node.age error in ses.pd function

[pabuveery]

I'm periodically running into an error when attempting to run ses.pd() on a large community matrix. The error reads: "function node.age only works with a rooted phylo object." However, my tree object is a rooted, ultrametric tree of 'phylo' class (is.rooted() and is.ultrametric() both return TRUE). Also, I'm having no trouble running pd() using the same 'phylo' tree object. Any insights into what might be going on?

The function I'm running is as follows:

passerine.1.ses.pd.subsample <- ses.pd(samp = passerine.1.picCleanComm.subsample, 
                         tree = passerine.picCleanTree, 
                         null.model = "taxa.labels", 
                         runs = 100)

Here, the samp object is a matrix with 25000 rows and 295 columns; the tree object is a phylogenetic tree with 297 tips, which is rooted and has branch lengths retained.

Please let me know also if more information is needed to help. Thank you very much for your help.

[kerby1998]

Hi, can you provide a reproducible example (that can be run directly within R console to troubleshoot)?

[lalisiglesias]

I'm having the same problem. Did you solve it?

[pabuveery]

Sorry, I missed the followup question back in November. Ultimately I ended up running the script on a remote high-power computing cluster and it worked, but no luck when running directly in desktop RStudio.

[lalisiglesias]

I think its a bug. I could calculate the sesPD when I adjusted the command to do 99 runs instead of the default (999). Have you tried this?

[skembel]

Hi, thanks for the followup, I am still unable to replicate this locally to help troubleshoot, could you please send the phylo and community objects you're using to get this error message? You can send them by direct message/email, or in this issue report thread as file attachments.