Re: [R-sig-phylo] Possible problem with Scaled likelihoods in ancestral state estimation

urface-of-fitted-m.html>) -- but if you'd like help, please send me your tree & data (or, even better, a saved .RData workspace) and I will take a look at your problem. All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/

Re: [R-sig-phylo] time axis in fan style phylogeny: arcs did not appear in eps file

Dear Felipe. It's possible that .eps doesn't support transparency. Have you tried plotting to a different device, e.g., .pdf or .png? Alternatively, you could undo the transparency by changing /make.transparent("blue",0.1)/ for just /"blue"/. All the best, Liam Liam

Re: [R-sig-phylo] Error in phytools rateshift

optimization iterations using /foreach/. When I get both of these fixes working I'll push the update to the /phytools/ GitHub and you can install the package from there. All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu

Re: [R-sig-phylo] Error in phytools rateshift

ools/ function /likeSurface.rateshift/. See more information here: http://blog.phytools.org/2016/08/function-to-plot-likelihood-surface-for.html. Unfortunately, it is also bound to be pretty slow for larger phylogenetic trees. Let us know if this is of help. Sincerely, Liam Liam J. Revell Professor of Biolo

Re: [R-sig-phylo] Error in phytools rateshift

explained variance in the tip taxa, rather than a genuine temporal rate shift. This could be due, for example, to measurement error / uncertainty in the species means for the trait we're studying. I hope this is helpful. All the best, Liam Liam J. Revell Professor of Biology, University of M

[R-sig-phylo] Evolution 2024 Symposium on Replicability & Reproducibility

h practices on the reliability of findings, & 'meta-science' (the science of science) to help ask if ecology & evolutionary biology are on the cusp of their own replication crisis & what can be done about it. -- Liam J. Revell Professor of Biology, University of Massachusetts Bosto

[R-sig-phylo] Postdoc at OIST

couraged to apply. -- Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/ Book: Phylogenetic Comparative Methods in R <https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r> (/Princeton University Press/, 2022)

Re: [R-sig-phylo] chronos ape substitution rate strict clock

ight. All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/ Book: Phylogenetic Comparative Methods in R <https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r> (/Princeton University Press/, 2022) O

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