Re: [R-sig-phylo] Rphylopars changing observed data values
Dear Nick, Although within-species error is not treated in the same way as in Rphylopars you can also impute missing values (and estimate ancestral states) for most multivariate models implemented in mvMORPH using the "estim" function (see ?estim). Best wishes, Julien De : R-sig-phylo de la part de Liam J. Revell Envoyé : lundi 20 juillet 2020 18:47 À : Nick Crouch ; r-sig-phylo@r-project.org Objet : Re: [R-sig-phylo] Rphylopars changing observed data values Dear Nick. I don't know what's going on with Rphylopars, but phytools also has a multivariate phylogenetic imputation function, phylo.impute. It's described here on my blog: http://blog.phytools.org/2019/03/phylogenetic-imputation-with.html (although, of course you should use the phytools version not the posted code). All the best, Liam Liam J. Revell Associate Professor, University of Massachusetts Boston Profesor Asistente, Universidad Católica de la Ssma Concepción web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org Academic Director UMass Boston Chile Abroad: https://www.umb.edu/academics/caps/international/biology_chile On 7/16/2020 10:47 AM, Nick Crouch wrote: > [EXTERNAL SENDER] > > Hi all, > > I'm trying to use Rphylopars to impute some missing data, but am having some > strange results with my empirical data. > > The phylopars should return a `data.frame` of the original data with the > missing (NA) values calculated given the phylogenetic data and evolutionary > model. However, my known values are being changed in the output. For example: > >> head(empirical.data) > species Trait > 1 Species_1 14.0 > 2 Species_2 12.0 > >> head(p_BM$anc_recon) > species Trait > 1 Species_1 12.0 > 2 Species_2 8.9 > > The function works fine when I use different combinations of simulated data: > * simulated traits + simulated phylogeny works fine > * simulated traits + empirical phylogeny works fine > * empirical data + simulated phylogeny works fine > > The phylogeny has no 0 branch lengths, is binary, and ultrametric. I have > tried log-transforming the data. I have also tried sequentially dropping one > tip at a time from the tree and re-running to see if any single tip is > causing the problem. Different models also have the same effect. > > If anyone has any thoughts i'd appreciate it. > > Nick > > -- > > Nick Crouch > https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fnickcrouch.github.io%2Fdata=02%7C01%7Cliam.revell%40umb.edu%7Cfb9cae70c8884b194ba308d82cc914ca%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637308589448752383sdata=hXkX5aboOGy3cJaK6QZBYAnm3kNrs%2Fqj2hAocX9MTKU%3Dreserved=0 > Postdoctoral scholar, Jablonski lab > The University of Chicago > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylodata=02%7C01%7Cliam.revell%40umb.edu%7Cfb9cae70c8884b194ba308d82cc914ca%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637308589448752383sdata=VO6CC1WW3FuZg3geh0vZAL7NADKfHuxXxftuMW%2FTic4%3Dreserved=0 > Searchable archive at > https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2Fdata=02%7C01%7Cliam.revell%40umb.edu%7Cfb9cae70c8884b194ba308d82cc914ca%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637308589448762381sdata=skztD9PMN5AVLUr03a1TXg2iNjWL9Aw5NvA3aYCvoyg%3Dreserved=0 > ___ 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/ ___ 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/
Re: [R-sig-phylo] Rphylopars changing observed data values
Dear Nick. I don't know what's going on with Rphylopars, but phytools also has a multivariate phylogenetic imputation function, phylo.impute. It's described here on my blog: http://blog.phytools.org/2019/03/phylogenetic-imputation-with.html (although, of course you should use the phytools version not the posted code). All the best, Liam Liam J. Revell Associate Professor, University of Massachusetts Boston Profesor Asistente, Universidad Católica de la Ssma Concepción web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org Academic Director UMass Boston Chile Abroad: https://www.umb.edu/academics/caps/international/biology_chile On 7/16/2020 10:47 AM, Nick Crouch wrote: [EXTERNAL SENDER] Hi all, I'm trying to use Rphylopars to impute some missing data, but am having some strange results with my empirical data. The phylopars should return a `data.frame` of the original data with the missing (NA) values calculated given the phylogenetic data and evolutionary model. However, my known values are being changed in the output. For example: head(empirical.data) speciesTrait 1 Species_1 14.0 2 Species_2 12.0 head(p_BM$anc_recon) speciesTrait 1 Species_1 12.0 2 Species_2 8.9 The function works fine when I use different combinations of simulated data: * simulated traits + simulated phylogeny works fine * simulated traits + empirical phylogeny works fine * empirical data + simulated phylogeny works fine The phylogeny has no 0 branch lengths, is binary, and ultrametric. I have tried log-transforming the data. I have also tried sequentially dropping one tip at a time from the tree and re-running to see if any single tip is causing the problem. Different models also have the same effect. If anyone has any thoughts i'd appreciate it. Nick -- Nick Crouch https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fnickcrouch.github.io%2Fdata=02%7C01%7Cliam.revell%40umb.edu%7Cfb9cae70c8884b194ba308d82cc914ca%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637308589448752383sdata=hXkX5aboOGy3cJaK6QZBYAnm3kNrs%2Fqj2hAocX9MTKU%3Dreserved=0 Postdoctoral scholar, Jablonski lab The University of Chicago [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylodata=02%7C01%7Cliam.revell%40umb.edu%7Cfb9cae70c8884b194ba308d82cc914ca%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637308589448752383sdata=VO6CC1WW3FuZg3geh0vZAL7NADKfHuxXxftuMW%2FTic4%3Dreserved=0 Searchable archive at https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2Fdata=02%7C01%7Cliam.revell%40umb.edu%7Cfb9cae70c8884b194ba308d82cc914ca%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637308589448762381sdata=skztD9PMN5AVLUr03a1TXg2iNjWL9Aw5NvA3aYCvoyg%3Dreserved=0 ___ 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/
[R-sig-phylo] Rphylopars changing observed data values
Hi all, I'm trying to use Rphylopars to impute some missing data, but am having some strange results with my empirical data. The phylopars should return a `data.frame` of the original data with the missing (NA) values calculated given the phylogenetic data and evolutionary model. However, my known values are being changed in the output. For example: > head(empirical.data) speciesTrait 1 Species_1 14.0 2 Species_2 12.0 > head(p_BM$anc_recon) speciesTrait 1 Species_1 12.0 2 Species_2 8.9 The function works fine when I use different combinations of simulated data: * simulated traits + simulated phylogeny works fine * simulated traits + empirical phylogeny works fine * empirical data + simulated phylogeny works fine The phylogeny has no 0 branch lengths, is binary, and ultrametric. I have tried log-transforming the data. I have also tried sequentially dropping one tip at a time from the tree and re-running to see if any single tip is causing the problem. Different models also have the same effect. If anyone has any thoughts i'd appreciate it. Nick -- Nick Crouch http://nickcrouch.github.io/ Postdoctoral scholar, Jablonski lab The University of Chicago [[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/
