Re: [R-sig-phylo] corHMM reconstruction not estimating internal node states

[Michael Foisy]

Hi Kev,

Thank you for your response!

Yes -- $States was a typo, sorry!  Nevertheless, unclassing the model (on
my end) showed issues with the node labels (NA) and estimated $states (NaN).

Jeremy Beaulieu advised me to try updating my version of corHMM -- he was
spot on; I was using an old version of the package!


For future reference, if someone reading this needs to update corHMM:
install.packages("devtools")
library(devtools)
install_github("thej022214/corHMM")


Thanks again - I'm excited to work with these tools! :)

,  Michael Foisy



MSc. Student

University of Toronto

michael.fo...@mail.utoronto.ca

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Re: [R-sig-phylo] corHMM reconstruction not estimating internal node states

[Arbuckle, Kevin]

Hi Michael,

When I run your code I get states for the nodes, so I'm not sure what the 
problem is. However, I notice in your message you tried to get the node states 
from $States, so I wonder if this is a typo or if this is the problem: the node 
reconstructions are in $states (note the lower case 's')?

Cheers,

Kev


--

Message: 1
Date: Fri, 26 Feb 2016 12:34:16 -0500
From: Michael Foisy 
To: r-sig-phylo@r-project.org
Subject: [R-sig-phylo] [corHMM reconstruction not estimating internal
nodestates]
Message-ID: