[R-sig-phylo] TreeTools limit on number of tips

Hi Martin and list members, Happy New Year. I'm trying to explore the phylogenetic tree space represented by a few thousands trees of ~2500 tips. The packages TreeTools and TreeDist, which hold the most advanced R functionality for such analysis (AFAIK) are limited to dealing with trees smaller

Re: [R-sig-phylo] ancestral state reconstruction with a complex discrete trait

Hi Chris, I sent this message a few days ago but can't see any sign that it was received so trying again. Apologies if anyone ends up seeing both. To the question- in addition to the other (good) solutions given in this thread, both HiSSE (R package) and BayesTraits (stand alone software) can

Re: [R-sig-phylo] suspected error in hisse:::TransMatMakerMuHiSSE()

. Take care all, Roi On Thu, 13 May 2021 at 20:42, roee maor wrote: > Dear Daniel, > > I understand from Jeremy that this issue has already been addressed in a > more recent version of the package, so I seem to have caused a fuss for no > reason. > Thanks for these

Re: [R-sig-phylo] suspected error in hisse:::TransMatMakerMuHiSSE()

org > > You can reach the person managing the list at > r-sig-phylo-ow...@r-project.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of R-sig-phylo digest..." > > > Today's Topics: > >

[R-sig-phylo] suspected error in hisse:::TransMatMakerMuHiSSE()

Dear Jeremy and list, I'm running a bunch of evolutionary models using the package hisse v1.9.13, and noticed some anomalous parameterisation. Specifically, I obtained erroneous model specification when defining a muCID model with 4 hidden states and varying among-state transition rates, i.e.:

Re: [R-sig-phylo] Problem date consensus phylogeny

Hi Alina, I'm not entirely sure I understand the problem, but perhaps phangorn::maxCladeCred() could help? I have used at some point to summarize 100 posterior mammal trees, and got a binary ultrametric tree. Note that my input trees were also fully binary and ultrametric, so if your results may

[R-sig-phylo] plotting geologic time scale on circular tree

Hi Jake, Liam and list, I have used function ring() in APE (see help for ape::phydataplot) to do this. It gives you full control over colours, transparency etc., but you'll have to manually specify the inner and outer radii of each 'donut'. >From my experience, block colours override the tree

[R-sig-phylo] Error in split MuSSE analysis (diversitree::make.musse.split)

Dear list, I'm trying to use MuSSE (package diversitree, FitzJohn 2012) to test for associations between diversification rates and a 3-state (discrete) character. I ran make.musse() for models where same rates affect the whole tree. I used this code from the diversitree tutorial, which worked