# pcls: Penalized Constrained Least Squares Fitting In mgcv: Mixed GAM Computation Vehicle with Automatic Smoothness Estimation

 pcls R Documentation

## Penalized Constrained Least Squares Fitting

### Description

Solves least squares problems with quadratic penalties subject to linear equality and inequality constraints using quadratic programming.

### Usage

pcls(M)


 M is the single list argument to pcls. It should have the following elements: yThe response data vector. wA vector of weights for the data (often proportional to the reciprocal of the variance). XThe design matrix for the problem, note that ncol(M$X) must give the number of model parameters, while nrow(M$X) should give the number of data. CMatrix containing any linear equality constraints on the problem (e.g.  \bf C in  {\bf Cp}={\bf c} ). If you have no equality constraints initialize this to a zero by zero matrix. Note that there is no need to supply the vector  \bf c, it is defined implicitly by the initial parameter estimates  \bf p. S A list of penalty matrices. S[[i]] is the smallest contiguous matrix including all the non-zero elements of the ith penalty matrix. The first parameter it penalizes is given by off[i]+1 (starting counting at 1). off Offset values locating the elements of M$S in the correct location within each penalty coefficient matrix. (Zero offset implies starting in first location) sp An array of smoothing parameter estimates. pAn array of feasible initial parameter estimates - these must satisfy the constraints, but should avoid satisfying the inequality constraints as equality constraints. AinMatrix for the inequality constraints  {\bf A}_{in} {\bf p} > {\bf b}_{in}. binvector in the inequality constraints. ### Details This solves the problem:  minimise~ \| { \bf W}^{1/2} ({ \bf Xp - y} ) \|^2 + \sum_{i=1}^m \lambda_i {\bf p^\prime S}_i{\bf p}  subject to constraints  {\bf Cp}={\bf c} and  {\bf A}_{in}{\bf p}>{\bf b}_{in}, w.r.t. \bf p given the smoothing parameters \lambda_i.  {\bf X} is a design matrix, \bf p a parameter vector, \bf y a data vector, \bf W a diagonal weight matrix,  {\bf S}_i a positive semi-definite matrix of coefficients defining the ith penalty and \bf C a matrix of coefficients defining the linear equality constraints on the problem. The smoothing parameters are the \lambda_i. Note that  {\bf X} must be of full column rank, at least when projected into the null space of any equality constraints.  {\bf A}_{in} is a matrix of coefficients defining the inequality constraints, while  {\bf b}_{in} is a vector involved in defining the inequality constraints. Quadratic programming is used to perform the solution. The method used is designed for maximum stability with least squares problems: i.e.  {\bf X}^\prime {\bf X} is not formed explicitly. See Gill et al. 1981. ### Value The function returns an array containing the estimated parameter vector. ### Author(s) Simon N. Wood simon.wood@r-project.org ### References Gill, P.E., Murray, W. and Wright, M.H. (1981) Practical Optimization. Academic Press, London. Wood, S.N. (1994) Monotonic smoothing splines fitted by cross validation SIAM Journal on Scientific Computing 15(5):1126-1133 ### See Also magic, mono.con ### Examples require(mgcv) # first an un-penalized example - fit E(y)=a+bx subject to a>0 set.seed(0) n <- 100 x <- runif(n); y <- x - 0.2 + rnorm(n)*0.1 M <- list(X=matrix(0,n,2),p=c(0.1,0.5),off=array(0,0),S=list(), Ain=matrix(0,1,2),bin=0,C=matrix(0,0,0),sp=array(0,0),y=y,w=y*0+1) M$X[,1] <- 1; M$X[,2] <- x; M$Ain[1,] <- c(1,0)
pcls(M) -> M$p plot(x,y); abline(M$p,col=2); abline(coef(lm(y~x)),col=3)

# Penalized example: monotonic penalized regression spline .....

# Generate data from a monotonic truth.
x <- runif(100)*4-1;x <- sort(x);
f <- exp(4*x)/(1+exp(4*x)); y <- f+rnorm(100)*0.1; plot(x,y)
dat <- data.frame(x=x,y=y)
# Show regular spline fit (and save fitted object)
f.ug <- gam(y~s(x,k=10,bs="cr")); lines(x,fitted(f.ug))
# Create Design matrix, constraints etc. for monotonic spline....
sm <- smoothCon(s(x,k=10,bs="cr"),dat,knots=NULL)[[1]]
F <- mono.con(sm$xp); # get constraints G <- list(X=sm$X,C=matrix(0,0,0),sp=f.ug$sp,p=sm$xp,y=y,w=y*0+1)
G$Ain <- F$A;G$bin <- F$b;G$S <- sm$S;G$off <- 0 p <- pcls(G); # fit spline (using s.p. from unconstrained fit) fv<-Predict.matrix(sm,data.frame(x=x))%*%p lines(x,fv,col=2) # now a tprs example of the same thing.... f.ug <- gam(y~s(x,k=10)); lines(x,fitted(f.ug)) # Create Design matrix, constriants etc. for monotonic spline.... sm <- smoothCon(s(x,k=10,bs="tp"),dat,knots=NULL)[[1]] xc <- 0:39/39 # points on [0,1] nc <- length(xc) # number of constraints xc <- xc*4-1 # points at which to impose constraints A0 <- Predict.matrix(sm,data.frame(x=xc)) # ... A0%*%p evaluates spline at xc points A1 <- Predict.matrix(sm,data.frame(x=xc+1e-6)) A <- (A1-A0)/1e-6 ## ... approx. constraint matrix (A%*%p is -ve ## spline gradient at points xc) G <- list(X=sm$X,C=matrix(0,0,0),sp=f.ug$sp,y=y,w=y*0+1,S=sm$S,off=0)
G$Ain <- A; # constraint matrix G$bin <- rep(0,nc);  # constraint vector
G$p <- rep(0,10); G$p[10] <- 0.1
# ... monotonic start params, got by setting coefs of polynomial part
p <- pcls(G);  # fit spline (using s.p. from unconstrained fit)

fv2 <- Predict.matrix(sm,data.frame(x=x))%*%p
lines(x,fv2,col=3)

######################################
######################################

## First simulate data...

set.seed(10)
f1 <- function(x) 5*exp(4*x)/(1+exp(4*x));
f2 <- function(x) {
ind <- x > .5
f <- x*0
f[ind] <- (x[ind] - .5)^2*10
f
}
f3 <- function(x) 0.2 * x^11 * (10 * (1 - x))^6 +
10 * (10 * x)^3 * (1 - x)^10
n <- 200
x <- runif(n); z <- runif(n); v <- runif(n)
mu <- f1(x) + f2(z) + f3(v)
y <- mu + rnorm(n)

## Preliminary unconstrained gam fit...
G <- gam(y~s(x)+s(z)+s(v,k=20),fit=FALSE)
b <- gam(G=G)

## generate constraints, by finite differencing
## using predict.gam ....
eps <- 1e-7
pd0 <- data.frame(x=seq(0,1,length=100),z=rep(.5,100),
v=rep(.5,100))
pd1 <- data.frame(x=seq(0,1,length=100)+eps,z=rep(.5,100),
v=rep(.5,100))
X0 <- predict(b,newdata=pd0,type="lpmatrix")
X1 <- predict(b,newdata=pd1,type="lpmatrix")
Xx <- (X1 - X0)/eps ## Xx %*% coef(b) must be positive
pd0 <- data.frame(z=seq(0,1,length=100),x=rep(.5,100),
v=rep(.5,100))
pd1 <- data.frame(z=seq(0,1,length=100)+eps,x=rep(.5,100),
v=rep(.5,100))
X0 <- predict(b,newdata=pd0,type="lpmatrix")
X1 <- predict(b,newdata=pd1,type="lpmatrix")
Xz <- (X1-X0)/eps
G$Ain <- rbind(Xx,Xz) ## inequality constraint matrix G$bin <- rep(0,nrow(G$Ain)) G$C = matrix(0,0,ncol(G$X)) G$sp <- b$sp G$p <- coef(b)
G$off <- G$off-1 ## to match what pcls is expecting
## force inital parameters to meet constraint
G$p[11:18] <- G$p[2:9]<- 0
p <- pcls(G) ## constrained fit
par(mfrow=c(2,3))
plot(b) ## original fit
b\$coefficients <- p
plot(b) ## constrained fit
## note that standard errors in preceding plot are obtained from
## unconstrained fit



mgcv documentation built on July 26, 2023, 5:38 p.m.