaults to one over the number of observations, which centers the prior for the basis function weights on the unit information prior.
w1	nominal weight for degree of interaction, used in generating candidate basis functions. Should be greater than 0.
w2	nominal weight for variables, used in generating candidate basis functions. Should be greater than 0.
beta.prior	what type of prior to use for basis coefficients, "g" or "jeffreys"
temp.ladder	temperature ladder used for parallel tempering. The first value should be 1 and the values should increase.
start.temper	when to start tempering (after how many MCMC iterations). Defaults to 1000 or half of burn-in, whichever is smaller.
curr.list	list of starting models (one element for each temperature), could be output from a previous run under the same model setup.
save.yhat	logical; should predictions of training data be saved?
small	logical; if true, returns a smaller object by leaving out curr.list and other unnecessary objects. Use in combination with save.yhat to get smaller memory footprint for very large models.
verbose	logical; should progress be displayed?
ret.str	logical; return data and prior structures

Details

Explores BASS model space by RJMCMC. The BASS model has

y = f(x) + \epsilon, ~~\epsilon \sim N(0,\sigma^2)

f(x) = a_0 + \sum_{m=1}^M a_m B_m(x)

and B_m(x) is a BASS basis function (tensor product of spline basis functions). We use priors

a \sim N(0,\sigma^2/\tau (B'B)^{-1})

M \sim Poisson(\lambda)

as well as the priors mentioned in the arguments above.

Value

An object of class 'bass'. The other output will only be useful to the advanced user. Rather, users may be interested in prediction and sensitivity analysis, which are obtained by passing the entire object to the predict.bass or sobol functions.

See Also

predict.bass for prediction and sobol for sensitivity analysis.

Examples

## Not run: 
####################################################################################################
### univariate example
####################################################################################################
## simulate data (Friedman function)
f<-function(x){
  10*sin(pi*x[,1]*x[,2])+20*(x[,3]-.5)^2+10*x[,4]+5*x[,5]
}
sigma<-1 # noise sd
n<-500 # number of observations
x<-matrix(runif(n*10),n,10) #10 variables, only first 5 matter
y<-rnorm(n,f(x),sigma)

## fit BASS, no tempering
mod<-bass(x,y)
plot(mod)
## fit BASS, tempering
mod<-bass(x,y,temp.ladder=1.3^(0:8),start.temper=1000)
plot(mod)

## prediction
npred<-1000
xpred<-matrix(runif(npred*10),npred,10)
pred<-predict(mod,xpred,verbose=TRUE) # posterior predictive samples
true.y<-f(xpred)
plot(true.y,colMeans(pred),xlab='true values',ylab='posterior predictive means')
abline(a=0,b=1,col=2)

## sensitivity
sens<-sobol(mod)
plot(sens,cex.axis=.5)

####################################################################################################
### functional example
####################################################################################################
## simulate data (Friedman function with first variable as functional)
sigma<-1 # noise sd
n<-500 # number of observations
nfunc<-50 # size of functional variable grid
xfunc<-seq(0,1,length.out=nfunc) # functional grid
x<-matrix(runif(n*9),n,9) # 9 non-functional variables, only first 4 matter
X<-cbind(rep(xfunc,each=n),kronecker(rep(1,nfunc),x)) # to get y
y<-matrix(f(X),nrow=n)+rnorm(n*nfunc,0,sigma)

## fit BASS
mod<-bass(x,y,xx.func=xfunc)
plot(mod)

## prediction
npred<-100
xpred<-matrix(runif(npred*9),npred,9)
Xpred<-cbind(rep(xfunc,each=npred),kronecker(rep(1,nfunc),xpred))
ypred<-matrix(f(Xpred),nrow=npred)
pred<-predict(mod,xpred) # posterior predictive samples (each is a curve)
matplot(ypred,apply(pred,2:3,mean),type='l',xlab='observed',ylab='mean prediction')
abline(a=0,b=1,col=2)
matplot(t(ypred),type='l') # actual
matplot(t(apply(pred,2:3,mean)),type='l') # mean prediction

## sensitivity
sens<-sobol(mod,mcmc.use=1:10) # for speed, only use a few samples
plot(sens) # functional variable labelled "a"

sens.func<-sobol(mod,mcmc.use=1:10,func.var=1)
plot(sens.func)

## End(Not run)

## minimal example for CRAN testing
mod<-bass(1:2,1:2,nmcmc=2,nburn=1)

BASS documentation built on July 9, 2023, 6:57 p.m.