[R-sig-phylo] iterative pruning from alignment and tree

Hi folks, I'm starting to use APE, and am trying to write a script to iteratively prune taxa from an alignment / tree combination and print the reduced datasets to separate files. I was thinking of using some combination of drop.tip + DNAbin, but I am unsure of how to link removing the tip

[R-sig-phylo] outputting values during taxon pruning

Hi, all. I'm working on a script that iteratively removes taxa from an initial total tree and re-searches for optimal (pruned) topologies after outputting a pruned alignment. I'm trying to get a few things to happen: First, the script iteratively checks to make sure that the taxon names match

[R-sig-phylo] phylogenetic tree diameter

Hi all, I'm using the ape package, and was wondering if there was a method in the package or code for calculating the diameter (http://mathworld.wolfram.com/GraphDiameter.html) of phylogenetic tree objects. I had been looking in to exporting trees from ape into a graph theory package (igraph),

[R-sig-phylo] problems with assign(), paste(), and data.frame() for folders containing trees

Hi folks, I am trying to recurse through several numbered subfolders in a directory. Each folder has many trees that I want to display summary values for. I have been expanding data frames using code with the structure name - rbind(name, newvals) to produce a data frame with n rows equal to

[R-sig-phylo] treefinder chronogram problems

Hi folks, I generated a quick chronogram in TreeFinder (attached) for an exploratory analysis in R. The tree appeared fine in the Treefinder plot window, but the branch length notation does not appear to be compatible with R plotting for a chronogram. The basal divergence time is 33.9 MYA

[R-sig-phylo] transform nexus SETS block into treefinder partition

Hi all, PartitionFinder selected a complex partitioning scheme that I would like to put into a TreeFinder analysis. As far as I know, TreeFinder ignores NEXUS SETS blocks, and so I would have to input the partitioning by hand. I do this normally for repetitive partitions, e.g. codon positions,

[R-sig-phylo] collapse descendants of a node to a polytomy

Hi folks, I'd like to collapse the descendants of a node, identified using something like node - mrca(tree)[A, B]. I did not see a function in ape, geiger, phyloch, or picante to do something like collapse.descendants(node). Is there a package with a function like this? Thanks! ~John John

Re: [R-sig-phylo] collapse descendants of a node to a polytomy

of Natural History www.johnssdenton.com From: Liam J. Revell [liam.rev...@umb.edu] Sent: Saturday, June 22, 2013 8:09 AM To: John Denton Cc: David Bapst; r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] collapse descendants of a node to a polytomy Hi John. Here

[R-sig-phylo] FW: tps format problem reading in R

Hi folks, I'm trying to read a tps file in the geomorph v1.1-1 R package using readland.tps(file), but every time I try the above, I get the error Error in dimnames(coords)[[3]] - imageID : 'dimnames' must be a list In addition: Warning message: In readland.tps(Lter_mean.TPS) : NAs introduced

[R-sig-phylo] drop trees from multiphylo list

Hi folks, I have a set of trees with tip states, generated by simulation, in a multiphylo object. I'd like to drop trees from the list based on a criterion (some trees do not exhibit all three tip states). I've tried the following (which is admittedly clumsy; I am not very familiar with

[R-sig-phylo] generate liability/threshold plot from ancThresh

Hi folks, I'm trying to generate the thresholds and liabilities plot, including the posterior support values, from Revell (2014) Evolution 68(3), Figure 6B. Does anybody have a script for this? I see the liabilities output from ancThresh(), but no thresholds. Thanks! ~John John S. S.

[R-sig-phylo] add geoscale to histogram or density plot

Hi all, I'd like to add a geoscale to a histogram/density plot, in a manner similar to axisGeo() or add.geoscale() in phyloch. Is there a function that can do this? Thanks! ~John John S. S. Denton, Ph.D. Department of Vertebrate Paleontology American Museum of Natural History

[R-sig-phylo] mcmcglmm with different classes of predictors

Hi all, I'm trying to analyze a dataset that has left-censored, right-censored, and categorical predictor variables and a univariate response in mcmcglmm. However, I am uncertain of how to specify the appropriate model command and priors. The response (rates) is a net diversification rate

[R-sig-phylo] extracting from mrbayes

Hi folks, I need to do some simulation using the Mkv model, and am wondering if there is a way to extract Mk Q-matrix values from mrbayes. A look at report lists revmat as an output, but I do not see any parameters in the .p files when I finish the run. Thanks, ~John John S. S. Denton,

[R-sig-phylo] evolve discrete characters on non-ultrametric tree?

Hi all, I'm curious to know whether there is a function for evolving discrete character data onto a non-ultrametric tree. I know sim.char() can technically produce output given a non-ultrametric tree, and the documentation does not specify that it is a requirement, but all the example trees I

[R-sig-phylo] maximum agreement subtrees?

Hi all, Is there a function in an existing package for calculating maximum agreement subtrees (MASTs)? Thanks! ~John John S. S. Denton, Ph.D. Department of Vertebrate Paleontology American Museum of Natural History www.johnssdenton.com [[alternative HTML version deleted]]

[R-sig-phylo] correlation of characters from stochastic maps

Hi all, I’m curious to know whether any packages implement character correlations and tests for significance of character correlation using the outputs of stochastic character mapping, such as make.simmap(), allowing for for characters with different numbers of states. I know the package

[R-sig-phylo] correlation of binary and multistate

Hi all, Does anybody know of a package that does character correlations between binary and multistate characters (and even better with the possibility of missing data)? Thanks! ~John ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org