[R-sig-phylo] abundance-weighted Faith phylogenetic diversity index

Dear list members, In order to calculate the abundance-weighted Faith phylogenetic diversity index, I ran the function "weighted.faith()" from the lefse package (link below) using a community data matrix and a phylogeny. But I got the following error. I would be appreciated if you could help me

[R-sig-phylo] Phylogenetic D-statistics

Hello everybody, I have calculated phylogenetic D-value for a binary trait (nitrogen-fixation) using a phylogenetic supertree. I have got D-value = 0.127 and the probability resulting from Brownian motion phylogenetic structure is P= 0.30. My question is what does it mean when you receive D-val

Re: [R-sig-phylo] plotting time-calibrated trees

Thnaks Liam. The problem is solved. -Original Message- From: Saleh Rahimlouye Barabi Sent: 30. september 2019. a. 16:32 To: Liam Revell; R-sig-phylo@r-project.org Subject: RE: [R-sig-phylo] plotting time-calibrated trees Dear Liam, Yes, It is the best solution. But I'm getting an

Re: [R-sig-phylo] plotting time-calibrated trees

#x27;by' argument Best Regards, Saleh -Original Message- From: Liam Revell [mailto:liam.rev...@umb.edu] Sent: 30. september 2019. a. 15:03 To: Saleh Rahimlouye Barabi; R-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] plotting time-calibrated trees Dear Saleh. You can do this using

[R-sig-phylo] molecular dating of a phylogenetic tree

Hello, Do you have any suggestion about any function in R for dating a phylogenetic tree based on a single node age (fixed node)? The calculation of the confidence intervals for each node would be beneficial. Best regards, Saleh Rahimlou Ph.D. Candidate Department of Botany and Ecology Universi

[R-sig-phylo] plotting time-calibrated trees

Hello, I have constructed a big time-calibrated tree (683 tip labels) using the ape::chronopl function. What is a good way of visualizing this tree in a circular way with time scale axis? Best, Saleh Rahimlou Ph.D. Candidate Department of Botany and Ecology University of Tartu 14A Ravila, 5041

[R-sig-phylo] cophylo

Hello, I want to plot two phylogenetic trees face-to-face using phytools::cophylo function. I see there is no possibility to connect 2 or 3 same taxa in a tree to one taxon in the other tree (attached). Is there anyway doing this in R? Best Saleh Rahimlou Ph.D. Candidate Department of Botany an

[R-sig-phylo] comparePhylo

Hello, I'm using comparePhylo() function from APE package in R. I want to know is there anyway to change the tip labels size when plotting it? Arguments like 'cex' does not work in this case. Best Saleh Rahimlou Ph.D. Candidate Department of Botany and Ecology University of Tartu 14A Ravila, 50