Re: [R-sig-phylo] corHMM reconstruction not estimating internal node states
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
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 $states (note the lower case 's')?
Cheers,
Kev
--
Message: 1
Date: Fri, 26 Feb 2016 12:34:16 -0500
From: Michael Foisy
To: r-sig-phylo@r-project.org
Subject: [R-sig-phylo] [corHMM reconstruction not estimating internal
nodestates]
Message-ID:
Content-Type: text/plain; charset="UTF-8"
Hello,
I'm running some precursor models in corHMM to understand the evolution of
a discrete binary character. Some example code using data(primates) below,
but what happens is the internal nodes are not being estimated ($States =
NaN). Also, when I unclass(precursor2.primates), the internal Node labels
are all "NA". Still solves the optimization, but I can't plot the
reconstruction!
library(corHMM)
data(primates)
#write precursor matrix (Marazzi et al., 2012):
precursor2.matrix <- matrix(data = c(NA, NA, 2, NA,
NA, NA, NA, NA,
1, NA, NA, 4,
NA, NA, 3, NA ),
nrow = 4, ncol = 4,
byrow = TRUE
)
rownames(precursor2.matrix) <- c("(0,R1)", "(1,R1)", "(0,R2)", "(1,R2)")
rownames(precursor2.matrix)
colnames(precursor2.matrix) <- c("(0,R1)", "(1,R1)", "(0,R2)", "(1,R2)")
colnames(precursor2.matrix)
#running the precursor-2 model:
precursor2.primates <- corHMM(primates$tree,primates$trait,rate.cat
=2,rate.mat=precursor2.matrix,node.states="marginal",diagn=FALSE)
unclass(precursor2.primates)
Am I neglecting something in the corHMM() function, or is there something
else going on? I run into the same NaN when running the precursor matrices
Beaulieu wrote into the corHMM notes.
Any help is appreciated! Thank you!
, Michael Foisy
MSc. Student
University of Toronto
michael.fo...@mail.utoronto.ca
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[R-sig-phylo] [corHMM reconstruction not estimating internal node states]
Hello,
I'm running some precursor models in corHMM to understand the evolution of
a discrete binary character. Some example code using data(primates) below,
but what happens is the internal nodes are not being estimated ($States =
NaN). Also, when I unclass(precursor2.primates), the internal Node labels
are all "NA". Still solves the optimization, but I can't plot the
reconstruction!
library(corHMM)
data(primates)
#write precursor matrix (Marazzi et al., 2012):
precursor2.matrix <- matrix(data = c(NA, NA, 2, NA,
NA, NA, NA, NA,
1, NA, NA, 4,
NA, NA, 3, NA ),
nrow = 4, ncol = 4,
byrow = TRUE
)
rownames(precursor2.matrix) <- c("(0,R1)", "(1,R1)", "(0,R2)", "(1,R2)")
rownames(precursor2.matrix)
colnames(precursor2.matrix) <- c("(0,R1)", "(1,R1)", "(0,R2)", "(1,R2)")
colnames(precursor2.matrix)
#running the precursor-2 model:
precursor2.primates <- corHMM(primates$tree,primates$trait,rate.cat
=2,rate.mat=precursor2.matrix,node.states="marginal",diagn=FALSE)
unclass(precursor2.primates)
Am I neglecting something in the corHMM() function, or is there something
else going on? I run into the same NaN when running the precursor matrices
Beaulieu wrote into the corHMM notes.
Any help is appreciated! Thank you!
, Michael Foisy
MSc. Student
University of Toronto
michael.fo...@mail.utoronto.ca
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