Nothing
csummary.dmm <-
function(object,traitset="all",componentset="all",bytrait=T,gls=F,digits=3, ...)
# csummary.dmm() - make component summary tables for a dmm object
{
if(!is.null(object$specific)) { # specific
retobj <- csummary_specific(object,traitset,componentset,bytrait,gls,digits,...)
class(retobj) <- "csumspecific.dmm"
return(retobj)
} # end if specific
else { # nonspecific
if(traitset[1] == "all"){
# traits <- dimnames(object$b)[[2]][1:ncol(object$b)]
traitpairs <- dimnames(object$variance.components)[[2]]
traits <- traitpairstotraits(traitpairs)
}
else {
traits <- traitset
traitpairs <- permpaste(traits)
}
l <- length(traits)
alltraitpairs <- dimnames(object$variance.components)[[2]]
if(componentset[1] == "all") {
components <- dimnames(object$variance.components)[[1]]
}
else {
components <- componentset
}
if(bytrait) {
ctables <- vector("list",l*l) # one table per traitpair
count <- 0
for(i in traits) {
for(j in traits) {
traitpair <- paste(i,":",j,sep="",collapse=NULL)
ij <- match(traitpair,alltraitpairs)
count <- count + 1
ci95lo <- object$variance.components[components,ij] - 1.96 * object$variance.components.se[components,ij]
ci95hi <- object$variance.components[components,ij] + 1.96 * object$variance.components.se[components,ij]
ctable <- data.frame(Traitpair=alltraitpairs[ij],
Estimate=object$variance.components[components,ij],
StdErr=object$variance.components.se[components,ij],
CI95lo=ci95lo,CI95hi=ci95hi,row.names=components)
ctables[[count]] <- ctable
}
}
}
else { # not bytrait
ctables <- vector("list",length(components)) # one table per component
count <- 0
for(i in components) {
count <- count + 1
ci95lo <- object$variance.components[i,traitpairs] - 1.96 * object$variance.components.se[i,traitpairs]
ci95hi <- object$variance.components[i,traitpairs] + 1.96 * object$variance.components.se[i,traitpairs]
ctable <- data.frame(Component=i,
Estimate=object$variance.components[i,traitpairs],
StdErr=object$variance.components.se[i,traitpairs],
CI95lo=ci95lo,CI95hi=ci95hi,row.names=traitpairs)
ctables[[count]] <- ctable
}
}
retobj <- list(ctables=ctables,traits=traits, components=components, bytrait=bytrait, gls=gls, digits=digits)
if(gls) {
if(bytrait) {
gctables <- vector("list",l*l) # one table per traitpair
count <- 0
for(i in traits) {
for(j in traits) {
traitpair <- paste(i,":",j,sep="",collapse=NULL)
ij <- match(traitpair,alltraitpairs)
count <- count + 1
ci95lo <- object$gls$variance.components[components,ij] - 1.96 * object$gls$variance.components.se[components,ij]
ci95hi <- object$gls$variance.components[components,ij] + 1.96 * object$gls$variance.components.se[components,ij]
ctable <- data.frame(Traitpair=alltraitpairs[ij],
Estimate=object$gls$variance.components[components,ij],
StdErr=object$gls$variance.components.se[components,ij],
CI95lo=ci95lo,CI95hi=ci95hi,row.names=components)
gctables[[count]] <- ctable
}
}
}
else { # not bytrait
gctables <- vector("list",length(components)) # one table per component
count <- 0
for(i in components) {
count <- count + 1
ci95lo <- object$gls$variance.components[i,traitpairs] - 1.96 * object$gls$variance.components.se[i,traitpairs]
ci95hi <- object$gls$variance.components[i,traitpairs] + 1.96 * object$gls$variance.components.se[i,traitpairs]
ctable <- data.frame(Component=i,
Estimate=object$gls$variance.components[i,traitpairs],
StdErr=object$gls$variance.components.se[i,traitpairs],
CI95lo=ci95lo,CI95hi=ci95hi,row.names=traitpairs)
gctables[[count]] <- ctable
}
}
retobj <- list(ctables=ctables,gctables=gctables,traits=traits, components=components, bytrait=bytrait, gls=gls, digits=digits)
}
retobj$call <- match.call()
class(retobj) <- "csummary.dmm"
return(retobj)
} #end else nonspecific
}
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