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Function.Design <- function(object, intercept=NULL,
digits=max(8,.Options$digits), ...)
{
# .Options$digits <- digits 14Sep00
oldopt <- options(digits=digits)
on.exit(options(oldopt))
if(.SV4. && ('cph' %in% object$fitFunction) && !length(intercept))
intercept <- -object$center # 7feb04
at <- object$Design
if(!length(at)) at <- getOldDesign(object)
name <- at$name
ac <- at$assume.code
p <- length(name)
nrp <- num.intercepts(object)
name.main <- name[ac!=9] #non-intercepts
pm <- length(name.main)
adj.to <- Getlim(at, allow.null=TRUE, need.all=TRUE)$limits['Adjust to',]
chr <- function(y, digits) if(is.category(y)||is.character(y))
paste('"',as.character(y),'"',sep='') else format.sep(y, digits)
adj.to <- unlist(lapply(adj.to,chr,digits=digits))
z <- paste('function(',paste(name.main,'=',adj.to,collapse=','), ') {', sep='')
#f$term.labels does not include strat
TL <- attr(terms(object),"term.labels")
#Get inner transformations
#from <- c("asis","pol","lsp","rcs","catg","scored","strat","matrx","I")
#from <- paste(from,"(\\(.*\\))",sep="")
from <- c('asis(*)','pol(*)','lsp(*)','rcs(*)','catg(*)','scored(*)',
'strat(*)','matrx(*)','I(*)')
to <- rep('*',9)
#trans <- paste("h(",translate(TL[ac!=9], from, "\\1"),")",sep="")
trans <- paste("h(",sedit(TL[ac!=9], from, to),")",sep="")
#change wrapping function to h()
h <- function(x,...) deparse(substitute(x))
for(i in (1:pm)) trans[i] <- eval(parse(text=trans[i]))
j <- trans!=name.main
if(any(j)) z <- paste(z, paste(name.main[j],'<-',trans[j],collapse=';'),
';',sep='')
interaction <- at$interactions
if(length(interaction)==0) interaction <- 0
parms <- at$parms
Two.Way <- function(prm,Nam,nam.coef,cof,coef,f,varnames,at,digits) {
i1 <- prm[1,1]; i2 <- prm[2,1]
num.nl <- any(prm[1,-1])+any(prm[2,-1])
#If single factor with nonlinear terms, get it as second factor
#Otherwise, put factor with most # terms as second factor
rev <- FALSE
if((num.nl==1 & any(prm[1,-1])) || (length(Nam[[i1]])>length(Nam[[i2]])))
{ i1 <- i2; i2 <- prm[1,1]; rev <- TRUE }
N1 <- Nam[[i1]]; N2 <- Nam[[i2]]
n1 <- nam.coef[[i1]]; n2 <- nam.coef[[i2]]
v <- ""
for(j1 in 1:length(N1)) {
nam1 <- nam.coef[[i1]][j1]
lN2 <- length(N2)
cnam <- if(rev) paste(nam.coef[[i2]],"*",nam1) else
paste(nam1, "*", nam.coef[[i2]])
mnam <- match(cnam, names(cof), nomatch=0)
act <- mnam[mnam>0]
lN2.act <- length(act)
#Check if restricted interaction between a rcs and another nonlinear
#var, i.e. >1 2nd term possible, only 1 (linear) there, and at first
#nonlinear term of rcs
if(lN2.act==1 & lN2>1 & at$assume.code[i1]==4 & j1==2) {
v <- paste(v,"+",N2[1],"*(",sep="")
cnam <- paste(nam.coef[[if(rev)i2 else i1]][1], "*",
nam.coef[[if(rev)i1 else i2]][-1])
## rev and re-order -1 1 4Dec00
vv <- attr(rcspline.restate(at$parms[[at$name[i1]]], c(0, coef[cnam]),
x=varnames[i1], digits=digits),'function.text')
v <- paste(v, vv, ')', sep='')
break
}
else if(lN2.act==1) {
vv <- paste(cof[act],"*",N1[j1],"*", N2[mnam>0], sep="")
v <- paste(v, vv, sep='')
}
else if(lN2.act>0) {
vv <- paste("+",N1[j1],"*(",sep="")
v <- paste(v, vv, sep='')
if(at$assume.code[i2]==4 & !any(mnam==0)) {
#rcspline, interaction not restricted
vv <- attr(rcspline.restate(at$parms[[at$name[i2]]], coef[act],
x=varnames[i2], digits=digits),
'function.text')
v <- paste(v, vv, ')', sep='')
}
else {
for(j2 in 1:lN2) {
l <- mnam[j2]
if(l>0) { #not a restricted-out nonlinear term
if(j2==1 && substring(cof[l],1,1)=="+") cof[l] <- substring(cof[l],2)
vv <- paste(cof[l],"*",N2[j2],sep="")
v <- paste(v, vv, sep='')
}
}
v <- paste(v, ")", sep='')
}
} }
v
}
Three.Way <- function(prm,Nam,nam.coef,cof,coef,f,at,digits){
i1 <- prm[1,1]; i2 <- prm[2,1]; i3 <- prm[3,1]
N1 <- Nam[[i1]]; N2 <- Nam[[i2]]; N3 <- Nam[[i3]]
v <- ""; l <- 0
for(j3 in 1:length(N3)) {
for(j2 in 1:length(N2)) {
for(j1 in 1:length(N1)) {
l <- l+1
v <- paste(v,cof[l], "*", N1[j1], "*", N2[j2],
"*", N3[j3], sep="")
}
}
}
v
}
Coef <- object$coef
if(nrp==1 | length(intercept)) {
cof <- if(!length(intercept))format.sep(Coef[1],digits) else
format.sep(intercept,digits)
z <- paste(z, cof, sep='')
}
Nam <- list(); nam.coef <- list()
assig <- object$assign #DesignAssign(at, f$non.slopes, formula(f)) ## 10Apr02
for(i in (1:p)) {
ass <- ac[i]
nam <- name[i]
prm <- at$parms[[nam]]
if(any(ass==c(5,7,8))) prm <- chr(at$parms[[nam]],digits=digits)
k <- assig[[TL[i]]] ## was f$assign 10Apr02
coef <- Coef[k]
nam.coef[[i]] <- names(coef)
cof <- format.sep(coef,digits)
cof <- ifelse(coef<=0, cof, paste("+", cof, sep=""))
switch(ass,
{ nam <- name[i]; Nam[[i]] <- nam
q <- paste(cof, '*', nam, sep="")
},
{ q <- ""; pow <- 1:prm
nams <- ifelse(pow==1,nam,paste(nam,"^",pow,"",sep=""))
Nam[[i]] <- nams
for(j in pow) q <- paste(q, cof[j], "*", nams[j], sep="")
},
{
q <- paste(cof[1], "*", nam, sep="")
nams <- nam
kn <- format.sep(-prm,digits)
for(j in 1:length(prm)) {
zz <- paste("pmax(", nam, if(prm[j]<0) "+" else NULL,
if(prm[j]!=0) kn[j] else NULL,
",0)", sep="")
nams <- c(nams, zz)
q <- paste(q, cof[j+1], "*", zz, sep="")
}
Nam[[i]] <- nams
},
{ q <- attr(rcspline.restate(prm, coef, x=nam, digits=digits),
'function.text')
if(coef[1]>=0) q <- paste('+',q,sep='')
nn <- nam
for(j in 1:(length(prm)-2)) {
nam <- paste(nam, "'", sep=""); nn <- c(nn, nam)
}
Nam[[i]] <- nn #Two.Way only needs first name
#for 2nd-order ia with 1 d.f. (restr ia)
#Three.Way needs original design matrix
} ,
{ nn <- paste('(',nam,'==',prm[-1],')',sep='')
## was prm[-1],, - R barked
Nam[[i]] <- nn
q <- ''
for(j in 1:(length(prm)-1)) {
vv <- paste(cof[j], nn[j], sep="*")
q <- paste(q, vv, sep="")
}
},
q <- '',
{
q <- paste(cof[1], "*", nam, sep="")
nams <- nam
for(j in 3:length(prm)) {
zz <- prm[j]
vv <- paste(cof[j-1], "*(", nam, "==", zz, ")", sep="")
nams <- c(nams, zz)
q <- paste(q, vv, sep="")
}
Nam[[i]] <- nams
},
#Strat factor doesn't exist as main effect, but keep variable
#names and their lengths if they will appear in interactions later
{ if(!length(Nam[[i]]) && any(interaction==i)) {
nam.coef[[i]] <- paste(name[i], "=", prm[-1], sep="")
## prm[-1] was oprm[-1] 26Mar01; thanks to
## Geskus, Ronald <RGeskus@gggd.amsterdam.nl>
Nam[[i]] <- prm[-1]
}
q <- "" },
{
if(prm[3,1]==0)
q <- Two.Way(prm,Nam,nam.coef,cof,coef,object, name, at, digits)
else q <- Three.Way(prm,Nam,nam.coef,cof,coef,object,at, digits)
},
{ nam <- names(coef)
q <- ""
nam <- paste("(", nam, ")", sep="")
Nam[[i]] <- nam
for(j in 1:length(prm)) {
vv <- paste(cof[j], '*', nam[j], sep="")
q <- paste(q, vv, sep="")
}
})
z <- paste(z, q, sep='')
}
z <- paste(z, '}')
eval(parse(text=z))
}
if(!.SV4.) {
Function.cph <-
function(object, intercept=-object$center, ...)
Function.Design(object, intercept=intercept, ...)
}
sascode <- function(object, file="", append=FALSE) {
chr <- function(y) if(is.category(y)||is.character(y))
paste('"',as.character(y),'"',sep='') else as.character(y)
n <- names(object)[names(object)!='']
# 14Sep00: In S+ 6.0, can't append to tty
for(i in n) if(file=='') cat(i,'=',chr(object[[i]]),';\n') else
cat(i,'=',chr(object[[i]]),';\n',file=file, append=append|i>1)
if(.R.) {
tf <- tempfile()
dput(object, file=tf)
object <- scan(file=tf, what='', sep='\n', quiet=TRUE)
object <- paste(paste(object[3:(length(object)-1)],collapse='\n'),';',sep='')
} else object <- paste(as.character(object[[length(object)]]), ';')
#com <- 'sed -e "s/pmax/max/g" -e "s/pmin/min/g" -e "s/==/=/g"
#-e "s/<-/=/g" -e "s/\\^/\*\*/g"'
#w <- sys(com, w)
object <- sedit(object, c('pmax','pmin','==','<-','^'),c('max','min','=','=','**'),
wild.literal=TRUE)
if(file=='') cat(object, sep='\n') else cat(object, sep="\n", file=file, append=TRUE)
invisible()
}
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