Hi Filipe,
I believe you cannot directly. When you use the "Map onto phylogeny" option
in MorphoJ, you will have appear in the scene tree the tree icon, and two
dataset icons below that. "BranchDiffs" and "IndContrasts". From the
MorphoJ helpGuide:
*Each analysis produces two output data sets: one with the values of the
changes along the branches of the phylogeny for the values of shape
variables, centroid sizes and covariates in the original dataset, and the
other with scores for phylogenetically independent contrasts (Felsenstein
1985) for the same variables.*
You could retroactively calculate node position in PC space based on the
IndCont and branch lengths. However it may be simpler to run
plotGMPhyloMorphoSpace in *geomorph* in R and extract the ancestral states
(which although are calculated by maximum likelihood using *phytools*
fastanc *) - note that the anc.states matrix returned are states prior to
PCA, so all you'd need to do is:
all.data <- rbind(two.d.array(mydata), anc.states) # combine tips and
nodes
pcdata <- prcomp(all.data)$x # PCA
Em
* ML and weighted squared change parsimony are equivalent assuming BM model
of evolution
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Emma Sherratt, PhD.
Postdoctoral Researcher in the Keogh Lab
<http://biology-assets.anu.edu.au/hosted_sites/Scott/>
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Research School of Biology
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On 17 May 2016 at 01:32, filipe oliveira <[email protected]> wrote:
> Hi,
>
> do you know how to save the PC values of the ancestral nodes estimated
> with Square change Parsimony in MorphoJ?
>
> Thank you.
> Best
> Filipe
>
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