will be found at:
https://fhl.uw.edu/courses/course-descriptions/course/evolutionary-quantitative-genetics-workshop-2023/
and more information, including details of the Workshop in recent
years, will be found at
https://eqgw.github.io
Joe Felsenstein and Steve Arnold
--
Joe Felsenstein
Ac-_tyBKyUS0BwdXHfS_bddA8mSgcsrMp6Nly1GJM-UkNMs09pABZP0gIb89WvlGmsVldrV5B-5tMdJeYl2P7XvDP1_L29Apw$
> Searchable archive at
> https://urldefense.com/v3/__http://www.mail-archive.com/r-sig-phylo@r-project.org/__;!!K-Hz7m0Vt54!lAc-_tyBKyUS0BwdXHfS_bddA8mSgcsrMp6Nly1GJM-UkNMs09pABZP0gIb89WvlGmsVldr
.
Joe
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> it make sense?
>
Well, I am afraid I am lost. Perhaps someone else here could explain the
issues to me ...
Joe
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Joe Felsenstein felse...@gmail.com, j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065,
it is clear what the
intended task is and why that makes sense.
Joe
--
Joe Felsenstein felse...@gmail.com, j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
[[alternative HTML version
u compute a linear
combination such as 2 log(wt) - 3 log(height). Which princip[al, le]
components machinery does.
Joe
--
Joe Felsenstein felse...@gmail.com, j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle,
f you had a principal component (usually misnamed a “principle” component)
it is in terms of a linear combination of characters, and I am deeply
puzzled how to give their units as they mix them.
Joe
--
Joe Felsenstein felse...@gmail.com, j...@gs.washington.edu
Department of Genome
. So crop yield has units of meters, and
variance of crop yield should have units of square meters.
That way lies madness ...
Joe
-
Joe Felsenstein felse...@gmail.com, j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 35506
or PHYLIP within R.
J.F.
-
Joe Felsenstein j...@gs.washington.edu
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just using likelihood computations -- I've
checked and the sampling does infer the same
covariances in that case. In this all-continuous
case the same issue of transforming to independent
characters also comes up.
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and
Oscar Inostraza --
Is the variable x also evolving on the tree? If so you need to use
standard phylogenetically-informed comparative methods to estimate the
variances and covariances of changes in both characters.
You may not be able to assume that y responds instantly to x.
J.F.
Joe
e most picturesque marine laboratory.
Joe
----
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logenetic PCA ?
See above. It does require MCMC, and cannot
simply be done with distances.
J.F.
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
___
ompatible. That will often
be the same, but not always. The latter is called the Nelson
Consensus Tree.
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065,
become correspondingly
different, and the model is still reversible. The
tree can be rerooted at any interior node
and the marginal ancestral states at that node
found by the usual likelihood "pruning"
algorithm.
J.F.
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sc
of taking ancestral state inferences as
observations.
The popular science press in particular demands a fly-on-the-wall
account of what happened in evolution, and giving them the ancestral
state inferences as if they were known precisely is a mistake.
Joe
Joe Felsenstein j
a,c) r(b,c)] / [(sqrt(1 - r(a,c)^2) sqrt(1 - r(b,c)^2)]
For likelihood ratio testing in a linear model,
one could compare the likelihoods of models
that did or did not have direct connection of
a and b. RA Fisher also derived a distribution
of the partial correlation coefficient.
Joe
Joe
he PCA machinery until after you
estimate these two covariance matrices.
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
___
R
the within-species sampling error.
The harder part is using that to correct one's estimate of the
covariances of the between-species change, which using ordinary
methods will have some within-species variation mixed in.
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences
pressibility should be much lower.
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
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after the
distance matrix is computed.
J.F.
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
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em that one either
estimates those separately for each pair of sequences, or jointly
estimates them from the whole dataset, without using a tree in the
process.
J.F.
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington
.
Application deadline March 1, 2017.
Application forms and details here:
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Web page:
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Instructors:
Dr. Joe Felsenstein
Department of Genome Sciences
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j...@gs.washington.edu
Dr
this with my own C programs, but it can be done in R too.
But what does it mean to be "scaled similarly" ?
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-50
ut how the environments changed along the tree. Not much
effect so far so you can expect more shots across the bow.
Joe
----
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
[[alter
>
> 1) Diversitree package BiSSE
> 2) Caper package using MacroCAIC
>
> Any suggestions would be greatly appreciated-
And what do these methods assume about how that "discrete binary predictor"
evolves along the tree?
Joe
-
j...@gs.washington.edu
Joe Felsenstein, D
model. American Naturalist 179:
145-156.
which is implemented in my program Threshml which can be called from Liam
Revell's Phytools R package. It also works for multiple threshold
characters and multiple continuous characters.
Joe
Joe Felsenstein j...@gs.washington.edu
Department
continuous and another discrete.
It is implemented in my program Threshml, which should be callable from
Liam Revell's "phytools" R package.
However it does not precisely answer the question you posed, but just asks
whether the two traits evolve in a correlated fashion.
J.
tivariate statistics book by Morrison.
I am not sure where Paul published this, but I think he did in an appendix to a
paper of his in some multiauthor volume.
J.F.
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University
some, but the type I
error rate stays the same.
If the 100 trees are something else, such as the personal opinions of 100
of your friends, then there is no statistical justification for this.
J.F.
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department
ive discussions in the book by John Wakeley. Also in the
elementary population genetics text by Nielsen and Slatkin.
J.F.
----
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065
way I figured out is the function dist.dna from the ape
> package. But I think it does not estimate distances between groups.
>
You want to use distances between groups? But you don't want to think
about coalescents?
J.F.
Joe Felsenstein j...@gs.washington.edu
Depar
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.
-
j...@gs.washington.edu
Joe Felsenstein, Department of Genome Sciences and Department
...@gs.washington.edu
Joe Felsenstein, Department of Genome Sciences and Department of Biology
Box 355065, University of Washington, Seattle, WA 98195-5065
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Warning: You'd have to ensure that the traits for which you are comparing
rates are evolving independently, so that they do not covary in their
evolutionary changes.
I assume Dean Adams's paper involves some way of coping with this. The
issue of log-transforms that Ted raised is very important,
are met.
J.F.
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
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to the true P value, one needs 4 times as many
permutations. And this need for more and more samples continues
indefinitely. There is no sudden change as one reaches a threshold number
of permutations.
But that's what you really meant, right?
Joe
---
Joe Felsenstein j...@gs.washington.edu
? There are parameterized
transformation such as y = (x^p - x^{-p})/(2p) or elsey = ( x^p
- 1) / p + 1 for which you could estimate the parameter p by ML.
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University
or
more states. But the possibilty should be mentioned here.
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
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mentioned by them, I gather
because the authors forgot about it until the last minute when writing the
review. Nevertheless it is getting increasing use.
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box
, it would then be possible to
view the tree in an application such as Adobe Acrobat Reader and zoom in on
it and see the tiny branches and their labels. Making multiple plots for
one tree would probably confuse the matter.
Or is there something I am missing here?
J.F.
Joe Felsenstein j
.
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
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to
model this. We have a version of Dnaml for PHYLIP that can do it, and hope
to release it soon.
As George Shireff saw, it is actually easy to do, and the computations are
not any slower.
J.F.
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology
that it really is G, etc., then
the four quantities you want at one site at one tip of the tree are the
four numbers in a column. (Which column depends on what you observed).
The rows have to add to 1; the columns don't have to.
J.F.
Joe Felsenstein j...@gs.washington.edu
Department of Genome
lengths between
closely-related species are an inadequate predictor of
how different the species means will be. In effect, the
model is wrong so some of the changes attributed to
between-species evolution are actually within-species
sampling variation (phenotypic variance).
Joe
Joe
of menus.
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
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think, for labeled histories.
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
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--
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences
in Windows using the Command Prompt tool, which you will
find in the Accessories menu that is found in the menu
opened by the All Programs tab in the Start Menu.
Joe
Joe Felsenstein, j...@gs.washington.edu
Dept. of Genome Sciences, Univ. of Washington
Box 355065, Seattle, WA 98195-5065 USA
.
The paper I saw was this one:
Hansen, Thomas F Bartoszek, Krzysztof (2012). Interpreting the evolutionary
regression: The interplay between observational and biological errors in
phylogenetic comparative studies. Systematic Biology 61 (3): 413-425. ISSN
1063-5157.
J.F.
Joe Felsenstein
package can call our program.
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
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if we find (chimp, bonobo) to be the cherry we
remove them, leaving a tree such as
(macacque, (gibbon, (orang, gorilla)));
so now (orang, gorilla) is a cherry.
Joe
Joe Felsenstein, j...@gs.washington.edu
Dept. of Genome Sciences, Univ. of Washington
Box 355065, Seattle, WA 98195-5065 USA
(gorilla, human) is a cherry.
Joe
Joe Felsenstein, j...@gs.washington.edu
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Box 355065, Seattle, WA 98195-5065 USA
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is the
likelihood and modeling equivalent problem.)
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
[[alternative HTML version deleted
of the distances
that had been invented up to that date, and explaining relationships between
them:
Zharkikh, A. 1994. Estimation of evolutionary
distances between nucleotide sequences.
Journal of Molecular Evolution 39: 315.329
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome
(there are parameterized families of them)
and use the likelihood to test values of the transform parameters (with
appropriate correction of the likelihood by having a Jacobian term).
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University
interesting but makes molecular change less clocklike.
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
[[alternative HTML version deleted
methods -- the set of most parsimonious
trees may have a consensus, which may well not be a most parsimonious tree.
People who see the consensus of most parsimonious trees may not realize that
the particular tree they are looking at is not most parsimonious.
J.F.
Joe Felsenstein j
.
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
(from 1 October 2012 to 10 December 2012 on sabbatical leave at)
Department of Statistics, University of California, Berkeley
if you use a prior, but if you are willing to
use a controversial prior. And in this case the prior is pretty
uncontroversial.
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065
to prove. In which case it is not
necessary to bring speciation rates or priors into it.
A reversible two-state model should be able to have its parameters
estimated on a given tree, clocklike or not.
Joe
Joe Felsenstein, j...@gs.washington.edu
Dept. of Genome Sciences, Univ
present-day y's on present-day x's. Lots of people are
doing it -- and they're all wrong.
*** whining off ***
Joe
Joe Felsenstein j...@gs.washington.edu
Dept of Genome Sciences and Dept of Biology, Univ. of Washington, Box 5065,
Seattle Wa 98195-5065
).Or have I
missed something here? So the expectation of the difference
is log likelihood *is* described by the AIC, right? And isn't it
(in view of Fisher's distribution) wrong too? That is what
disturbs me and makes me feel there is something I don't
understand about the AIC argument.
Joe
Joe
hypotheses, and the main
point of the AIC is to deal with non-nested hypotheses. To make matters
worse, in my field the AIC has the reputation of too easily favoring the
most complex hypothesis, so maybe we should be subtracting more than
2D, not less.
Clueless in Seattle.
Joe
Joe Felsenstein
i.i.d. from a distribution.
Of course, even correlations of rates of evolution among neighboring
sites violates this.
Whether and how number of species comes in is trickier.
Joe
Joe Felsenstein j...@gs.washington.edu
Dept of Genome Sciences and Dept of Biology, Univ. of Washington
),
when people measure the residual of a character regressed on
environmental variables,
then casually assume that it is undergoing Brownian Motion, when the
environmental variables may have been different in the past. That's
probably not an issue here.
Joe
Joe Felsenstein j
regression.
I worry. Why are we to assume that current phenotypes are distributed around
optima that are based on *current* environmental variables?
Joe
---
Joe Felsenstein, j...@gs.washington.edu
Department of Genome Sciences and Department of Biology
University of Washington
Box 355065
Seattle
hypothesis about the value of the grand mean, of course
REML is inappropriate.
An example would be simple one-way ANOVA which is actually a REML analysis, and
it does test means of the groups.
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology
the statistical method you did
that, and then going ahead with the analysis is a Big Mistake.
J.F.
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
.
J.F.
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
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).
Just complaining that the Brownian stochastic process is no good is
insufficient.
If we want to add the fossils to the calculation, then they will of
course
pressure the Brownian Motion process to change more in their vicinity,
which may help some.
Joe
Joe Felsenstein j
(and they
are not aware how hard they are).
Just understand, when you raise legitimate concerns, that us
model-analyzers are also used to getting a lot of these unreasonable
demands too, and may be grumpy as a result.
Joe
Joe Felsenstein j...@gs.washington.edu
Dept of Genome Sciences and Dept
phenotypes in the fossils
that seem incompatible with the Brownian Motion assumption?
Joe
Joe Felsenstein j...@gs.washington.edu
Dept of Genome Sciences and Dept of Biology, Univ. of Washington,
Box 5065, Seattle Wa 98195-5065
[[alternative HTML version deleted
to approach it. If you can calculate the likelihood of
trees, one way would be to not bother fitting any ancestral values:
just try different lengths for the branch that connects the fossil to
the tree, and see which one maximizes the likelihood.
Joe
Joe Felsenstein j
-species analyses is more difficult yet. I
hope to release an R package later this year to do the one-character analysis
(it is not too hard to put one together yourself in the meantime).
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department
this
for all interior nodes will be no worse than about twice
that of a single pass through the tree.
However people may prefer to use PGLS, which if
properly done should give the proper estimates for
all nodes. There is some discussion of this in
Rohlf's 2001 paper in Evolution.
Joe
Joe
BM on the logs and then
looks at the original phenotype scale, you *would* expect that as the
variance among species increases, so does the mean of the species
means.
Joe
Joe Felsenstein j...@gs.washington.edu
Dept of Genome Sciences and Dept of Biology, Univ. of Washington,
Box 5065
method ought to
be able to handle identical sequences.
2. A high bootstrap support (or another form of support) associated
with a zero-length branch is an indication that something's wrong
there.
Again, it can be a problem even when the branch lengths
are nonzero.
Joe
Joe Felsenstein, j
.
J.F.
Joe Felsenstein, j...@gs.washington.edu
Dept. of Genome Sciences, Univ. of Washington
Box 355065, Seattle, WA 98195-5065 USA
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that it was already estimating.
Joe
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Box 355065, Seattle, WA 98195-5065 USA
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that (determined by
the BD process), then that is even easier using the time-
transformation trick.
I do not know the R packages well enough to know whether one of them
implements this, but I am sure someone will comment on that.
Joe
Joe Felsenstein, j...@gs.washington.edu
Dept. of Genome Sciences
book) is that it gives you
a direct idea of how many groups born at each time
are missing from the tree owing to having gone extinct
before reaching the present day.
J.F.
Joe Felsenstein, j...@gs.washington.edu
Dept. of Genome Sciences, Univ. of Washington
Box 355065, Seattle, WA 98195-5065
method called polymorphism
parsimony but it makes specific assumptions -- namely that polymorphism is
hard to retain along a lineage, easy to lose but hard to regain.
So do you want assume that, or what?
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences
it will return all the binary trees compatible with
that. It is also much slower than PAUP*.
It would get you a file of Newick trees.
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA
). It is only the more
recent researchers who don't know it.
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
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from finite distance matrices or set infinite values to a large value.
But one should return a warning as these samples are likely to be
biased.
Exactly.
J.F.
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box
often it may go very small but not zero.
In either case, it seems to me you can do a LRT versus a star with one
d.f.
Can you? Is the value of zero contained within the range of possible
values, or at its extreme? I think for LRT you need contained within.
Joe
Joe Felsenstein j
of the distances.
Joe
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Department of Genome Sciences and Department of Biology
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Box 355065
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don't have a
non-arbitrary way to do that.
Joe
Joe Felsenstein, j...@gs.washington.edu
Dept. of Genome Sciences, Univ. of Washington
Box 355065, Seattle, WA 98195-5065 USA
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. Wartren Wagner mentions patristic distance
in a 1968 review in Bioscience, but does not
claim it.
4. JS Farris's paper showing that the cophenetic
correlation is minimized when we achieve a least
squares fit of tree to distances is in 1969 in
Systematic Zoology.
Joe
Joe Felsenstein, j
(reduced or restricted maximum
likelihood) on the full covarying Brownian motion model. If PGLS gets
identical results to that, then that proves the identity to contrasts analysis.
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology
characters, and multiply
the values at each node by that.)
This way you don't need a nodes x nodes covariance matrix.
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
be straightforward to simulate (continous) traits under
the available models of evolution.
Keep in mind that one can't always assume that the variances (say
of Brownian motion) are equal in all characters, so the correlations
aren't quite enough.
Joe
Joe Felsenstein, j...@gs.washington.edu
Dept
measures the same character in different species,
is that not good enough? My curiousity is because I suspect that
if Stephane had coded his characters 0/1 before trying to analyze
them, they would then be accepted as made of homology hypotheses.
J.F.
Joe Felsenstein j...@gs.washington.edu
arbitrary opinion of mine, which they are (barely) willing to tolerate.
I suppose the matter will become one of open discussion some day.
Anyway, back to R.
J.F.
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box
important anyway.
J.F.
Joe Felsenstein, j...@gs.washington.edu
Dept. of Genome Sciences, Univ. of Washington
Box 355065, Seattle, WA 98195-5065 USA
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. Then the regression
might just be a simple linear one.
Joe
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
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answered questioning this as a good resampling
procedure. Just to be the Voice Of Orthodoxy, let me add ...
Whatever its merits, it isn't the same as parametric
bootstrapping. That involves simulating data along a tree,
not shuffling data among leaves.
J.F.
Joe Felsenstein j
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