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Small follow-up to rate-by-state method
This is a follow-up to my earlier post on attempting to measure the influence of the state of one continuous trait on the Brownian rate of a second.First, the posted code had a small bug. Basically...
View ArticleApplying countSimmap to a set of trees
I just received the following email request about the function countSimmap that counts the transitions on a mapped tree that's been created or read into memory:I was wondering if this function...
View ArticleNew version of countSimmap for "multiPhylo" objects
I just posted a new version of countSimmap for an object of class "multiPhylo" that uses the method described in a recent post. Here's a quick demo:>Â require(phytools)>Â source("utilities.R")>...
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Using plotBranchbyTrait to plot different style trees
A recent commenter pointed out something that I hadn't realized about the new phytools function, plotBranchbyTrait - that is, that it can be used to plot different styles of tree and that the branch...
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New, totally rewritten version of make.simmap; new phytools build
I just posted a totally rewritten version of the phytools function make.simmap for stochastic character mapping on trees. Rich Glor reported that there might be a bug in older versions of make.simmap...
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Awesome new version of phenogram (in my opinion)
The phytools function phenogram does a projection of the phylogeny into a space defined by a morphological trait axis (on y) and time since the root (on x). This is a neat visualization, but it's most...
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New option in fancyTree for visualizing the uncertainty of ancestral states
A few weeks ago I posted about visualizing uncertainty in ancestral state reconstructions using phenogram. Well, this seems like a neat thing to be able to do easily, so I have added it as a new method...
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Anolis phenogram of body size using spread.labels
The post title pretty much says it all. I was playing with the new version of the phytools function phenogram and here is the result - a traitgram of (log) body-size in Greater Antillean Anolis in...
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New CRAN version of phytools
I just submitted a new version of phytools (phytools 0.2-30) to CRAN. Hopefully there are no major issues and it is accepted promptly by the CRAN gatekeepers.** If so, then it should percolate through...
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Conditional scaled likelihoods in ace & on not using them for ancestral state...
A not very well appreciated attribute of ace(...,type="discrete") is that the scaled likelihoods returned in the matrix $lik.anc are the scaled conditional likelihoods from the "pruning" algorithm of...
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Coloring all the nodes of a subtree the same color in a phylomorphospace plot
A recent user comment asks:Is there a way to use getDescendents() to color the tips that descend from a certain node (including or excluding the node colors) to use in phylomorphospace()? And if there...
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A little more on ancestral state estimation
What is true of marginal ancestral state estimates is that (for a reversible model of evolution) they are equivalent to the conditional scaled likelihoods at the root node of the tree. This is stated...
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Function to summarize the results of stochastic mapping
To address a user request I just quickly wrote a new utility function, describe.simmap, to summary the results from stochastic maps on one or multiple trees. It computes the total number of transitions...
View ArticleBug fix for describe.simmap
There was a small bug in this new function to summarize the results of stochastic mapping that I posted yesterday, describe.simmap, for describe.simmap(...,plot=TRUE). The fixed version of this, plus...
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New version of describe.simmap with informative message
I just posted a new version of describe.simmap that prints an informative message and returns the results invisibly (if message is set to TRUE). This can be used on a single tree simulated with...
View ArticleMarginal ancestral state reconstruction using multiple methods
Rob Lanfear asks:"A quick question to follow up on your two posts, and some recent discussion on the R list: do you have a good feeling for the quickest implementation to do this on large trees? (Happy...
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Estimating ancestral states when tips are uncertain
I recently received an email with the following content (among other things):"Have you ever considered developing algorithms for inferring character states for taxa that are missing data? I looked at...
View ArticleRandom trees for a set of taxa
A phytools user recently asked:"Is there any function in your package that can randomize the shape of a phylogeny? e.g. randomize the topology of a phylogenetic tree?I'm going to liberally interpret...
View ArticleSmall update to phylosig
The following query was recently posted to the bioinformatics question & answer site, BioStar:"I use phytools to analyse phylogenetic signal in different tree topologies. In likelihood ratio test...
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phytools expands into industrial networking solutions....
OK, the post title is an April Fools' Day joke; however imagine my horror at discovering yesterday that phytools is in fact a real, brand new, private commercial company formed in 2013 as a subsidiary...
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