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Some useful updates to contMap & densityMap
The most common error reported by users of contMap&densityMap is the following:Error in while (x > trans[i]) { : missing value where TRUE/FALSE neededThis is usually (but not always) due to the...
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New version of plotTree.wBars that permits positive & negative phenotypic...
A couple of weeks ago I posted a new function (1, 2) to plot bars at the tips of a circular or square phylogram. One limitation of this function is that because the bars are plotted 'growing' out of...
View Articlephytools blog no longer permits anonymous comments
Basically, the post title says it all. The phytools blog was getting so many spam comments (and more & more of it was getting through the automatic blogger spam filters) that it was starting to...
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New version of fancyTree for type="scattergram"
I just fixed a small bug in fancyTree(...,type="scattergram") that can cause axis labels to suddenly appear inside the multi-panel plot when edited using an external application. Just as a reminder,...
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Locating the phylogenetic postion of the Yeti: Placing cryptic, recently...
I recently returned from teaching in the AnthroTree 2014 Workshop. This is a course organized by Charlie Nunn that is designed to (in brief) introduce anthropologists to basic & advanced methods in...
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Plotting a slanted cladogram using phytools
I inadvertently discovered the algorithm for plotting a right-facing slanted cladogram this evening. Basically, to get the vertical position of each internal node we just assign heights 1 through N to...
View ArticleGeneric rep (replicate) function for objects of class "phylo"&"multiPhylo"
Again, working on something else, I realized that there is no generic rep (replicate elements of vectors or lists) function for objects of class "phylo" or "multiPhylo". These were straightforward to...
View ArticlePerforming stepwise phylogenetic regression in R
A colleague asked the following:"Is there a way to do a multiple stepwise regression on continuous data that incorporates phylogenetic information and selects the best model based on an AICc...
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Coloring edges in phylomorphospace3d
A recent R-sig-phylo query asked the following about phytools function phylomorphospace3d (for projecting a tree into a three-dimensional morphospace):"[Is t]here is a possbility to color some specific...
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Constraining internal node values using make.simmap
A phytools user asked the following question:"I know I can constrain the state of the root node, but is it possible to also constrain the state at specific internal nodes?"This is possible, although it...
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Computing the average trait value for the set of taxa descended from each node
A recent comment asked if there was an easy way to substitute the raw average value of the tips descended from a node for ancestral states obtained via ancestral state reconstruction when using the...
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Alternative node placements in plotted trees using plotTree & plotSimmap
Felsenstein (2004; pp. 574-576) gives four different node placements for square phylograms. The most commonly used node placement what Felsenstein calls intermediate, i.e., the node is placed at the...
View ArticleUpdates to phylomorphospace3d & locate.yeti; new version of phytools
I just posted a new version of phytools. This can be downloaded from the phytools page & installed from source; however I have also submitted this version (phytools 0.4-20) to CRAN, so hopefully it...
View ArticleBug fix in make.simmap for multi-state data and non-reversible model of...
In response to an R-sig-phylo query about stochastic mapping in phytools I wrote:I can answer the three questions that pertain to phytools:(1) The function make.simmap has a bug for non-reversible...
View ArticleNew version of read.newick that can read root node labels
The phytools function read.newick is a slower, but slightly more robust Newick tree reader than read.tree in the ape package - specifically in that it permits certain types of 'badly conformed' Newick...
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Principal components rotation of ancestral states; or ancestral state...
I recently fielded the following query:From what I understand, the phylomorphospace function allows the mapping of the phylogeny on a morphospace defined by 2 characters/traits. However, I'm using...
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New user controls in phylo.to.map
I just posted a version of the phytools function phylo.to.map, which can be used to project a tree onto a geographic map. Based on some user feedback, including at the Latin American Macroevolutionary...
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Update to locate.yeti permitting the missing tip to attach below the root node
I just updated the phytools function locate.yeti (a method to attach a missing tip to an ultrametric base tree using continuous character data) so that the missing leaf is now permitted to attach below...
View ArticleBug fix for S3 plotting method for objects of class "describe.simmap"
In recent phytools versions the phytools function describe.simmap returns an object of class "describe.simmap" which, if plotted, shows a phylogeny with posterior probabilities from stochastic mapping...
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Improvements/bug-fixes in plotBranchbyTrait
Unlike most of the phylogeny plotting functions of phytools which use the multifunctional plotting function plotSimmap internally, the phytools function plotBranchbyTrait is nothing more than a fancy...
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