Nothing
anova.lmp<-
function(object, ...)
{
if(length(list(object, ...)) > 1)
stop("The first argument cannot be an array or list.")
#return(anova.lmlist(object, ...))
#REW
mo<-NCOL(object$resid)
if (mo>1)
respNames<-colnames(object$residuals)
else
respNames<- deparse(formula(object)[[2]])
#REW
for (id in 1:mo) {
resid<-as.matrix(object$resid)[,id]
effects<-as.matrix(object$effects)[,id] #REW replaced these and added id indexes throughout
w <- object$weights
ssr <- sum(if(is.null(w)) resid^2 else w*resid^2)
dfr <- df.residual(object)
p <- object$rank
if(p > 0) {
p1 <- 1:p
comp <- effects[p1]
asgn <- object$assign[object$qr$pivot][p1]
nmeffects <- c("(Intercept)", attr(object$terms, "term.labels"))
tlabels <- nmeffects[1 + unique(asgn)]
ss <- c(unlist(lapply(split(comp^2,asgn), sum)), ssr)
df <- c(unlist(lapply(split(asgn, asgn), length)), dfr)
} else {
ss <- ssr
df <- dfr
tlabels <- character(0)
}
ms <- ss/df
#begin REW
if (is.null(object$perm))
doPerm<-FALSE
else {
perm=object$perm$perm
doPerm<-(perm=="Prob" || perm=="SPR" || perm=="Exact")
}
if (doPerm){
table<-data.frame(df,ss,ms)
const<-attr(object$terms,"intercept")
P<-c(as.vector(object$perm$P[,id]),NA) # as.vector() pervents warning message about class of coulumn in table
#table<-table[1:length(P),,drop=FALSE] # get rid of residual row, but keep table a matrix
perm<-object$perm$perm
if (perm=="Prob") {
table$Mn<-c(as.vector(object$perm$Mn[,id]),NA)
table$P<-P
dimnames(table) <- list(c(tlabels, "Residuals"),
c("Df","R Sum Sq", "R Mean Sq", "Iter", "Pr(Prob)"))
}
else if (perm=="SPR") {
table$Mn<-c(as.vector(object$perm$Mn[,id]),NA)
table$P<-P
table$accept<-c(as.vector(object$perm$accept),NA)
dimnames(table) <- list(c(tlabels, "Residuals"),
c("Df","R Sum Sq", "R Mean Sq", "Iter", "Pr(SPR)" ,"Accept"))
}
else { #Exact
table$P<-P
dimnames(table) <- list(c(tlabels, "Residuals"),
c("Df","R Sum Sq", "R Mean Sq", "Pr(Exact)"))
}
if (const)
table<-table[-1,,drop=FALSE]
print(structure(table, heading = c("Analysis of Variance Table\n",
paste("Response:", respNames[id])),
class= c("anova", "data.frame")))# was "tabular"
}
else{
f <- ms/(ssr/dfr)
P <- pf(f, df, dfr, lower.tail = FALSE)
table <- data.frame(df, ss, ms, f, P)
table[length(P), 4:5] <- NA
dimnames(table) <- list(c(tlabels, "Residuals"),
c("Df","R Sum Sq", "R Mean Sq", "F value", "Pr(>F)"))
if(attr(object$terms,"intercept")) table <- table[-1, ]
print(structure(table, heading = c("Analysis of Variance Table\n",
paste("Response:", respNames[id], object$info)),
class= c("anova", "data.frame")))# was "tabular"
}
}
#end REW
}
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