Aloha all, Well if all youʻre doing is plotting data, then sure, you can have a change of axes and something in g will still be in g with log-transformed axes.
But does this apply to fitting models of BM or OU? The model is assuming that the "errors" or the small jumps in phenotype comes from a normal distribution. So by fitting a model on log-transformed data will assume that those changes come from a different distribution, on log(g). This has potentially deep implications, suggesting that the magnitude of the changes in the original scale would be larger for large values of g that for small values of g when on a log-scale. That would imply basically that itʻs easier to get a lot larger or a lot smaller in a single step if youʻre already big. This might make sense especially for genome size evolution, for example, where big changes in size arise by chromosomal duplication or transposable element activity, etc. Anyway, log-transformation is commonly applied to biological data. As for the units of time, yes I agree with Joe - it is the units that the depth of the tree is in. If it is time calibrated, then it is time. Otherwise it is generally mutations per branch length. Marguerite On Fri, Mar 19, 2021 at 2:20 PM Joe Felsenstein <j...@gs.washington.edu> wrote: > Marguerite asked: > > > First - Joe - what do you mean by log(grams) has no units? The units of > grams is a unit, so log(mass) will have units of log-gm. As log is not the > same as 1/gm, log(gm) cannot be unit-free. > > I looked it up on Wikipedia, and was assured by it that Marguerite is > right, log(weight) has the same units as weight, except you're > supposed to call them log-gm. > > > I do think that unless there is a calibration with time, the tree > branch lengths are not in units of time but in units of base > substitutions per site. > > And I remain confused on what the units are, if you compute a linear > combination such as 2 log(wt) - 3 log(height). Which princip[al, le] > components machinery does. > > Joe > ------ > Joe Felsenstein felse...@gmail.com, j...@gs.washington.edu > Department of Genome Sciences and Department of Biology, > University of Washington, Box 355065, Seattle, WA 98195-5065 USA > -- ____________________________________________ Marguerite A. Butler Professor Department of Biology 2538 McCarthy Mall, Edmondson Hall 216 Honolulu, HI 96822 Office: 808-956-4713 Dept: 808-956-8617 Lab: 808-956-5867 FAX: 808-956-4745 http://butlerlab.org http://manoa.hawaii.edu/biology/people/marguerite-butler http://www2.hawaii.edu/~mbutler [[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/
