Nothing
tt.Summary <-
function(tabtabres,trees,focal){
no.trees<-length(c(trees[focal]))
treeComp<-c(trees[focal])
num.edges<-NA
for(Tr in 1:no.trees){#
thisTre<-treeComp[[Tr]]
num.edges[Tr]<-sum(thisTre$edge[,2]>length(thisTre$tip.label))
}
n<-sum(num.edges)
colNames<-c("k","Groups")
totgroups<-(dim(tabtabres)[2]-2)/5
ratetocalc<-totgroups
rowtocal<-dim(tabtabres)[1]
P1s<-seq(from=3,to=dim(tabtabres)[2],by=5)
P2s<-seq(from=4,to=dim(tabtabres)[2],by=5)
mIDs<-seq(from=7,to=dim(tabtabres)[2],by=5)###Changed this from from=6 to from=7
rAtes<-array(dim=c(rowtocal,ratetocalc))
ratcn<-NA
for (i in 1:ratetocalc){
ratcn[i]<-paste("g",i,"_rate",sep="")
}
for (i in 1:rowtocal){
for(j in 1:ratetocalc){
p.1<-tabtabres[i,P1s[j]]
p.2<-tabtabres[i,P2s[j]]
m.id<-tabtabres[i,mIDs[j]]
if(is.na(m.id)==TRUE){rAtes[i,j]<-NA}
else{
if(m.id==1){rAtes[i,j]<-p.1}
if(m.id==2)rAtes[i,j]<-calc.rate.weib(c(p.1,p.2))
if(m.id==3)rAtes[i,j]<-calc.rate.lnorm(c(p.1,p.2))
if(m.id==4)rAtes[i,j]<-calc.rate.vrat(c(p.1,p.2))}
}
}
colnames(rAtes)<-ratcn
for (i in 1:totgroups){
P1n<-paste("g",i,"_P1",sep="")
P2n<-paste("g",i,"_P2",sep="")
Lin<-paste("g",i,"_LL",sep="")
Min<-paste("g",i,"_mod.id",sep="")
npn<-paste("g",i,"_n.param",sep="")
colNames<-c(colNames,P1n,P2n,Lin,Min,npn)
}
col.liks<-seq(5,length(colNames),5)
col.nparm<-seq(7,length(colNames),5)
lik.sums<-apply(tabtabres[,col.liks],1,sum,na.rm=TRUE)
nparm.sums<-apply(tabtabres[,col.nparm],1,sum,na.rm=TRUE)
aic<-(-2*lik.sums)+(2*nparm.sums)
aicc<-aic+((2*nparm.sums*(nparm.sums+1))/(n-nparm.sums-1))
dAICc<-aicc-min(aicc)
result<-data.frame(tabtabres,nparm.sums,lik.sums,aic,aicc,dAICc)
colnames(result)<-c(colNames,"total.param","LL","AIC","AICc","dAICc")
result<-cbind(result[,1:(length(result[1,])-5)],rAtes,result[,(length(result[1,])-4):length(result[1,])])
return(result)
}
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