Hi Nathan, Although it is still possible to impute the missing data prior to the analysis, you can fit multivariate models with missing cases (NA values), using the mvMORPH (development version) from my gitHubhttps://github.com/JClavel/mvMORPH/ Non-ultrametric trees (trees with fossil species) are also allowed and you can compute the root state using the "param" list. HTH, Julien
Short example derived after the code of the help page of mvOU:data2<-data# put some missing casesdata2[8,2]<-NAdata2[25,1]<-NA #then you can fit both data2 or data mvOU(tree, data2) > From: [email protected] > To: [email protected] > Date: Thu, 4 Jun 2015 21:22:46 +0000 > CC: [email protected] > Subject: Re: [R-sig-phylo] Constraining node values in an OUCH analysis > > Hi Daniel, > > There�s a difference between a method being able to handle fossil data, that > is a dataset consisting of a non-ultrametric tree an data for all tips > including non contemporaneous ones, and a method allowing you to directly > specify trait values at nodes. Most trait evolution methods allow you to do > the former (I don�t know for sure but I expect OUCH does). For the latter, > which you want to do, there is a function in geiger (described in Slater, > Harmon, and Alfaro 2012 Evolution), that allows you to place informative > prior probability distributions on node trait values based on the fossil > record. But this only allows for fitting simple models and not complex OU > scenarios you might want to test. As a hack, I�d suggest adding zero length > branches to all nodes in your tree and assigning your reconstructed node > values to these. This will produce identical results to specifying node > values directly. Zero length branches can be problematic for matrix > operations required to compute likelihoods in R and so you might need to > explore minimally short branch lengths (10^-5 time units has worked for me in > the past). This all should have the same effect as specifying node values, > but Aaron will need to confirm that it would work in OUCH. > > I would question though whether this is a good strategy - you�re assuming > your ML estimates of node states , presumably inferred under BM, are robust > enough to be fixed for subsequent macroevolutionary analyses. Given how dicey > ASRs are, even when you include fossil data, this seems a big stretch. If > this is a route you really want to go, perhaps explore using a restricted set > of inferred node states - for example only those nodes in the extant taxon > tree that are directly ancestral to a fossil taxon, to explore how much this > approach influences your results. > > g > ------------------------------------------------------------ > Graham Slater > Peter Buck Post-Doctoral Fellow > Department of Paleobiology > National Museum of Natural History > The Smithsonian Institution [NHB, MRC 121] > P.O. Box 37012 > > > (202) 633-1316 > [email protected]<mailto:[email protected]> > www.fourdimensionalbiology.com<http://www.fourdimensionalbiology.com> > > > > > > On Jun 4, 2015, at 2:50 PM, Daniel Fulop > <[email protected]<mailto:[email protected]>> wrote: > > Isn't at least some of this functionality in mvSLOUCH and/or geiger? > ...it's definitely the case that mvSLOUCH can handle missing data at the > tips, and I think fossil data can be incorporated in it and geiger as > well. At least Slater 2013 has code for incorporating fossils in geiger > or modified geiger functions. > > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - > [email protected]<mailto:[email protected]> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/[email protected]/ > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/[email protected]/ [[alternative HTML version deleted]]
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