Hi Ted, The R library brms had many distributional families including a log-normal hurdle distribution. I think this is the one you want as it sounds like you have a continuous, positive horn length measurement along with your animals that lack horns. It looks like this family has an extra “hu” parameter to model the hurdle process. If your measurements are not continuous but are instead counts or bounded by 0&1, you could look into some of the zero-inflated models like zi-poisson or zi-beta respectively. There’s also a zi-gamma distribution family option which could work for you. There is lots of talk out there on when to use hurdle vs zero-inflated families. Importantly, you can set up a phylogenetic regression using any of these families. Just search “brms phylogenetic” for the excellent vignette. This method will require going Bayesian, but this is probably a good idea regardless given your small sample size and relatively complex model as you can use regularizing priors to avoid overfitting.
(Just FYI priors may require a bit of extra thought and care in log-normal distribution families and the outputs may need to be transformed via exp(beta). But I’ve never used this family so I’m not totally sure). Jon On Tue, Aug 24, 2021 at 5:01 AM <r-sig-phylo-requ...@r-project.org> wrote: > Send R-sig-phylo mailing list submissions to > r-sig-phylo@r-project.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > or, via email, send a message with subject or body 'help' to > r-sig-phylo-requ...@r-project.org > > You can reach the person managing the list at > r-sig-phylo-ow...@r-project.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of R-sig-phylo digest..." > > > Today's Topics: > > 1. hurdle models (Ted Stankowich) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 24 Aug 2021 01:05:33 +0000 > From: Ted Stankowich <theodore.stankow...@csulb.edu> > To: "r-sig-phylo@r-project.org" <r-sig-phylo@r-project.org> > Subject: [R-sig-phylo] hurdle models > Message-ID: > < > by5pr12mb4820249e759c5ecb4466a4c9f6...@by5pr12mb4820.namprd12.prod.outlook.com > > > > Content-Type: text/plain; charset="us-ascii" > > Hi all, > We're doing an analysis of horn evolution in female ungulates where some > taxa (30+ species) lack horns entirely and others have horns of varying > lengths, so it is a mixture of a discrete and continuous variable. > > We want to run a phylogenetic analysis on our dataset, and many have > suggested run a "two part" model or "hurdle" model since we have a zero > inflation within our continuous data. > > We have attempted the "hurdle" function using the "pscl" package, but > consistently receive this error message: > Error in hurdle(log10Hornmm ~ LogSHexp..mm., data = HabPrac) : > invalid dependent variable, non-integer values > > Is it possible to run a phylogenetic analysis using a hurdle model or are > there other recommendations for dedicated phylo models? We have attached a > plot of our data. We don't want to degrade it into a discrete 0/1 trait, as > we already tested it this way in a previous paper. We really would like to > capture the continuous nature of the horn length in those species that have > it, while still accounting for the many species lacking horns distributed > throughout the tree (there are several independent evolutionary origins of > female horns). > > Apologies if we've just missed an obvious phylo model that's commonly used. > > Thanks! > Dr. Ted Stankowich > Associate Professor > Associate Chair > Department of Biological Sciences > California State University Long Beach > www.csulb.edu/mammallab<http://www.csulb.edu/mammallab> > [cid:image001.png@01D79849.898888A0] > > > > Thanks, > Ted Stankowich > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > https://stat.ethz.ch/mailman/private/r-sig-phylo/attachments/20210824/c6cfda71/attachment-0001.html > > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image001.png > Type: image/png > Size: 23778 bytes > Desc: image001.png > URL: < > https://stat.ethz.ch/mailman/private/r-sig-phylo/attachments/20210824/c6cfda71/attachment-0001.png > > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: FemaleBovid Plot 1.pdf > Type: application/pdf > Size: 9400 bytes > Desc: FemaleBovid Plot 1.pdf > URL: < > https://stat.ethz.ch/mailman/private/r-sig-phylo/attachments/20210824/c6cfda71/attachment-0001.pdf > > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > > ------------------------------ > > End of R-sig-phylo Digest, Vol 163, Issue 1 > ******************************************* > -- Jonathan A. Nations NSF Postdoctoral Researcher Slater Lab <https://fourdimensionalbiology.com/>, University of Chicago | Research Associate Field Museum of Natural History <https://www.fieldmuseum.org/science/research> [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
