Hi Yan,

Yes, you are right: this modification can be done. In the meantime, you can fix the code with:


fix(read.nexus)

Find this line (#117):

    if (Ntree == 1) {

and change it to:

    if (FALSE) {

save and close. Tell me if you still have problem.

Best,

Emmanuel

Le 27/12/2016 à 21:15, Yan Wong a écrit :
Hi

I’m doing some analysis in which I produce a variable number of phylogenetic 
trees with the same tips in a nexus file, then import them into R for analysis 
(these are trees along a genome). The name of each tree is meaningful (it is a 
position along the genome). However, in a few simulations, the nexus file has 
only a single tree in it. In this case, read.nexus returns not a multiPhylo 
object, but a single tree, with the name of the tree lost. I wonder if it would 
be sensible to have a force.multi option to read.nexus(), by default set to 
FALSE (to retain compatibility), but which, if set to TRUE, returns a 
multiPhylo object even if there is only one tree in the file?

Yan
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