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Hypothesis testing using fitDiversityModel
A user had this question about using the function fitDiversityModel (which implements an ML version of the method in Mahler et al. (2010) to test hypotheses about phenotypic diversification:I have one...
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Faster inversion of square symmetric positive-definite matrices
For square, symmetric, positive-definite matrices (like covariance matrices) there is a method for faster matrix inversion that uses inversion of the Cholesky matrix. This is described here and...
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Function setNames
I can't believe I just discovered the function setNames in the 'stats' package. All it is is a wrapper to combine the two lines of code required to create a vector & assign its names. (It can also...
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New version of threshDIC
I just posted a new version of threshDIC for computing the Deviance Information Criterion from the object returned by ancThresh. The previous version (of threshDIC not ancThresh) just plain doesn't...
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Plotting densityMap to PDF
A phytools user asks:In the densityMap graphic you sent me it seemed like you had spread the branches apart some to make the tree more readable. Is that true? If so, could you tell me how?! I have...
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Specifying pie colors in ancThresh & plotThresh
A phytools user contacted me to express difficulty in controlling pie colors at nodes using the new phytools functions for ancestral character estimation under the threshold model, ancThresh and...
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Two years of blogging
Just as the title of this post would suggest, phytools blog is two years old** today. (**More or less - as I noted last year, I had a few earlier placeholder posts, but my first serious entry was dated...
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Processing .tps morphometric files in R
This has absolutely nothing to do with phylogenetics, but today (New Year's day 2013!) I've been starting the year with some R programming to pull data out of the raw output files from a program...
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Adding new tips at random to a phylogeny
A friend and colleague contacted me recently with the request (somewhat abbreviated), below:What I'm interested in doing is adding a given number of tips at random to a tree. I've done a comparison...
View ArticleNew version of pgls.Ives
I just posted a new version of the phytools function pgls.Ives, which is a function to fit the regression model of Ives et al. (2007) incorporating sampling error in the estimation of species means...
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Note on polytomies and internal branches of zero length in ancestral...
Just a quick note on the use of polytomous trees vs. arbitrarily fully-resolved trees with branches of zero length in phytools functions for ancestral character estimation such as anc.Bayes, anc.ML,...
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A comment on the distribution of residuals (and data) for phylogenetic ANOVA
I get inquiries (with some regularity) about "testing for normality in phylogenetic (i.e., species) data" before phylogenetic regression or ANOVA; or about "satisfying the assumptions of parametric...
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Robinson-Foulds distance and NNI
A colleague just asked me:Do you know of a way in R to calculate the topological difference between 2 trees as the (ed. minimum) number of nearest-neighbor interchanges required to go from one to the...
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Reordering the columns of $mapped.edge for a set of stochastically mapped trees
I recently got the following comment to a recent post on the blog:I am trying to play with your make.simmap function, but I found that in all the simulations, colnames(tree$mapped.edge) show a...
View ArticleAddendum to the relationship between NNIs and Robinson-Foulds distance
In a previous post I commented that, for a broad range of trees and simulated NNIs, the minimum number of NNIs to get between two topologies seemed to be equal to (one half) the Robinson-Foulds...
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New version of phytools (0.2-16)
I just posted a new, non-CRAN phytools version (0.2-16). There are not a huge number of updates in this version from the last non-CRAN phytools version (0.2-15), but the updates since the last CRAN...
View ArticleNew version of function for MRP supertree estimation
I just posted a new version of the phytools function mrp.supertree for supertree estimation via Matrix Representation Parsimony (MRP). The main update for the user is that now control of optimization,...
View ArticleMore on MRP supertree estimation in phytools
In a post from earlier today, I described some of the updates in a new version of the phytools function mrp.supertree. The two main changes are as follows: (1) now the user can decide which parsimony...
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Updated phylANOVA
A user phytools user recently contacted me with the bug report that for a tree with multifurcations they received the following error from the function phylANOVA:Error in pic(y, tree) : 'phy' is not...
View ArticleFix to fastAnc
A colleague recently reported bad behavior in the fast ancestral character estimation function fastAnc that he hypothesized was due to the fact that I extracted the total number of tips in the tree...
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