Re: [R-sig-phylo] Iterating though multiple FASTA files via rbind.DNAbin

Hi Jarrett, This has been working for me using the package ‘apex': x <- read.multiFASTA(files) # creates a multiDNA object genes <- x@dna[] # creates a list with your loci. I hope this helps. Best Gustavo Em qui., 12 de mar. de 2020 às 11:18, Jarrett Phillips < phillipsjarre...@

[R-sig-phylo] ape matrix manipulation

this outside of R but I am sure should be a better way to do this. Thanks Gustavo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

[R-sig-phylo] Fitzpatrick and Turelli 2006 - phylogenetic signal in range overlap

. Gustavo Bravo LSU Museum of Natural Science ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] Fitzpatrick and Turelli 2006 - phylogenetic signal in range overlap

Rob, Excellent! Thank you so much for the hint. Cheers, Gustavo On 4/7/11 8:15 PM, Rob Lanfear wrote: Hi Gustavo, This is implemented in the package phyloclim, and the function is age.range.correlation(). Here's the description from the help file: This function can be used to test

[R-sig-phylo] Phylogenetic Regression in R (Grafen method)

Hello, I`m analysing data for 300 anuran species. I want to run an ANCOVA using phylogenetic regression method (Grafen, 1989). Does any one know about a function or script to do it? Thanks, Gustavo Paterno ___ R-sig-phylo mailing list - R-sig-phylo@r

Re: [R-sig-phylo] Phylogenetic Regression in R (Grafen method)

I understand, pgls does not give you contrasts, is that right? Thanks again, Gustavo Paterno I`m using Pyron phlogeny, so i dono have any politomy in my data estrutur On Dec 3, 2013, at 1:20 PM, Gustavo Paterno paterno...@gmail.com wrote: Hello, I`m analysing data for 300 anuran species

[R-sig-phylo] Phylogenetic regression available in R (Grafen, 1989)

Hello all, I just got the confirmation that the Grafen method for phylogenetic regression (Grafen, 1989) was implemented in R ! The package “phyreg” has lots of details in help. Best wishes for all. Gustavo Paterno ___ R-sig-phylo mailing list - R-sig

Re: [R-sig-phylo] Phylogenetic regression available in R (Grafen, 1989)

the contrasts have been taken across each higher node, the design matrix for the model has lower rank than it did before, which is called losing a degree of freedom in the numerator (it is transferred to the denominator) Best wishes, Gustavo Paterno On Mar 7, 2014, at 6:06 AM, Emmanuel Paradis

Re: [R-sig-phylo] Installing diversitree on OS X Mavericks, R 3.1.0

installing diversitree on Mavericks. I hope there is a workaround or anything like that. Please let me know if you need any other information. Thank you all very much in advance for any help. Regards, Gustavo Burin Ferreira, Msc. Instituto de Biociências Universidade de São Paulo

Re: [R-sig-phylo] Installing diversitree on OS X Mavericks, R 3.1.0

Dear Jonathan, the last solution worked perfectly! Thank you very very much! Best, *Gustavo Burin Ferreira, **Msc.* Instituto de Biociências Universidade de São Paulo Tel: (11) 98525-8948 On Tue, May 27, 2014 at 6:30 PM, Jonathan Chang jonathan.ch...@ucla.eduwrote: Actually I suppose

[R-sig-phylo] Exponential function on make.bd.t

! Regards, *Gustavo Burin Ferreira, **Msc.* Instituto de Biociências Universidade de São Paulo Tel: (11) 98525-8948 [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r

Re: [R-sig-phylo] Exponential function on make.bd.t

Hi Richard, Thank you very much for the information! I will do my best to do it by myself, and will let you know if it worked or if I will need some more help. Thanks once again for the help! Cheers, On May 30, 2014 5:19 AM, Rich FitzJohn rich.fitzj...@gmail.com wrote: Hi Gustavo, This used

Re: [R-sig-phylo] dist.nodes crashing with big trees

eone can help me with that, I'll appreciate it! Thanks again for the help so far! Best, *Gustavo Burin Ferreira, **Msc.* Instituto de Biociências Universidade de São Paulo Tel: (11) 98525-8948 On Fri, Oct 16, 2015 at 5:06 PM, Nick Matzke <mat...@nimbios.org> wrote: > Hi! I re-did