Hi Sandra.
This can be done using phytools. Both stochastic character mapping and
marginal ancestral state reconstruction using the re-rooting method can
accept uncertain tip states. (In the case of missing data this would
just be specified as a equal prior probability of being in any of the
sampled states.)
More information can be found on my blog here:
http://blog.phytools.org/2013/03/estimating-ancestral-states-when-tips.html
(for stochastic mapping) or here:
http://blog.phytools.org/2013/04/estimating-ancestral-states-when.html
(for marginal ancestral state reconstruction). Please make sure you have
the latest version of phytools (at least the latest CRAN version, if not
the most recent version here: http://www.phytools.org/nonstatic/) and
let me know if you have any questions.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 6/11/2013 9:58 AM, sandra goutte wrote:
Hello everyone,
I am new to the r-sig-phylo mailing list; I have looked up in the archives,
but i haven't found any answer to my question, so here it is:
I have a tree with 156 tips, and various data sets (morphology, ecology,
behavioral data; continuous and discrete), but i have missing data, that is
tips that don't have associated data. On top of that, i don't have the same
number of species in each data set. So my question is: is there a way to
deal with missing data WITHOUT having to remove the species with missing
data? Ideally i would like to be able to represent ancestral states of all
data types on a single tree.
I have tried ace and gee and both functions fail when tips are attributed
NAs.
Any help would be greatly apreciated!
Cheers,
Sandra.
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