Taiwo Ojurongbe
2007-Mar-02 10:11 UTC
[R] Dice dissimilarity output and 'phylo' function in R
Dear All, I get some problems using the 'phylo' and dissimilarity functions in R. I converted an output from 'hclust' into an order of phylo so as to be able to use the 'consensus' function on it. Each time I submit the consensus codes, my computer hangs. When I tried to see what the contents of the object converted into order phylo is, I get the message "Phylogenetic tree with 0 tips and 7 internal nodes. Tip labels: NULL Rooted; includes branch lengths". So I guess this explains why the consensus function does not work. Another thing I noticed in the output from the 'dissimilarity' function is that when I compared the distances computed in R with that from NTSYS or SAS, for example dice and jaccard coefficients I realised that the dice distances are very different while the jaccard distances are the same with those from these other softwares. The codes I used for a small example are shown below: samptest4<- scan (file = "samp-test4.txt") samptest4<- matrix(data = samptest4,nrow=8, ncol=4, byrow=T) library(MASS) library(arules) library(ape) #CFI<- numeric (M) CFI <- function(ctree) { (ctree$Nnode -1)/(length(ctree$tip.label) - 2) } #calculation of dissimilarities & construction of trees# #Calc Jacc disimi# disjacc <- dissimilarity(samptest4, y=NULL,method="jaccard") #Calc Dice disimi# disdice <- dissimilarity(samptest4, y=NULL,method="dice") #Construct Jacc dendro# tjacc<- hclust(disjacc, method = "average") tjaccphylo<- as.phylo(tjacc) #Construct Dice dendro# tdice<- hclust(disdice, method = "average") tdicephylo<- as.phylo(tdice) pdf (file = paste("TJD4", ".pdf", sep = "")) par(mfrow = c(1,2)) plot (tjacc, hang = -1) plot (tdice, hang = -1) dev.off() #Construct consensus tree# ctree<-consensus(tdicephylo,tjaccphylo) plot(ctree) CFI(ctree) I will appreciate any help in solving these problems. Thank you and best regards, Taiwo ____________________________________________________________________________________ Don't pick lemons.