Hi Sérgio.
Liam is right. But we do expect the normalised residuals to be
approximately Normal. You can calculate the normalised residuals by
pre-multiplying the raw residuals by the inverse of the Cholesky
decomposition of the phylogenetic variance-covariance matrix, and then
dividing by the
Hi David.
The diagonal of Q is defined such that row sum (or sometimes the column
sum) is zero. This is the case for any transition rate matrix of a
continuous time Markov chain & is required so that matrix exponentiation
of Q*t give the matrix P[i,j] in which i,j gives the probability of
goi
Liam-
Yes, that works! I apparently confused the sort of model matrix needed
by rTraitDisc with the sort needed by ace.
Here's a full working example, for future posterity:
#
library(ape)
library(phytools)
data(bird.orders)
#make a matrix for a 4 step trait
model<-matrix(c(0,1,
Hi David.
I think the problem may be that you're specifying the model matrix
incorrectly. The model matrix is an integer matrix in which each number
is a different rate type and the diagonal is zeroes.
So, for instance, for a single-rate ordered model with four states you
would do:
model<-
corHMM should be able to do this as long as the states are defined in the
transition matrix (rate.mat.maker() to start, then modify). BioGeoBEARS
could do this (since it has to for biogeography: not all combos of
ancestral areas are observed at the tips), and one of its models might be
equivalent t
Liam,
Ah, I see, rerootingMethod(), unlike ace, will accept a matrix
representation of discrete trait values.
However, it doesn't appear that one can define a model matrix still?
Outside of molecular data, the missing state issue is often for
ordered data, hence the need to define a model matrix.
Hi David.
Actually, if I understand correctly, this does work in phytools. I
suspect it can be set up in phangorn as well - Klaus can probably
explain how.
So, if I understand correctly, you want to get marginal ancestral states
for a character that can assume, say, states "A", "C", "G", & "
Hello all,
(I'm a troublemaker today.)
Sometimes, in ordered discrete data, there are states we know might
exist as intermediary between observed states but aren't observed
themselves. I suppose this is probably common for meristic data. At
least to me, it seems like it should be possible to reco
Hi Sérgio.
It might be worth pointing out that we do not expect that the residuals
from a phylogenetic regression to be normal. I described this with
respect to the phylogenetic ANOVA on my blog
(http://blog.phytools.org/2013/02/a-comment-on-distribution-of-residuals.html),
but this applies e
Sergio,
You can fit a non-Gaussian phylo regression with MCMCglmm.
HTH,
Dan.
> On Jun 17, 2015, at 9:40 AM, Sergio Ferreira Cardoso
> wrote:
>
> Hello all,
>
> I'm having a problem with a Multiple Regression PGLS analysis that I'm
> performing. The residuals are not normal and it's dif
Hello all,
I'm having a problem with a Multiple Regression PGLS analysis that I'm
performing. The residuals are not normal and it's difficult to bring them
to normality. In these cases, are there any alternatives to the linear
model? I know that for non-phylogenetic analyses other models exist, bu
Hello all,
Following up on discussion from Monday, I've been trying to figure out
how the tree I shared broke ape's rules for 'phylo' objects. It turns
out, it doesn't, really (other than having single nodes), at least not
as defined by checkValidPhylo or as described in the formatTree PDF.
#
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