Hi all, Not exactly phylogenetic, but I've recently uncovered some odd behavior with `pcoa` in `ape` and I was curious if anyone understood what was going on.
Usually, if you don't have negative eigenvalues and aren't using a correction, `pcoa` will return the raw eigenvalues. However, I've found if there are negative eigenvalues and no correction is used, even though no correction is applied, the function will still return some corrected relative eigenvalues, and cumulative corrected eigenvalues. What correction was used in this case is not clear. Here's some output using an example dataset from paleotree to demonstrate the weirdness, both without correction argument specified and with it specified as "none". ``` > library(ape) > library(paleotree) > > data(graptDisparity) > dmat<-graptDistMat > res<-pcoa(dmat) > str(res) List of 5 $ correction: chr [1:2] "none" "1" $ note : chr "No correction was applied to the negative eigenvalues" $ values :'data.frame': 183 obs. of 6 variables: ..$ Eigenvalues : num [1:183] 3.22 2.72 1.9 1.74 1.41 ... ..$ Relative_eig : num [1:183] 0.217 0.183 0.128 0.117 0.095 ... ..$ Rel_corr_eig : num [1:183] 0.0495 0.0424 0.031 0.0287 0.0241 ... ..$ Broken_stick : num [1:183] 0.0319 0.0264 0.0236 0.0218 0.0204 ... ..$ Cum_corr_eig : num [1:183] 0.0495 0.0919 0.1229 0.1517 0.1758 ... ..$ Cumul_br_stick: num [1:183] 0.0319 0.0583 0.082 0.1038 0.1242 ... $ vectors : num [1:183, 1:72] 0.0143 -0.1818 -0.1011 0.104 0.101 ... ..- attr(*, "dimnames")=List of 2 .. ..$ : chr [1:183] "'Bulmanograptus' macilentus" "'Monograptus' arciformis" "'Monograptus' austerus" "'Paramplexograptus' kiliani" ... .. ..$ : chr [1:72] "Axis.1" "Axis.2" "Axis.3" "Axis.4" ... $ trace : num 14.8 - attr(*, "class")= chr "pcoa" > > data(graptDisparity) > dmat<-graptDistMat > res<-pcoa(dmat,correction="none") > str(res) List of 5 $ correction: chr [1:2] "none" "1" $ note : chr "No correction was applied to the negative eigenvalues" $ values :'data.frame': 183 obs. of 6 variables: ..$ Eigenvalues : num [1:183] 3.22 2.72 1.9 1.74 1.41 ... ..$ Relative_eig : num [1:183] 0.217 0.183 0.128 0.117 0.095 ... ..$ Rel_corr_eig : num [1:183] 0.0495 0.0424 0.031 0.0287 0.0241 ... ..$ Broken_stick : num [1:183] 0.0319 0.0264 0.0236 0.0218 0.0204 ... ..$ Cum_corr_eig : num [1:183] 0.0495 0.0919 0.1229 0.1517 0.1758 ... ..$ Cumul_br_stick: num [1:183] 0.0319 0.0583 0.082 0.1038 0.1242 ... $ vectors : num [1:183, 1:72] 0.0143 -0.1818 -0.1011 0.104 0.101 ... ..- attr(*, "dimnames")=List of 2 .. ..$ : chr [1:183] "'Bulmanograptus' macilentus" "'Monograptus' arciformis" "'Monograptus' austerus" "'Paramplexograptus' kiliani" ... .. ..$ : chr [1:72] "Axis.1" "Axis.2" "Axis.3" "Axis.4" ... $ trace : num 14.8 - attr(*, "class")= chr "pcoa" ``` Obviously if there are negative eigenvalues, a correction should probably be applied (although perhaps this is a bit of a philosophical matter), but still its unclear why the corrected eigenvalues are calculated, or how they are calculated. They are clearly different from the uncorrected values. Cheers, -Dave Bapst -- David W. Bapst, PhD Asst Research Professor, Geology & Geophysics, Texas A & M University Postdoc, Ecology & Evolutionary Biology, Univ of Tenn Knoxville https://github.com/dwbapst/paleotree [[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/
