Sure they are different. I forgot to mention that.
In comparative analyses, the expected quantity of trait change (= the
variance in the VCV matrix) is given by the product of the rate of
evolution of the trait with branch length. So using a non-ultrametric
tree is a way to assume different rates of evolution for each branch.
With an ultrametric tree, you somehow assume a "clock-like" trait
evolution (i.e., the quantity of change from the root of the tree to the
tips is the same).
BTW, the first command you give below should be (misplaced right
parenthesis):
vcv(chronoMPL(nonultrametric_tree), cor = TRUE)
Best,
Emmanuel
Le 29/10/2016 à 13:12, Shinichi Nakagawa a écrit :
Dear Emmanuel
Many thanks for your swift reply.
If we get a correlation matrix, via chronoMPL [i.e.
vcv(chronoMPL(nonultrametric_tree,cor=T))], this correlation matrix is
different from a correlation matrix obtained directly from vcv [i.e.
vcv(nonultrametric_tree, cor=T)].
Could you enlighten me about differences and why chronoMPL method might
be preferred?
Best wishes and thanks in advance.
Shinichi
On Sat, Oct 29, 2016 at 8:50 PM, Emmanuel Paradis
<emmanuel.para...@ird.fr <mailto:emmanuel.para...@ird.fr>> wrote:
Dear Shinichi,
A fast solution is provided by the function chronoMPL in ape; it does
not require calibration points (see the references in the help page of
this function for the assumptions). The function chronos (also in ape)
is another possibility but it needs at least one calibration point
(though this can be fixed to unity at the root).
Note that a correlation matrix can be calculated from a non-ultrametric
tree: see the function vcv.
Best,
Emmanuel
Le 29/10/2016 à 05:26, Shinichi Nakagawa a écrit :
> Dear List
>
> We would like make several non-ultrametic trees (based on
molecular data;
> downloaded from treeBASE) into ultrametric trees using R. Could
you advice
> us what is the best and the most general way of doing this please?
>
> We would like to use resultant ultrametric trees in phyologenetic
> comparative analysis (by turning into correlation matrices).
>
> Best wishes,
>
> Shinichi Nakagawa
>
> [[alternative HTML version deleted]]
>
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