Extracting all subtrees of a given size & larger
An R-sig-phylo query asked the following:I'd like to sample independent subclades of greater than N tips from a phylogenetic tree much greater than N, say (number of tips >= 10*N). I can extract all...
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Version of getCladesofSize that also works for multifurcating trees
As promised earlier, I have figured out how to allow the function getCladesofSize (which gets all the subtrees of a phylogeny that cannot be further subdivided into two subtrees of size greater in size...
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extract.clade for tree with a mapped discrete character
A phytools reader recently asked the following via the general comments page:I have used make.simmap to obtain 1000 stochastic maps for a larger clade. It contains two sister-clades. My main interest...
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New version of phytools on CRAN
A new version of phytools (0.2-70) is now available on CRAN. It can be downloaded & installed from source. Package binaries should be built and percolate through the CRAN mirror repositories over...
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Plotting the structure of a circular ("fan") tree
Rafael Maia asks:It would be really cool if simmap and densityMap trees could be plotted as radial (type='fan' in plot.phylo) trees. I find it much easier to visualize the patterns when the tree is...
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Plotting a circular discrete character mapped tree, part II: The colors
Now that we've figured out how to plot the structure of a circular (i.e., "fan") tree, the next step is segmenting our plotted edges by a discrete character & then plotting segment by color. Here's...
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New version of plotSimmap with type="fan"
Today I posted twice (1, 2) in response to Rafael Maia's early morning query about plotting stochastic mapped trees in a circular style. My earlier posts were about plotting the structure of a circular...
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Creating a type="fan" densityMap or contMap plot
I have not yet added the "type" argument to functions densityMap or contMap; however it is already possible to create a circular densityMap or contMap style tree. Here's how:>...
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Raster image files from circular trees in R
There is some noticeablealiasing in circular (type="fan") trees exported directly from R in a raster format such as .png or .jpg. This can be overcome by exporting instead in a lossless vector format...
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Some minor improvements to plotSimmap(...,type="fan") and a few other updates
I just posted a new version of plotSimmap and a new minor phytools version (phytools 0.2-74). The updates mainly do the following: (1) allows user control over close to the full range of plotting...
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Minor fixes to plotSimmap
I just fixed a couple of very minor issues with plotSimmap(...,type="fan"): specifically, lwd was not properly controlling the line width of edges; and ftype="off" (which should turn the labels off)...
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Circular trees in densityMap and contMap
In an earlier post I showed how plotSimmap(...,type="fan") could be used to plot densityMap or contMap style plots using the object of class "densityMap" or "contMap" returned invisibly by each...
View ArticleBug fix in make.simmap(...,Q="mcmc")
I just posted a new version of make.simmap and a new phytools build (phytools 0.2-77). This version fixes a bug affecting make.simmap(...,Q="mcmc"). In this method, the transition matrix Q is sampled...
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New CRAN version of phytools
There is a new version of phytools (phytools 0.2-80) now available on CRAN. It will probably take a few days for the Mac OS & Windows binaries to be compiled and to percolate through the mirror...
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On the annoying task of adding a legend to a plotted stochastic mapping tree
Today (actually yesterday, now) - in part because I've committed to writing this book chapter on plotting comparative data - I undertook the task of figuring out how to add a color legend to a plotted...
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plotSimmap(...,type="phylogram") now compatible with nodelabels() in ape
I have just posted a new version of the phytools function plotSimmap (and a new phytools package version, phytools 0.2-82) that can be compatible with the ape functions nodelabels, edgelabels, and...
View ArticleNew version of findMRCA
I just posted a new version of findMRCA. This function finds the most recent common ancestor (MRCA) for a set of taxa. Now it can instead (optionally) return the height above the root of the MRCA of a...
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Simple tree plotter
As I mentioned in a prior post I am writing a book chapter on visualization for phylogenetic comparative biology. As I component of this, I discuss the basics of plotting a couple of different types of...
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Even simpler phylomorphospace
As I mentioned yesterday, I'm working a book chapter on PCM visualization methods. A very small section of that chapter gives an introduction to programming such methods in R. To that end I described a...
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Overlaying a posterior density map from stochastic mapping on your...
Thinking about phylomorphospaces for the first time in a bit last night, when I realized that we can now use phytools to pretty easily overlay a posterior density map from stochastic mapping (e.g.,...
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