Hi Liam, Thank you very much! But this would work only with categorical data, wouldn't it? Most of my data is continuous though....
Best, Sandra. 2013/6/11 Liam J. Revell <liam.rev...@umb.edu> > 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<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<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/<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/<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. >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> R-sig-phylo mailing list - R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/r-sig-phylo<https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> >> Searchable archive at http://www.mail-archive.com/r-** >> sig-ph...@r-project.org/<http://www.mail-archive.com/r-sig-phylo@r-project.org/> >> >> > -- PhD Student Muséum National d'Histoire Naturelle Département Systématique et Évolution USM 601 / UMR 7205 Origine, Structure et Évolution de la Biodiversité Reptiles & Amphibiens - Case Postale 30 25 rue Cuvier F-75005 Paris Tel : +33 (0) 1 40 79 34 90 Mobile: +33 (0) 6 79 20 29 99 [[alternative HTML version deleted]]
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