New version of fastAnc; new build of phytools
I just posted a new version of the function fastAnc for (relatively) fast ancestral character estimation. The function is previously described here. The main addition to this new version is that now...
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Function to get the sister(s) of a node or tip
I just posted a new utility function, getSisters, that takes as input a tree and a node or tip number or label, and returns the sister node or tip numbers or labels. It has two modes: mode="number",...
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New version of phytools on CRAN (phytools 0.2-20)
A new version of phytools (phytools 0.2-20) is now on CRAN. Presently you can download the source code for this version from the phytools homepage or phytools CRAN page and install from source. Windows...
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Visualizing uncertainty in a 'traitgram'
For a variety of a reasons, I've been thinking about clever ways to try and visualize uncertainty in ancestral state estimates. Here is one attempt using an adaptation of the phytools function...
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Type I error and power of the 'phylogenetic ANOVA'
There are a couple of different statistical methods that are commonly referred to as the phylogenetic ANOVA.The phylogenetic ANOVA is generally meant to refer to the simulation approach of Garland et...
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'Tangled trees' from add.random
Today I received the following bug report about the relatively new phytools function add.random:I had a question about the add.random function you posted on your phytools blog a few weeks ago....
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More on 'untangling' misplotted trees
I just posted a new function, untangle, which attempts to "untangle" branch crossing resulting from bind.tree or other functions.It has two different methods: method="reorder" and method="read.tree"...
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New version of package for numerical analyses in evolutionary biology
I just added a new function to my little R package 'popgen' for numerical analyses and simulation in evolution and population genetics (see my previous post on this here). The function is called...
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On the shape of trees with random taxa addition or subtraction
Since I have a new function for add tips at random to a tree; and it is even easier to write a function to drop tips randomly from the tree - i.e., here it is:drop.random<-function(tree,n=1)...
View ArticleNew function to write trees with ancestral states and CIs
A phytools user today requested the ability to output ancestral state estimates (and confidence intervals) to file within a Newick string. Specifically, he had the following suggestion:It would be...
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New phytools build and rep() function for "phylo" objects
I just posted a new minor version of 'phytools' (phytools 0.2-22). You can download it here, and install from source.Relative to the last minor version, this version has only the new function...
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Function to count transitions from a mapped tree
To address a user request I just posted a simple function, countSimmap (code here), to count the number of transitions (in total and by type) on a discrete character mapped tree such as a...
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Using bind.tip (or bind.tree) on a tree with node labels
Just a quick point of (searchable) clarification for both phytools bind.tip and the ape function bind.tree (bind.tip, after all, uses bind.tree interally; 1, 2). Regardless of whether or not your tree...
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New version of matchNodes; new minor phytools version
I just made a couple of small updates to matchNodes (1, 2). I wrote this function primarily to be called internally by fastAnc, for which it works just fine, but I've since been frustrated when trying...
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New version of phylomorphospace with user control of x & y limits (and other...
A phytools user today requested user control of x and y limits in phylomorphospace. Currently phylomorphospace sets xlim and ylim based on the range of tip and ancestral values for x&y and this...
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New version of plotSimmap (& plotTree) for plotting leftward facing phylogenies
I was working on fixing some bugs in the phytools function phenogram when I suddenly realized how easy it would be to add left-direction plotted trees to the function plotSimmap. We do this with two...
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Significant update to phenogram
The phytools function phenogram does a projection of the phylogeny into a space defined by time since the root (on the x axis) and phenotype (on y). It has some nice features, for instance it can map...
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Neat new function to color branches by trait value
I had a user request yesterday for a function that would plot edge colors by probability - for example, if we have a value on [0, 1] for each edge in the tree - how do we use a built-in color palette...
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Investigating whether the rate of one continuous trait is influenced by the...
Yesterday, the following query was submitted to the R-SIG-phylo email listserve:I have a continuous dependent variable (e.g. range size) and a few "independent" variables (e.g. body mass,...
View ArticleNew phytools version (phytools 0.2-25)
I just posted a new minor phytools release, phytools 0.2-25, that can be downloaded and installed from source.> install.packages("phytools_0.2-25.tar.gz",type="source", repos=NULL)* installing...
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