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# Design FEH 1Aug90, re-written 21Oct91
#
# Augments S formula language to include:
#
# name - name[i] = name of ith original variable in x
# label - label[i] = label of ith original variable (=name if none)
# assume - assume(original x)
# assume.code - coded version of assume (1-9, 9=added interaction)
# parms - parms(original x)
# for interaction effects parms[[i]] is a matrix with dim
# 3 x (1+# interaction terms). First element in pair
# is 1 if first factor is represented as an expanded
# non-linear term, 0 otherwise (this applies to polynomial,
# lspline, rcspline, scored). Second element applies to
# second factor in interaction effect. Third element
# applies to third factor (0 if second order interaction)
# First column contains factor numbers involved in interaction.
# limits - limits(original x)
# values - For continuous variables with <=10 unique values, is
# vector of values. NULL otherwise.
# interactions - 3 x k matrix of factor numbers
#
# Cannot have interactions between two stratification factors.
#
#
#23Feb95 - added logic to remove cluster() factors
#
Design <- function(mf, allow.offset=TRUE, intercept=1) {
Terms <- attr(mf, "terms")
Term.labels <- attr(Terms,'term.labels')
#iscluster <- if(length(Term.labels)) substring(Term.labels,1,8)=='cluster('
# else FALSE 5jan04
# Problem: offsets not included in term.labels in R
#For some reason, model frame sometimes has a blank name if using %ia%
namx <- names(mf)
if(any(namx=="")) {
namx <- names(mf) <- c(namx[1],Term.labels)
dimnames(mf)[[2]] <- namx
dimnames(attr(Terms,"factors"))[[1]] <- namx
}
wts <- if(any(namx=='(weights)'))(1:length(namx))[namx=='(weights)']
else 0 # 4jun02
if(length(Terms)==0) inner.name <- NULL else {
#Handle case where a function has two arguments that are names,
#e.g. rcs(x,knots) -> want x only
inner.name <- unique(var.inner(Terms))
# var.inner is stripped down version of terms.inner (see Design.trans)
#Note: these exclude interaction terms and %ia% terms
}
response.pres <- attr(Terms, 'response') > 0 # 3Jun99
offs <- attr(Terms, "offset")
if(!length(offs)) offs <- 0
if(offs>0 & !allow.offset)
stop("offset variable not allowed in formula")
factors <- attr(Terms, "factors")
if(length(factors) && response.pres) factors <- factors[-1,,drop=FALSE]
attr(Terms, "intercept") <- intercept
fname <- flabel <- name <- strt <- asm <- len <-
fname.incl.dup <- ia <- funits <- NULL # funits 20May99
parm <- nonlinear <- limits <- values <- list()
scol<-1
colnam <- list()
#Corrected 23Jun95 - if user used name 'dist' get would return 'dist'
XDATADIST <- .Options$datadist
if(length(XDATADIST))
{
if(!exists(XDATADIST)) stop(paste("dataset",XDATADIST,
"not found for options(datadist=)"))
datadist <- if(.R.) eval(as.name(XDATADIST)) else
eval(as.name(XDATADIST), local=FALSE) #27May99 9Apr02
Limits <- datadist$limits
Limnames <- dimnames(Limits)[[2]]
}
nc <- 0
options(Design.attr=NULL, TEMPORARY=FALSE) #Used internally by asis, rcs, ...
anyfactors <- ncol(mf) > 1*response.pres #3Jun99
i1.noia <- 0
if(anyfactors)for(i in (response.pres+1):ncol(mf)) {
## if(i!=offs && i!=wts && !iscluster[i-response.pres]) { #3Jun99 5jan04
if(i != offs && i !=wts) {
i1 <- i - response.pres #3Jun99
xi <- mf[[i]]
z <- attributes(xi)
assu <- z$assume.code
if(!length(assu) || assu!=9) i1.noia <- i1.noia+1
if(!length(assu)) {#Not processed w/asis,et
nam <- inner.name[i1.noia]
lab <- attr(xi, "label")
ord <- is.ordered(xi) && all.is.numeric(levels(xi)) #21Jun99
if(!length(lab) || lab=="") lab <- nam
if(ord) {
xi <- scored(xi, name=nam, label=lab)
attr(mf[,i],"contrasts") <- attr(xi,"contrasts")
}
else if(is.character(xi) | is.category(xi)) {
## | is.factor(xi)) 21Feb02
if(is.ordered(xi) &&
.Options$contrasts[2]!='contr.treatment')
warning(paste('Variable',nam,'is an ordered factor.\n',
'You should set options(contrasts=c("contr.treatment","contr.treatment"))\nor Design will not work properly.'))
## warning 6may03
xi <- catg(xi, name=nam, label=lab)
}
else if(is.matrix(xi)) xi <- matrx(xi, name=nam, label=lab)
else xi <- asis(xi, name=nam, label=lab)
z <- c(z,attributes(xi))
}
za <- z$assume.code
zname <- z$name
fname.incl.dup <- c(fname.incl.dup, zname)
if(!length(fname) || !any(fname==zname)) { #unique factor
nc <- nc+1
fname <- c(fname,zname)
flabel <- c(flabel,z$label)
##funits <- was here 9Jun99 (see 5 down)
asm <- c(asm,za)
colnam[[i1]] <- z$colnames
if(za!=8) name <- c(name, colnam[[i1]])
if(za!=9) {
funits <- c(funits, if(length(z$units))z$units else '')
if(length(z$parms)) parm[[zname]] <- z$parms
if(length(XDATADIST))
{
limits[[zname]] <- if(any(Limnames==zname)) {
j <- match(zname, Limnames, 0) #require EXACT match
Limits[,j[j>0]]
}
else rep(NA,7)
j <- match(zname, names(datadist$values), 0)
if(j>0) {
values[[zname]] <- datadist$values[[j]]
l1 <- levels(xi); l2 <- datadist$values[[j]] #20May99
if(length(l1) && ((length(l1) != length(l2)) ||
any(sort(l1) != sort(l2))))
warning(paste('Variable',zname,'has levels',paste(l1,collapse=' '),
'which do not match levels given to datadist (',
paste(l2,collapse=' '),'). datadist values ignored.'))
values[[zname]] <- l1
}
}
}
if(length(nonl <- z$nonlinear)) nonlinear[[zname]] <- nonl
if(za==9) {
iia <- match(z$ia, fname)
if(any(is.na(iia)))stop(paste(paste(z$ia,collapse=" "),
"cannot be used in %ia% since not listed as main effect"))
ia <- cbind(ia, c(iia,0))
parms <- rbind(z$parms,0)
parms[,1] <- c(iia,0)
if(length(parms)) parm[[zname]] <- parms
}
}
nrows <- if(is.matrix(xi))nrow(xi) else length(xi)
}
}
#Save list of which factors where %ia% interactions (before adding automatic ias
which.ia <- (1:length(asm))[asm==9]
#Add automatically created interaction terms
if(anyfactors) {
# if((nrow(factors)-(offs>0)-sum(iscluster))!=length(fname.incl.dup))5jan04
nrf <- if(!length(factors)) 0 else if(.R.) nrow(factors) else
nrow(factors) * (ncol(factors) > 0)
## S-Plus, if only offset in model, has factors as 2 rows 0 cols 5jan04
if(nrf || length(fname.incl.dup))
if((nrf-(offs > 0)) != length(fname.incl.dup))
stop("program logic error 1")
## added length(factors) 5jan04
if(length(factors)) for(i in 1:ncol(factors)) {
f <- factors[,i] #3Jun99 was -1,i
j <- (1:length(f))[f>0]
nia <- length(j)
if(nia>1) {
fn <- fname.incl.dup[j]
jf <- match(fn,fname.incl.dup)
if(any(is.na(jf))) stop("program logic error 2")
nc <- nc + 1
asm <- c(asm,9)
if(nia==2)ialab <- paste(fn[1],"*",fn[2])
else if(nia==3)ialab <- paste(fn[1],"*",fn[2],"*",fn[3])
else stop("interaction term not second or third order")
fname <- c(fname, ialab)
flabel <- c(flabel, ialab)
if(sum(asm[jf]==8)>1)
stop("cannot have interaction between two strata factors")
nn <- list()
for(k in 1:nia) {
if(asm[jf[k]]==5 | asm[jf[k]]==8)
nn[[k]] <- paste(fn[k],"=",parm[[fname[jf[k]]]][-1],sep="")
else if(asm[jf[k]]==7) {
nn[[k]] <- c(fn[k], paste(fn[k],"=",
parm[[fname[jf[k]]]][c(-1,-2)],sep=""))
}
else nn[[k]] <- colnam[[jf[k]]]
}
if(nia==2) nn[[3]] <- ""
parms <- jf
if(length(jf)==2) parms <- c(parms, 0)
nonlin <- NULL
nl1 <- nonlinear[[fname[jf[1]]]]
nl2 <- nonlinear[[fname[jf[2]]]]
#Strata factors don't have nonlinear duplicated for # levels - 1
if(asm[jf[1]]==8) nl1 <- rep(FALSE, length(parm[[fname[jf[1]]]])-1)
if(asm[jf[2]]==8) nl2 <- rep(FALSE, length(parm[[fname[jf[2]]]])-1)
if(nia==2) nl3 <- FALSE
else if(asm[jf[3]]==8) nl3 <- rep(FALSE, length(parm[[fname[jf[3]]]])-1)
else nl3 <- nonlinear[[fname[jf[3]]]]
n1 <- nn[[1]]
n2 <- nn[[2]]
n3 <- nn[[3]]
#model.matrix makes auto-products move first variable fastest, etc.
for(j3 in 1:length(n3)) {
for(j2 in 1:length(n2)) {
for(j1 in 1:length(n1)) {
parms <- cbind(parms,c(nl1[j1],nl2[j2],nl3[j3]))
nonlin <- c(nonlin, nl1[j1] | nl2[j2] | nl3[j3])
if(nia==2)name <- c(name, paste(n1[j1],"*",n2[j2]))
else name <- c(name, paste(n1[j1],"*",n2[j2],"*",n3[j3]))
}}}
#If was 2-way interaction and one of the factors was restricted %ia%,
#adjust indicators
k <- match(jf, which.ia, 0)
if(any(k>0)) {
if(nia==3) stop("cannot have 2-way interaction with an %ia% interaction")
k <- jf[k>0]
wparm <- parms[,1]==k; wparm[3] <- TRUE
parms[wparm,] <- parm[[fname[k]]][1:2,,drop=FALSE]
jf <- parms[,1]
nonlin <- apply(parms, 2, any)[-1]
}
if(length(jf)==2) {jf <- c(jf, 0); parms[3,] <- 0}
ia <- cbind(ia, jf)
if(length(parms)) parm[[ialab]] <- parms
if(length(nonlin)) nonlinear[[ialab]] <- nonlin
}}}
if(!.R.) attr(mf,"names") <- NULL ## was needed at all? 8Apr02
if(anyfactors) {
if(length(XDATADIST))
limits <- structure(limits, row.names=c("Low:effect","Adjust to",
"High:effect",
"Low:prediction","High:prediction","Low","High"),class="data.frame")
#data.frame converts variables always NA to factor!
if(length(funits) != sum(asm!=9)) warning('program logic warning 1')
else names(funits) <- fname[asm!=9]
atr <- list(name=fname, label=flabel, units=funits, colnames=name,
assume=c("asis","polynomial","lspline","rcspline","category",
"","scored","strata","interaction","matrix")[asm],
assume.code=as.integer(asm), parms=parm, limits=limits,
values=values,nonlinear=nonlinear,
interactions=structure(ia,dimnames=NULL))
}
else atr <- list(name=NULL, assume=NULL, assume.code=NULL, parms=NULL)
#attr(Terms,"Design") <- atr 13Apr01 (plus next 4)
#attr(mf,"terms") <- Terms
#attr(mf,"offset") <- offs
attr(mf, 'Design') <- atr
mf
}
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