Liam,
The package MASS has the function mvrnorm that simulates from a
multivariate normal distribution. Its help page says:
The matrix decomposition is done via 'eigen'; although a Choleski
decomposition might be faster, the eigen decomposition is stabler.
The package mvtnorm (on C
esearch on Evolution
http://nere.bio.uci.edu/
(A University of California Multicampus Research Project)
Original message
Date: Tue, 19 May 2009 14:19:12 -1000
From: Marguerite Butler
Subject: Re: [R-sig-phylo] Trait simulations
To: r-sig-phylo@r-project.org
>Hi S
Hi Sam and Jeremy,
On May 19, 2009, at 11:34 AM, Sam Brown wrote:
>
>
>> I was just wondering if there is a package or function in R that
>> can simulate
>> two continuous traits with a user-specified correlation coefficient
>> using a
>> known tree topology, branch lengths, and a model of Br
> I was just wondering if there is a package or function in R that can simulate
> two continuous traits with a user-specified correlation coefficient using a
> known tree topology, branch lengths, and a model of Brownian motion (or even
> OU, if possible)?
I stumbled across the ouch package yes
Hi Jeremy,
Perhaps you've already figured this out. There may be a function
available in R to do this, but if not, in principle for BM it should be
fairly easy to do this "manually."
First, read your tree in:
tree<-read.tree(FILE, etc.) % put filename or paste in tree
then compute the ph
Hi all~
I was just wondering if there is a package or function in R that can simulate
two continuous traits with a user-specified correlation coefficient using a
known tree topology, branch lengths, and a model of Brownian motion (or even
OU, if possible)?
All the best,
Jeremy Beaulieu
