Nothing
## this is the new implementation of the Penalized B-splines smoother
## Mikis Stasinopoulos, Bob Rigby based on Simon Woods's idea
## created 19-12-2012
#------------------------------------------------------
## fixing df is ammended on 3-10-16 MS
##-----------------------------------------------------
## adding max.df on 24-7-2018 MS
## methods
# / | \
## fix lambda fix df estimate lambda
## | | swith(ML
## | | GAIC
## | | GCV
## | | if df>max.df
## | | fix df to max.df
## \ | /
## \ | /
# \ | /
## output
##########################################################################
##########################################################################
#-------------------------------------------------------------------------------
pb <- function(x, df = NULL, lambda = NULL, max.df = NULL, control=pb.control(...), ...)
{
# -------------------------------------------------------------------------
#--------------------------------------------------------------------------
## local function
## creates the basis for p-splines
## Paul Eilers' function
#-------------------------------------------------------------------------
bbase <- function(x, xl, xr, ndx, deg, quantiles=FALSE)
{
tpower <- function(x, t, p)
# Truncated p-th power function
(x - t) ^ p * (x > t)
# DS xl= min, xr=max, ndx= number of points within
# Construct B-spline basis
# if quantiles=TRUE use different bases
dx <- (xr - xl) / ndx # DS increment
if (quantiles) # if true use splineDesign
{ # this is not working and should be taken out
knots <- sort(c(seq(xl-deg*dx, xl, dx),quantile(x, prob=seq(0, 1, length=ndx)), seq(xr, xr+deg*dx, dx)))
B <- splineDesign(knots, x = x, outer.ok = TRUE, ord=deg+1)
n <- dim(B)[2]
attr(B, "knots") <- knots[-c(1:(deg-1), (n-(deg-2)):n)]
return(B)
}
else # if false use Paul's
{
knots <- seq(xl - deg * dx, xr + deg * dx, by = dx)
P <- outer(x, knots, tpower, deg)# calculate the power in the knots
n <- dim(P)[2]
D <- diff(diag(n), diff = deg + 1) / (gamma(deg + 1) * dx ^ deg) #
B <- (-1) ^ (deg + 1) * P %*% t(D)
attr(B, "knots") <- knots[-c(1:(deg-1), (n-(deg-2)):n)]
# I think what I need is xl, xr, ndx, deg
# quantiles should be eliminated
# why I do not save all knots?
B
}
}
#--------------------------------------------------------------------------
#--------------------------------------------------------------------------
# the main function starts here
scall <- deparse(sys.call())
no.dist.val <- length(table(x))
if (is.matrix(x)) stop("x is a matric declare it as a vector")
lx <- length(x)
control$inter <- if (lx<99) 10 else control$inter # this is to prevent singularities when length(x) is small:change to 99 30-11-11 MS
control$inter <- if (no.dist.val<=control$inter) no.dist.val else control$inter
xl <- min(x)
xr <- max(x)
xmax <- xr + 0.01 * (xr - xl)
xmin <- xl - 0.01 * (xr - xl)
## create the basis
X <- bbase(x, xmin, xmax, control$inter, control$degree, control$quantiles) #
# getting the base out assign("X", X, envir = .GlobalEnv)
r <- ncol(X)
## the penalty matrix
D <- if(control$order==0) diag(r) else diff(diag(r), diff=control$order)
## ------ if df are set
if(!is.null(df)) # degrees of freedom
{
if (df>(dim(X)[2]-2))
{df <- 3;
warning("The df's exceed the number of columns of the design matrix", "\n", " they are set to 3") }
if (df < 0) warning("the extra df's are set to 0")
df <- if (df < 0) 2 else df+2
}
## -------- check max.df (new 7-2018 MS)
if (is.null(max.df)) max.df <- dim(X)[2]
if (max.df>(dim(X)[2]))
{
max.df <- dim(X)[2]
warning("The max.df's are set to", dim(X)[2], "\n")
}
## here we get the gamlss environment and a random name to save
## the starting values for lambda within gamlss()
## get gamlss environment
#--------
rexpr<-regexpr("gamlss",sys.calls())
for (i in 1:length(rexpr)){
position <- i
if (rexpr[i]==1) break}
gamlss.environment <- sys.frame(position)
#--------
## get a random name to use it in the gamlss() environment
#--------
sl <- sample(letters, 4)
fourLetters <- paste(paste(paste(sl[1], sl[2], sep=""), sl[3], sep=""),sl[4], sep="")
startLambdaName <- paste("start.Lambda",fourLetters, sep=".")
## put the starting values in the gamlss()environment
#--------
assign(startLambdaName, control$start, envir=gamlss.environment)
#--------
xvar <- x #rep(0,length(x)) # only the linear part in the design matrix the rest pass as artributes
attr(xvar, "control") <- control
attr(xvar, "D") <- D
attr(xvar, "X") <- X
attr(xvar, "df") <- df
attr(xvar, "max.df") <- max.df
attr(xvar, "call") <- substitute(gamlss.pb(data[[scall]], z, w))
attr(xvar, "lambda") <- lambda
attr(xvar, "gamlss.env") <- gamlss.environment
attr(xvar, "NameForLambda") <- startLambdaName
attr(xvar, "Name") <- deparse(substitute(x))
attr(xvar, "class") <- "smooth"
xvar
}
#--------------------------------------------------------------------------
#--------------------------------------------------------------------------
# control function for pb()
##-------------------------------------------------------------------------
pb.control <- function(inter = 20, degree= 3, order = 2, start=10, quantiles=FALSE,
method=c("ML","GAIC", "GCV"), k=2, ...)
{
## Control function for pb()
## MS Tuesday, March 24, 2009
## inter : is the number of equal space intervals in x
## (unless quantiles = TRUE is used in which case the points will be at the quantiles values of x)
## degree: is the degree of the polynomial
## order refers to differences in the penalty for the coeficients
## order = 0 : white noise random effects
## order = 1 : random walk
## order = 2 : random walk of order 2
## order = 3 : random walk of order 3
# inter = 20, degree= 3, order = 2, start=10, quantiles=FALSE, method="loML"
if(inter <= 0) {
warning("the value of inter supplied is less than 0, the value of 10 was used instead")
inter <- 10 }
if(degree <= 0) {
warning("the value of degree supplied is less than zero or negative the default value of 3 was used instead")
degree <- 3}
if(order < 0) {
warning("the value of order supplied is zero or negative the default value of 2 was used instead")
order <- 2}
if(k <= 0) {
warning("the value of GAIC/GCV penalty supplied is less than zero the default value of 2 was used instead")
k <- 2}
method <- match.arg(method)
list(inter = inter, degree = degree, order = order, start=start,
quantiles = as.logical(quantiles)[1], method= method, k=k)
}
#--------------------------------------------------------------------------
#--------------------------------------------------------------------------
gamlss.pb <- function(x, y, w, xeval = NULL, ...)
{
# -------------------------------------------------------------------------
# functions within
# a simple penalised regression
# this is the original matrix manipulation version but it swiches to QR if it fails
regpen <- function(y, X, w, lambda, D)# original
{
# p <- dim(X)[2]
# qrX <- qr(sqrt(w)*X, tol=.Machine$double.eps^.8)
# R <- qr.R(qrX)
RD <- rbind(R,sqrt(lambda)*D) # 2p x p matrix
svdRD <- svd(RD) # U 2pxp D pxp V pxp
## take only the important values
rank <- sum(svdRD$d>max(svdRD$d)*.Machine$double.eps^.8)
U1 <- svdRD$u[1:p,1:rank] # U1 p x rank
# I am not sure what are consequances in introducing this ???
y1 <- t(U1)%*%Qy # t(Q)%*%(sqrt(w)*y) # rankxp pxn nx1 => rank x 1 vector
# beta <- svdRD$v[,1:rank] %*%diag(1/svdRD$d[1:rank])%*%y1
beta <- svdRD$v[,1:rank] %*%(y1/svdRD$d[1:rank])
# 1/(svdRD$d^2)
#print((svdRD$v)%*%t(svdRD$v), digits=1)
HH <- (svdRD$u)[1:p,1:rank]%*%t(svdRD$u[1:p,1:rank])
df <- sum(diag(HH))
fit <- list(beta = beta, edf = df)
return(fit)
}
#-------------------------------------------------------------------------
## function to find lambdas miimizing the local GAIC
fnGAIC <- function(lambda, k)
{
fit <- regpen(y=y, X=X, w=w, lambda=lambda, D)
fv <- X %*% fit$beta
GAIC <- sum(w*(y-fv)^2)+k*fit$edf
# cat("GAIC", GAIC, "\n")
GAIC
}
#-------------------------------------------------------------------------
## function to find the lambdas which minimise the local GCV
fnGCV <- function(lambda, k)
{
I.lambda.D <- (1+lambda*UDU$values)
edf <- sum(1/I.lambda.D)
y_Hy2 <- y.y-2*sum((yy^2)/I.lambda.D)+sum((yy^2)/((I.lambda.D)^2))
GCV <- (n*y_Hy2)/(n-k*edf)^2
GCV
}
#--------------------------------------------------------------------------
## local function to get edf from lambda
# edf_df <- function(lambda)
# {
# G <- lambda * t(D) %*% D
# H <- solve(XWX + G, XWX)
# edf <- sum(diag(H))
# # cat("edf", edf, "\n")
# (edf-df)
# }
## local function to get df using eigen values
edf1_df <- function(loglambda)
{
lambda <- exp(loglambda)
I.lambda.D <- (1+lambda*UDU$values)
edf <- sum(1/I.lambda.D)
(edf-df)
}
#------ new 22-7-18------- to get max.df
edf2_df <- function(loglambda)
{
lambda <- exp(loglambda)
I.lambda.D <- (1+lambda*UDU$values)
edf <- sum(1/I.lambda.D)
(edf-max.df)
}
##------------------------------------------------------------------------
# the main function starts here
# get the attributes
#w <- ifelse(w>.Machine$double.xmax^.5,.Machine$double.xmax^.5,w )
if (is.null(xeval)) # if no prediction
{
X <- if (is.null(xeval)) as.matrix(attr(x,"X")) #the trick is for prediction
else as.matrix(attr(x,"X"))[seq(1,length(y)),]
Name <- as.character(attr(x, "Name"))
D <- as.matrix(attr(x,"D")) # penalty
lambda <- as.vector(attr(x,"lambda")) # lambda
df <- as.vector(attr(x,"df")) # degrees of freedom
max.df <- as.vector(attr(x,"max.df")) # degrees of freedom
control <- as.list(attr(x, "control"))
gamlss.env <- as.environment(attr(x, "gamlss.env"))
startLambdaName <- as.character(attr(x, "NameForLambda"))
order <- control$order # the order of the penalty matrix
N <- sum(w!=0) # DS+FDB 3-2-14
n <- nrow(X) # the no of observations
p <- ncol(D) # the rows of the penalty matrix
qrX <- qr(sqrt(w)*X, tol=.Machine$double.eps^.8)
R <- qr.R(qrX)
Q <- qr.Q(qrX)
Qy <- t(Q)%*%(sqrt(w)*y)
tau2 <- sig2 <- NULL
# now the action depends on the values of lambda and df
#-------------------------------------------------------------------------
lambdaS <- get(startLambdaName, envir=gamlss.env) ## geting the starting value
if (lambdaS>=1e+07) lambda <- 1e+07 # MS 19-4-12
if (lambdaS<=1e-07) lambda <- 1e-07 # MS 19-4-12
# cat(lambda, "\n")
# case 1: if lambda is known just fit -----------------------------------
if (is.null(df)&&!is.null(lambda)||!is.null(df)&&!is.null(lambda))
{
fit <- regpen(y, X, w, lambda, D)
fv <- X %*% fit$beta
} # case 2: if lambda is estimated --------------------------------------
else if (is.null(df)&&is.null(lambda))
{ #
# cat("----------------------------","\n")
lambda <- lambdaS # MS 19-4-12
# if ML --------------------------------------------------------------ML
switch(control$method,
"ML"={
for (it in 1:50)
{
fit <- regpen(y, X, w, lambda, D) # fit model
gamma. <- D %*% as.vector(fit$beta) # get the gamma differences
fv <- X %*% fit$beta # fitted values
sig2 <- sum(w * (y - fv) ^ 2) / (N - fit$edf) # DS+FDB 3-2-14
tau2 <- sum(gamma. ^ 2) / (fit$edf-order)# see LNP page 279
if(tau2<1e-7) tau2 <- 1.0e-7 # MS 19-4-12
lambda.old <- lambda
lambda <- sig2 / tau2 # maybe only 1/tau2 will do since it gives exactly the EM results see LM-1
if (lambda<1.0e-7) lambda<-1.0e-7 # DS Saturday, April 11, 2009 at 14:18
if (lambda>1.0e+7) lambda<-1.0e+7 # DS 29 3 2012
# cat("iter tau2 sig2",it,tau2, sig2, '\n')
if (abs(lambda-lambda.old) < 1.0e-7||lambda>1.0e10) break
assign(startLambdaName, lambda, envir=gamlss.env)
#cat("lambda",lambda, '\n')
}
},
# "ML-1"={ #------------------------------------------------------------ML-1
# for (it in 1:50)
# {
# fit <- regpen(y, X, w, lambda, D) # fit model
# gamma. <- D %*% as.vector(fit$beta) # get the gamma differences
# fv <- X %*% fit$beta # fitted values
# sig2 <- 1 # sum(w * (y - fv) ^ 2) / (N - fit$edf)
# tau2 <- sum(gamma. ^ 2) / (fit$edf-order)# Monday, March 16, 2009 at 20:00 see LNP page 279
# if(tau2<1e-7) tau2 <- 1.0e-7
# lambda.old <- lambda
# lambda <- sig2 / tau2 # 1/tau2
# if (lambda<1.0e-7) lambda<-1.0e-7 # DS Saturday, April 11, 2009 at 14:18
# if (lambda>1.0e+7) lambda<-1.0e+7 # DS 29 3 2012
# if (abs(lambda-lambda.old) < 1.0e-7||lambda>1.0e7) break
# assign(startLambdaName, lambda, envir=gamlss.env)
# }
# },
# "EM"={ #------------------------------------------------------------ EM
# for (it in 1:500)
# {
# fit <- regpenEM(y, X, w, lambda, order, D)
# gamma. <- D %*% as.vector(fit$beta)
# vgamma <- sum(diag(D%*%fit$V%*%t(D))) # this is crucial for estimating the variance of gamma Monday, March 23, 2009
# fv <- X %*% fit$beta
# tau2 <- ((sum(gamma.^ 2))+vgamma)/length(gamma.)
# if(tau2<1e-7) tau2 <- 1.0e-7
# lambda.old <- lambda
# lambda <- 1 / tau2
# #if (lambda<1.0e-7) lambda<-1.0e-7 # DS Saturday, April 11, 2009
# if (lambda<1.0e-7) lambda<-1.0e-7 # DS Saturday, April 11, 2009 at 14:18
# if (lambda>1.0e+7) lambda<-1.0e+7 # DS 29 3 2012
# # cat("iter sigma_t^2",it, tau2, "lambda",lambda, '\n')
# if (abs(lambda-lambda.old) < 1.0e-7||lambda>1.0e7) break
# }
# #cat("lambda",lambda, '\n')
# assign(startLambdaName, lambda, envir=gamlss.env)
# },
"GAIC"= { #------------------------------------------------------------ GAIC
lambda <- nlminb(lambda, fnGAIC, lower = 1.0e-7, upper = 1.0e7, k=control$k)$par
fit <- regpen(y=y, X=X, w=w, lambda=lambda, D)
fv <- X %*% fit$beta
assign(startLambdaName, lambda, envir=gamlss.env)
},
"GCV"={ #----------------------------------------------------------- GCV
wy <- sqrt(w)*y
y.y <- sum(wy^2)
Rinv <- solve(R)
S <- t(D)%*%D
UDU <- eigen(t(Rinv)%*%S%*%Rinv)
yy <- t(UDU$vectors)%*%Qy #t(qr.Q(QR))%*%wy
lambda <- nlminb(lambda, fnGCV, lower = 1.0e-7, upper = 1.0e7, k=control$k)$par
fit <- regpen(y=y, X=X, w=w, lambda=lambda, D)
fv <- X %*% fit$beta
assign(startLambdaName, lambda, envir=gamlss.env)
})
# new 22-7-2018 MS ----------------------------------------- check max.df
# now we check whether the fitted df are greater that max.df
if (fit$edf > max.df)
{
Rinv <- try(solve(R), silent = TRUE)
if (any(class(Rinv) %in% "try-error"))
stop("The B-basis for ",Name," is singular, transforming the variable may help","\n")
S <- t(D)%*%D
UDU <- eigen(t(Rinv)%*%S%*%Rinv, symmetric=TRUE, only.values=TRUE)
loglambda <- if (sign(edf2_df(-30))==sign(edf2_df(30))) 30
else uniroot(edf2_df, c(-30,30))$root
lambda <- exp(loglambda)
fit <- regpen(y, X, w, lambda, D)
if (abs(fit$edf-max.df)>0.1) warning("the target df's are not acheived, try to reduce the no. of knot intervals \n in pb(). eg. inter=10")
fv <- X %*% fit$beta
assign(startLambdaName, lambda, envir=gamlss.env)
}
#---------- the max.df is finished here----------------------------------
}
else # case 3 : if df are required------------------------------------DF
{
Rinv <- try(solve(R), silent = TRUE)
if (any(class(Rinv) %in% "try-error"))
stop("The B-basis for ",Name," is singular, transforming the variable may help","\n")
S <- t(D)%*%D
UDU <- eigen(t(Rinv)%*%S%*%Rinv, symmetric=TRUE, only.values=TRUE)
loglambda <- if (sign(edf1_df(-30))==sign(edf1_df(30))) 30
else uniroot(edf1_df, c(-30,30))$root
# lambda <- if (sign(edf1_df(0))==sign(edf1_df(100000))) 100000 # in case they have the some sign
# else uniroot(edf1_df, c(0,100000))$root
# if (any(class(lambda)%in%"try-error")) {lambda<-100000}
lambda <- exp(loglambda)
fit <- regpen(y, X, w, lambda, D)
if (abs(fit$edf-df)>0.1) warning("the target df's are not acheived, try to reduce the no. of knot intervals \n in pb(). eg. inter=10")
fv <- X %*% fit$beta
}#end of case 3 --------------------------------------------------------
# I need to calculate the hat matrix here for the variance of the smoother
# but this is working
#Version 1 --------------------------------------------------
# RD <- rbind(R,sqrt(lambda)*D) # 2p x p matrix
# svdRD <- svd(RD) # U 2pxp D pxp V pxp
# ## take only the important values
# rank <- sum(svdRD$d>max(svdRD$d)*.Machine$double.eps^.8)
# U1 <- svdRD$u[1:p,1:rank] # U1 p x rank
# HAT <- Q%*%U1%*%t(U1)%*%t(Q)
# lev <- diag(HAT) # lev1=lev
# #-end -----------------------------------------------------------
# #Version 2 --------------------------------------------------
# RD <- rbind(R,sqrt(lambda)*D) # 2p x p matrix
# svdRD <- svd(RD) # U 2pxp D pxp V pxp
# # ## take only the important values
# rank <- sum(svdRD$d>max(svdRD$d)*.Machine$double.eps^.8)
# U1 <- svdRD$u[1:p,1:rank] # U1 p x rank
# U1U1T <- U1%*%t(U1)
# lev <- rep(0, N)
# for (i in 1:N) lev[i] <- Q[i, ]%*%U1U1T%*%Q[i, ]
# #-end -----------------------------------------------------------
# #Version 3 --------------------------------------------------
# RD <- rbind(R,sqrt(lambda)*D) # 2p x p matrix
# svdRD <- svd(RD) # U 2pxp D pxp V pxp
# # # ## take only the important values
# rank <- sum(svdRD$d>max(svdRD$d)*.Machine$double.eps^.8)
# #U1 <- svdRD$u[1:p,1:rank] # U1 p x rank
# betavcov <- svdRD$v%*%diag(svdRD$d^(-2))%*%t(svdRD$v)
# lev3 <- rep(0, N)
# for (i in 1:N) lev3[i] <- X[i, ]%*%betavcov%*%X[i, ]
# this verion is not working???
# #-end -----------------------------------------------------------
#Version 4 --------------------------------------------------
waug <- as.vector(c(w, rep(1,nrow(D))))
xaug <- as.matrix(rbind(X,sqrt(lambda)*D))
lev <- hat(sqrt(waug)*xaug,intercept=FALSE)[1:n] # get the hat matrix
# MIKIS: conclusion is that version 4 the R hat is the faster
#-end -----------------------------------------------------------
lev <- (lev-.hat.WX(w,x)) # subtract the linear since is already fitted
var <- lev/w # the variance of the smootherz
# # se <- sqrt(diag(solve(XWX + lambda * t(D) %*% D)))
suppressWarnings(Fun <- splinefun(x, fv, method="natural"))
coefSmo <- list( coef = fit$beta,
fv = fv,
lambda = lambda,
edf = fit$edf,
sigb2 = tau2,
sige2 = sig2,
sigb = if (is.null(tau2)) NA else sqrt(tau2),
sige = if (is.null(sig2)) NA else sqrt(sig2),
method = control$method,
name = Name,
knots = attr(X,"knots"),
fun = Fun)
class(coefSmo) <- "pb"
list(fitted.values=fv, residuals=y-fv, var=var, nl.df =fit$edf-2,
lambda=lambda, coefSmo=coefSmo )
}
else # for prediction
{
position <- 0
rexpr <- regexpr("predict.gamlss",sys.calls())
for (i in 1:length(rexpr)){
position <- i
if (rexpr[i]==1) break}
# cat("New way of prediction in pb() (starting from GAMLSS version 5.0-3)", "\n")
gamlss.environment <- sys.frame(position)
param <- get("what", envir=gamlss.environment)
object <- get("object", envir=gamlss.environment)
TT <- get("TT", envir=gamlss.environment)
smooth.labels <- get("smooth.labels", envir=gamlss.environment)
# ls(envir=gamlss.environment)
pred <- getSmo(object, parameter= param, which=which(smooth.labels==TT))$fun(xeval)
# pred <- getSmo(object, parameter= param, which=which(TT%in%smooth.labels))$fun(xeval)
# ll <- dim(as.matrix(attr(x,"X")))[1]
# nx <- as.matrix(attr(x,"X"))[seq(length(y)+1,ll),]
# pred <- drop(nx %*% fit$beta)
pred
}
}
#-------------------------------------------------------------------------------
plot.pb <- function(x,...)
{
plot(x$coef, type="h", xlab="knots", ylab="coefficients")
abline(h=0)
}
#-------------------------------------------------------------------------
coef.pb <- function(object, ...)
{
as.vector(object$coef)
}
#-------------------------------------------------------------------------
fitted.pb<- function(object, ...)
{
as.vector(object$fv)
}
#-------------------------------------------------------------------------
print.pb <- function (x, digits = max(3, getOption("digits") - 3), ...)
{
cat("P-spline fit using the gamlss function pb() \n")
cat("Degrees of Freedom for the fit :", x$edf, "\n")
cat("Random effect parameter sigma_b:", format(signif(x$sigb)), "\n")
cat("Smoothing parameter lambda :", format(signif(x$lambda)), "\n")
}
#-------------------------------------------------------------------------
knots.pb <- function(Fn, ...)
{
as.vector(Fn$knots)
}
#-----------------------------------------------------------------------------
# END
#-----------------------------------------------------------------------------
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