Hi,
I agree that model testing between ARD vs MK models is going to be misleading
when the process is really described by a threshold model (and sorry for
ignoring that set of simulations by Jarrod previously; somehow I misfiled that
email and didn't see it).
The threshold model has nice ways
correction: the last sentence should have read
I wonder how that would work in this case. I think these are important
questions going forward.
On Thu, Aug 16, 2012 at 11:00 PM, Matt Pennell wrote:
> Hey all,
>
> This has been a really fantastic discussion. Mark, you make some really
> excellent
Hey all,
This has been a really fantastic discussion. Mark, you make some really
excellent points in response to my earlier comments. I think you are
correct in this.
The question that arises out of Jarrod and Dan's simulations (which I have
just run) is whether a model selection criteria would b
Hi all-
A couple of points. I am actually less concerned about the Type I error rates I
gave in that previous message for the equal rates markov process, even though I
think they are real (e.g., I can corroborate them using Diversitree). I don't
think it is an issue of ascertainment bias, but
Mark Holder wrote:
With respect to Jarrod's simulations, I have a few thoughts:
1. I don't understand the claim (in the original email) that "its
fairly straightforward to prove that asymmetric transition rates
cannot be identified using data collected on the tips of a
phylogeny" It seem
Hi all,
I'm a bit more concerned with Dan's elevated Type-1 error rates than Jarrod's
example.
With respect to Jarrod's simulations, I have a few thoughts:
1. I don't understand the claim (in the original email) that "its
fairly straightforward to prove that asymmetric transiti
Hi All-
This is an interesting discussion. I think there is clearly something going on.
I do not get catastrophic Type I error rates from this exercise (only
'elevated') with discrete char simulations (an equal rates markov process) -
see below. However, Jarrod's latent model seems reasonable
Hi,
I can see that there is information when the rates depend on
speciation, because there is variation in the number of speciation
events the species have experienced in their evolutionary history
(from the root). However, if it is a purely time based process there
is no variation in tim
Dear Jarrod,
It's not R, but I think very helpful - this is from the Mesquite
documentation at
http://mesquiteproject.org/mesquite_folder/docs/mesquite/CharacterEvolution
/AncestralStates.html -
"As of version 1.1 of Mesquite, the AsymmMk model has two options
for the handling
Jarrod and Dan,
While I see what Dan is saying and I agree that evaluating this with
non-phylogenetic data is not entirely useful, I think you have stumbled
upon a known issue but one that is not widely appreciated.
While the MK model is a useful model for discrete characters in many ways,
it may
HI Jarrod-
It isn't immediately obvious to me why the exercise below reflects something
problematic. In the first scenario, you have a random binary state but with
strong differences in frequency. Because there is effectively no phylogenetic
signal (as data are simply random), this suggests a
Hi,
I have had a few replies off-list which have made me try and clarify
what I mean. I think the distinction needs to be made between two
types of probability: the probability that an outcome is 0 or 1 Pr(y|
\theta) and the probability density of \theta, Pr(\theta | \gamma),
indexed by
Hi,
I'm using the function haploNet in the package pegas to create haplotype
networks. Does anyone knows if it is possible to: 1) also plot missing
haplotypes, 2) include the mutational steps (i.e. not only a longer line,
but ticks or blank circles) and, 3) if possible a reference to the position
Hi,
I have been helping someone with some analyses and came across some
routines to estimate asymmetric transition rates between discrete
characters. This surprised me because its fairly straightforward to
prove that asymmetric transition rates cannot be identified using data
collected on
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