I have received phishing spam through the R-sig-phylo mailing list
(pretending I had expressed interest in renting something from them) from
anya_phill...@casetotours.xyz
disguised as a reply to my comment. So that address should immediately be
removed from the list.
Joe
-
j...@gs.washingto
Dear Grace,
the problem may derive from your specification of the priors. Usually you don’t
specify the prior for B in MCMCglmm. The problem may also be related to the
size of your dataset. Estimation of effects can be difficult with binary data,
when the dataset is small. Below is a small exam
There's also corDISC in corHMM (disclosure: I'm a coauthor on the package).
It does Pagel 1994 with two or three binary characters, allows for user set
root states (I believe the canonical Pagel (1994) assumes equal freq at the
root, I don't know if phytools uses this same assumption [a lot of prog
Hello,
I agree with Joe that Pagel’s 1994 method might be a good option to analyze the
data. I would only include a word of caution that the method can be sensitive
to the sample sizes in each of the states (i.e. 0,0 ; 0,1 ; 1,1 ; 1,0 :
environment yes/no & degrades carbon yes/no) so you should
Grace,
The package phytools includes a function fitPagel if that is the method
that you want to use. He has a post on his blog that discusses his
implementation so it won't be a black box for you:
http://blog.phytools.org/2014/12/r-function-for-pagels-1994-correlation.html
cheers
Heath
On Wed
I do not know offhand whether there is an R implementation, but how about
Mark Pagel's 1994 method for testing whether two 0/1 characters changing
along a ohylogeny are changing independently?
J.F.
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j...@gs.washington.edu
Joe Felsenstein, Department of Genome Sciences and Department of Biolog
Grace,
Maybe this easiest thing to do is just try phylogenetic logistic regression,
which is appropriate for binary dependent variables regardless of the form of
the independent variables. You can use phyloglm in the phylolm package, or
binaryPGLMM in the ape package.
Cheers, Tony
On 2/9/1
Hello,
I have characterized a few hundred bacteria from two environments and want to
know if the bacteria from one environment is more likely to show a trait than
the bacteria isolated from the other environment. So my data is binary in both
the independent and in the dependent variable: "envir