Re: [R-sig-phylo] weirdness in confidence intervals returned by ace, pic option
On Wed, Mar 23, 2011 at 10:24 PM, Emmanuel Paradis emmanuel.para...@ird.fr wrote: Hi Nick, With method = pic, the CIs are computed using the expected variances under the model, so they depend only on the tree. I've added a paragraph in the man page to explain this. Cheers, Emmanuel Obviously, though, if one set of tip data ranges from 100-1000, and another set of tip data ranges from 0.001-1, and both are mapped on the same tree, the variances confidence intervals will be different at the estimated internal nodes for each trait. But I was getting identical confidence intervals across ~20 traits of widely different magnitudes -- and then when I rescaled the trait data, the problem went away, and each trait had different-sized CIs like you would expect. It was as if there some bizarre bug where there was a memory error or some such and the same CI values were getting copied from one trait to the next in some situations. It's probably pointless to discuss, though, unless someone else can replicate the problem I saw with the code I posted. If the problem disappears on other computers, then it's a local problem. R.app sometimes throws messages about memory errors and the like for no apparent reason (not specifically associated with this, though), so it might not even be an APE issue. Cheers! Nick Nick Matzke wrote on 22/03/2011 12:30: Hi all, This isn't crucial to my work at the moment since I am not using the PIC option of ace to do ancestral character estimation. But while trying it out I noticed a very weird result that I can't explain...basically when I run ace on my raw trait values, I get the same sized confidence interval (97.5% CI minus 2.5% confidence interval) for all of my (drastically different) traits. ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] reading nexus file from treebase?
Hello, I can't get read.nexus (ape) or readNexus (phylobase) to read nexus files downloaded from treebase with URLs parsed from xml files. I can't manually edit each file as I want to read a lot of these files. Is there an easy fix? One of the files is copied below. Thanks! Scott Chamberlain Rice University, EEB Dept. #NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Downloaded on March 24, 2011; 16:32 GMT TreeBASE (cc) 1994-2008 Study reference: Brown R., Yang Z. 2010. Bayesian Dating of Shallow Phylogenies with a Relaxed Clock. Systematic Biology, 59(2): 119-131. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10165] BEGIN TAXA; TITLE M4787; DIMENSIONS NTAX=16; TAXLABELS Chalcides_coeruleopunctatus_E2806.20 Chalcides_coeruleopunctatus_E2806.22 Chalcides_manueli_E2506.1 Chalcides_mionecton_mionecton_E2506.10 Chalcides_mionecton_mionecton_E2506.12 Chalcides_mionecton_trifasciatus_E2506.18 Chalcides_polylepis_E14124.1 Chalcides_polylepis_E14124.2 Chalcides_polylepis_E2506.21 Chalcides_sexlineatus_bistriatus_E2806.6 Chalcides_sexlineatus_sexlineatus_E2806.8 Chalcides_simonyi_E3007.2 Chalcides_sphenopsiformis_E8121.26 Chalcides_sphenopsiformis_E8121.27 Chalcides_viridanus_E2806.10 Chalcides_viridanus_E2806.14 ; END; BEGIN TREES; TITLE Tb10793; LINK TAXA = M4787; TREE Fig._3c = [R] ((Chalcides_sphenopsiformis_E8121.26,Chalcides_sphenopsiformis_E8121.27),(((Chalcides_viridanus_E2806.10,Chalcides_viridanus_E2806.14),((Chalcides_sexlineatus_bistriatus_E2806.6,Chalcides_sexlineatus_sexlineatus_E2806.8),(Chalcides_coeruleopunctatus_E2806.22,Chalcides_coeruleopunctatus_E2806.20))),(Chalcides_simonyi_E3007.2,((Chalcides_mionecton_trifasciatus_E2506.18,(Chalcides_mionecton_mionecton_E2506.12,Chalcides_mionecton_mionecton_E2506.10)),(Chalcides_manueli_E2506.1,(Chalcides_polylepis_E14124.1,(Chalcides_polylepis_E14124.2,Chalcides_polylepis_E2506.21))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr6136] END; [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] reading nexus file from treebase?
Hi Scott, Which version of phylobase are you using and which architecture? I can read the file on my machine. Cheers, -- François On Thu, Mar 24, 2011 at 12:39, Scott Chamberlain myrmecocys...@gmail.comwrote: Hello, I can't get read.nexus (ape) or readNexus (phylobase) to read nexus files downloaded from treebase with URLs parsed from xml files. I can't manually edit each file as I want to read a lot of these files. Is there an easy fix? One of the files is copied below. Thanks! Scott Chamberlain Rice University, EEB Dept. #NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Downloaded on March 24, 2011; 16:32 GMT TreeBASE (cc) 1994-2008 Study reference: Brown R., Yang Z. 2010. Bayesian Dating of Shallow Phylogenies with a Relaxed Clock. Systematic Biology, 59(2): 119-131. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10165] BEGIN TAXA; TITLE M4787; DIMENSIONS NTAX=16; TAXLABELS Chalcides_coeruleopunctatus_E2806.20 Chalcides_coeruleopunctatus_E2806.22 Chalcides_manueli_E2506.1 Chalcides_mionecton_mionecton_E2506.10 Chalcides_mionecton_mionecton_E2506.12 Chalcides_mionecton_trifasciatus_E2506.18 Chalcides_polylepis_E14124.1 Chalcides_polylepis_E14124.2 Chalcides_polylepis_E2506.21 Chalcides_sexlineatus_bistriatus_E2806.6 Chalcides_sexlineatus_sexlineatus_E2806.8 Chalcides_simonyi_E3007.2 Chalcides_sphenopsiformis_E8121.26 Chalcides_sphenopsiformis_E8121.27 Chalcides_viridanus_E2806.10 Chalcides_viridanus_E2806.14 ; END; BEGIN TREES; TITLE Tb10793; LINK TAXA = M4787; TREE Fig._3c = [R] ((Chalcides_sphenopsiformis_E8121.26,Chalcides_sphenopsiformis_E8121.27),(((Chalcides_viridanus_E2806.10,Chalcides_viridanus_E2806.14),((Chalcides_sexlineatus_bistriatus_E2806.6,Chalcides_sexlineatus_sexlineatus_E2806.8),(Chalcides_coeruleopunctatus_E2806.22,Chalcides_coeruleopunctatus_E2806.20))),(Chalcides_simonyi_E3007.2,((Chalcides_mionecton_trifasciatus_E2506.18,(Chalcides_mionecton_mionecton_E2506.12,Chalcides_mionecton_mionecton_E2506.10)),(Chalcides_manueli_E2506.1,(Chalcides_polylepis_E14124.1,(Chalcides_polylepis_E14124.2,Chalcides_polylepis_E2506.21))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr6136] END; [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] weirdness in confidence intervals returned by ace, pic option
Ah -- I get it now. Even my rescaled trait data have the same width 95% CI, e.g. my CI for a particular node could be mean +/- 2.345 whether my input trait data ranges from 0.3-0.5, or 400-800. My fix with scaled data occurred because I was back-transforming, which scaled the size of the 95% CI with the size of the mean. So I guess neither of these options is a real estimate of the CI, unlike when one runs ace, method=ML. I noticed the same behavior using ace, method=gls, so that should be noted as well. I have been using method=ml for ancestral character estimation, the width of its CIs vary as you might expect, so I was just surprised when PIC GLS didn't exhibit the same behavior. Cheers, Nick On 3/24/11 12:21 AM, Nick Matzke wrote: On Wed, Mar 23, 2011 at 10:24 PM, Emmanuel Paradis emmanuel.para...@ird.fr wrote: Hi Nick, With method = pic, the CIs are computed using the expected variances under the model, so they depend only on the tree. I've added a paragraph in the man page to explain this. Cheers, Emmanuel ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] sort trees by constraint?
Dear all, I am wondering if there is some way using R to sort a file of multiple trees (i.e., BEAST output) to either 1) return all trees that match a constraint topology (backbone or full topology) or 2) return all trees that have a monophyletic clade of a list of taxa. Any help much appreciated! Just joined the list... looking forward to it! -Brad PhD Student Harvard Herbaria ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] reading nexus file from treebase?
Scott, readNexus (phylobase) can read your tree but not read.nexus (ape). The problem is the two lines inserted within the TREES block: BEGIN TREES; TITLE Tb10793; LINK TAXA = M4787; TREE Fig._3c = [R] If you delete them, it's OK. FigTree also cannot read this file. Cheers, Emmanuel François Michonneau wrote on 25/03/2011 00:35: Hi Scott, Which version of phylobase are you using and which architecture? I can read the file on my machine. Cheers, -- François On Thu, Mar 24, 2011 at 12:39, Scott Chamberlain myrmecocys...@gmail.comwrote: Hello, I can't get read.nexus (ape) or readNexus (phylobase) to read nexus files downloaded from treebase with URLs parsed from xml files. I can't manually edit each file as I want to read a lot of these files. Is there an easy fix? One of the files is copied below. Thanks! Scott Chamberlain Rice University, EEB Dept. #NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Downloaded on March 24, 2011; 16:32 GMT TreeBASE (cc) 1994-2008 Study reference: Brown R., Yang Z. 2010. Bayesian Dating of Shallow Phylogenies with a Relaxed Clock. Systematic Biology, 59(2): 119-131. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10165] BEGIN TAXA; TITLE M4787; DIMENSIONS NTAX=16; TAXLABELS Chalcides_coeruleopunctatus_E2806.20 Chalcides_coeruleopunctatus_E2806.22 Chalcides_manueli_E2506.1 Chalcides_mionecton_mionecton_E2506.10 Chalcides_mionecton_mionecton_E2506.12 Chalcides_mionecton_trifasciatus_E2506.18 Chalcides_polylepis_E14124.1 Chalcides_polylepis_E14124.2 Chalcides_polylepis_E2506.21 Chalcides_sexlineatus_bistriatus_E2806.6 Chalcides_sexlineatus_sexlineatus_E2806.8 Chalcides_simonyi_E3007.2 Chalcides_sphenopsiformis_E8121.26 Chalcides_sphenopsiformis_E8121.27 Chalcides_viridanus_E2806.10 Chalcides_viridanus_E2806.14 ; END; BEGIN TREES; TITLE Tb10793; LINK TAXA = M4787; TREE Fig._3c = [R] ((Chalcides_sphenopsiformis_E8121.26,Chalcides_sphenopsiformis_E8121.27),(((Chalcides_viridanus_E2806.10,Chalcides_viridanus_E2806.14),((Chalcides_sexlineatus_bistriatus_E2806.6,Chalcides_sexlineatus_sexlineatus_E2806.8),(Chalcides_coeruleopunctatus_E2806.22,Chalcides_coeruleopunctatus_E2806.20))),(Chalcides_simonyi_E3007.2,((Chalcides_mionecton_trifasciatus_E2506.18,(Chalcides_mionecton_mionecton_E2506.12,Chalcides_mionecton_mionecton_E2506.10)),(Chalcides_manueli_E2506.1,(Chalcides_polylepis_E14124.1,(Chalcides_polylepis_E14124.2,Chalcides_polylepis_E2506.21))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr6136] END; [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
