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New function cladelabels
I just added a new function cladelabels to the phytools package. This function is in some ways analogous to nodelabels, tiplabels, etc. in ape. It basically implements the method I gave here, while...
View ArticleFunction to quickly compute the height above the root of a pair of taxa
Today I received the following phytools user request:I've been using your phytools package (and the findMRCA function with type="height" to find the height of a specific node in a phylogenetic tree....
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Rphylip now on CRAN!
Rphylip, an R interface for J. Felsenstein's PHYLIP phylogeny methods program package, is now on CRAN.Rphylip is a collaborative project with Scott Chamberlain at Simon Fraser University. Although I...
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Plotting a right-facing round phylogram
Don't ask me why I'm working on this. Here's how to do it:roundPhylogram<-function(tree){ n<-length(tree$tip.label) # reorder cladewise to assign tip positions cw<-reorder(tree,"cladewise")...
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roundPhylogram now in phytools
A slightly more fully functional version of roundPhylogram (described on the blog earlier today) is now part of the phytools package. The function source code can be viewed here, and updated phytools...
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Putting a barplot next to a plotted tree
Today a phytools user contacted me about creating a plot that looks like this. Well, I'm not going to try to duplicate this exactly, but here is a quick demo about how to put a bar plot next to a...
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New version of Rphylip with Rseqboot & demo
I just submitted a new version (Rphylip 0.1-23) of the Rphylip package ('an R interface for PHYLIP') to CRAN. This version fixes a couple of bugs in the first CRAN version - including taxon name length...
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New function to paint individual branch or branches of the tree
A few days ago I received the following email:"I have recently come across your excellent paper entitled "On the analysis of evolutionary change along single branches in a phylogeny". In that you...
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New options & methods for ltt95
A couple of days ago I received the following comment about the phytools function ltt95:"I'm using ltt95 function with the times method and log transformed y axis, but I get reversed ages (both in the...
View ArticleComputing the height above the root of a node in the tree
phytools already has a function that computes the height of all the nodes in the tree: nodHeights. If we only want to know the height of one node, then using this function is very inefficient, for...
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New print & plot methods for describe.simmap
I just added new print & plot methods to phytools for the object returned by describe.simmap, a function designed to summarize the results of stochastic mapping conducted with the phytools function...
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New option to offset tip labels in contMap and densityMap
In response to a recent Facebook request I just added the option to offset tip labels in the phytools functions contMap and densityMap. This is simple. Because plot.contMap and plot.densityMap (the...
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New postdoc in phylogeny methods
I am hiring a new postdoc in phylogenetic comparative methods. The job advertisement is below:-----------------------------------Postdoctoral research associate in phylogenetic comparative methodsA...
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Dropping tips while retaining the ancestors of remaining extant tips as...
Luke Mahler asked the following:"Do you know of a way to drop a terminal branch from a phylogeny, yet preserve the node it came from as a singleton node? I initially thought drop.tip(trim.internal=F)...
View ArticleFixed drop.tip.singleton
Here is a fixed version of the function I just posted to drop leaves while retaining all ancestral nodes of remaining extant taxa as singletons:drop.tip.singleton<-function(tree,tip){...
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New version of phytools submitted to CRAN
I just submitted a new version of phytools (phytools 0.4-05) to CRAN. Some updates in the current version relative to the previous CRAN version include the following:1. A new function, cladelabels, to...
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contMap with missing data
Today a phytools user emailed with the following question:"I am still having difficulty running an analysis on the evolution of a continuous character with a partial data set (I have character states...
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Plotting bars at the tips of a circular tree
Today Matt Helmus posted the following request to the R-sig-phylo mailing list:"Does anyone know of R code (or perhaps another program) to plot bars across the tips of a radial/fan phylogeny?...
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Plotting bars at the tips of a tree, part II
Earlier today, I responded to an R-sig-phylo request to be able to plot bars showing phenotypic trait values for species at the times of a circular or 'fan' tree. I have now added this function...
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Changing the color ramp in contMap or densityMap
I recently received the following question:"Would it be possible in contMap to specify our own color ramp instead of stuck with the default red-to-blue?"This cannot yet be done automatically, but it is...
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