reading BEAST output trees into R

[Jacob Berv]

Hi all,

What do people use to read the nexus/beast formatted tree output from beast into R? the ape read.nexus and read.tree functions result in an "Error in start:end : NA/NaN argument." 

I refer to the raw BEAST output - ie the posterior distribution of trees, not the treeannotator output. I want to randomly subsample the posterior distribution using the function described here:

http://coleoguy.blogspot.ru/2012/09/randomly-sampling-trees.html

But I can't get R to read the BEAST output.

Any ideas?

Jake

[Jacob Berv]

I've also tried the read.beast function in the phyloch package and I get the same error. 

Jake

[Santiago Sánchez]

Hi Jacob,

Usually, read.nexus() can read BEAST annotated trees without a problem. read.beast() is failing because it uses the read.nexus() function internally. My guess is that there is something wrong with the tree structure its self. Does FigTree open your file without error? If it does, try exporting the tree as nexus or phylip, and try reading these files again with read.nexus() or read.tree(). Does your tree have negative branch lengths? Something else that you can try is summarizing your tree again with the heights = "ca" option.

Hope this helps,

Santiago

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Santiago Sánchez-Ramírez

Department of Ecology and Evolutionary Biology, University of Toronto

Department of Natural History (Mycology), Royal Ontario Museum

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[Jacob Berv]

Hi Santiago - 

It turned out that read.nexus() couldn't parse the files because they did not terminate with the 'End;' output (the runs were stopped prematurely). I was able to get them to load into R using read.nexus() but then I learned that read.nexus() doesn't parse most of the branch info that beast writes to the newick format - so I ended up writing a python script that does what I want without losing any of the branch data.

Jake

[r.j.c.bi...@rug.nl]

> But I can't get R to read the BEAST output. Any ideas?

To parse the .trees files to obtain a list of phylogenies (those in the posterior), I currently use the `beast2out.read.trees` function from the https://github.com/olli0601/rBEAST package.

A package with the same functionality is https://github.com/beast-dev/RBeast , but I have not checked that one out yet.

[mira...@umn.edu]

Jake, did you figure it out? I use Phyloch in R.

Hernán

On Saturday, January 24, 2015 at 7:48:02 PM UTC-5, Jacob Berv wrote:

[Patrick Strutzenberger]

My preferred way is 'read.annotated.nexus' in the ‘OutbreakTools’ package.

cheers

Patrick

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[r.j.c.bi...@rug.nl]

For BEAST, treeio's 'read.beast' function appears robust.
For BEAST2, tracerer supports reading all the different BEAST2 output files.

[Santiago Sánchez]

You can also checkout 'read.beast.annot' from: https://github.com/santiagosnchez/rBt

It has some added features, like edge index ordering, to plot and annotate you trees over branches instead of nodes.

There are other useful features, like potting HPD bars on nodes.

You will need to install the package using: 

library(devtools)

install_github("santiagosnchez/rBt")

On Fri, Apr 13, 2018 at 8:45 AM <r.j.c.bi...@rug.nl> wrote:

For BEAST, treeio's 'read.beast' function appears robust.
For BEAST2, tracerer supports reading all the different BEAST2 output files.

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==========================

Santiago Sanchez-Ramirez, PhD

Postdoctoral Associate

Ecology and Evolutionary Biology

University of Toronto

https://sites.google.com/view/sanchez-ramirez-s/home

==========================