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Phylogenetic Tools for Comparative Biology: Comments
http://blog.phytools.org/p/comments.html
Phylogenetic Tools for Comparative Biology. This page is for general comments about the blog. Please feel free to post suggestions, questions, or comments about the blog material, my R functions page, or phylogenetic comparative methods generally. August 24, 2011 at 8:51 AM. October 3, 2011 at 6:23 PM. So far as I can tell, the above comment is spam - but since it is the only one Ive got (as of 10/3/2011) on a whole page dedicated to comments, I have chosen to leave it up. September 28, 2012 at 5:42 PM.
blog.phytools.org
Phylogenetic Tools for Comparative Biology: Small update to control legend text in contMap
http://blog.phytools.org/2015/05/small-update-to-control-legend-text-in.html
Phylogenetic Tools for Comparative Biology. Thursday, May 14, 2015. Small update to control legend text in contMap. I just added a small update to the phytools function. For mapping a continuous characters evolution on the tree. Now the user has control over the legend title. This was possible before (e.g., see Figure 4.4 here. Just trickier and required a separate call to. Code for this update is here. And it will be in future versions of phytools. Heres a quick demo:. Posted by Liam Revell. About how a...
blog.phytools.org
Phylogenetic Tools for Comparative Biology: PGLS with measurement or sampling error in the dependent variable, y
http://blog.phytools.org/2015/05/pgls-with-measurement-or-sampling-error.html
Phylogenetic Tools for Comparative Biology. Friday, May 8, 2015. PGLS with measurement or sampling error in the dependent variable, y. In the following demo I show one way to do phylogenetic generalized least squares (PGLS) assuming a Brownian motion model for the variance-covariance structure of the residual error, for conditions in which there is measurement error in the estimation of y. The dependent variable in our model, but not our x. But not in our factor or factors. Now, next, I start with an ill...
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Phylogenetic Tools for Comparative Biology: March 2015
http://blog.phytools.org/2015_03_01_archive.html
Phylogenetic Tools for Comparative Biology. Tuesday, March 31, 2015. Intensive short course on phylogenetic comparative methods in R. We are pleased to announce a new graduate-level intensive short course on the use of R for phylogenetic comparative analysis. The course will be four days in length and will take place at the Hotel Ilha Flata. In Ilhabela, Sao Paulo State, Brazil, from the 2nd to the 5th of July, 2015. This course is funded by the National Science Foundation. University of California, Los ...
blog.phytools.org
Phylogenetic Tools for Comparative Biology: Robinson-Foulds distance and NNI
http://blog.phytools.org/2013/02/robinson-foulds-distance-and-nni.html
Phylogenetic Tools for Comparative Biology. Wednesday, February 6, 2013. 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 other? And then compute RF distance for each tree (using phangorn: RF.dist. Here is the result:. One random NNI step. 1] 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20. This will eventually even...
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Phylogenetic Tools for Comparative Biology: August 2014
http://blog.phytools.org/2014_08_01_archive.html
Phylogenetic Tools for Comparative Biology. Friday, August 29, 2014. Counting edges from a Newick string. I just posted a new phytools source build ( phytools 0.4-32. Featuring the newly updated. Is a simple tree-reading function - basically redundant with. In the ape package, but slightly more tolerant of "badly conformed" Newick strings. Unfortunately, it is quite slow - although some improvements. To the code have dramatically decreased run-time for the function. As it uses the same basic structure.
blog.phytools.org
Phylogenetic Tools for Comparative Biology: Bug fix for phenogram when ftype="off"
http://blog.phytools.org/2015/05/bug-fix-for-phenogram-when-ftypeoff.html
Phylogenetic Tools for Comparative Biology. Tuesday, May 19, 2015. Bug fix for phenogram when ftype="off". In developing an exercise recently, I discovered a small bug that was introduced into the function. When I changed (in the latest phytools) version the optional argument. This bug causes the function to crash if labels are turned off using. Under the default conditions. Heres how it manifests using simulated tree and data:. Phenogram(tree,x,ftype=off) # doesnt work. OK, thats it for now. Subscribe t...
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Phylogenetic Tools for Comparative Biology: October 2014
http://blog.phytools.org/2014_10_01_archive.html
Phylogenetic Tools for Comparative Biology. Tuesday, October 28, 2014. Alternative implementations of fitContinuous. A colleague contacted me today about “alternative implementations” of geigers. Function that he could use to check parameter estimation, and maybe to speed calculations as. Can be somewhat slow (although is evidently quite robust now) for some models. Well, I dont know about speeding things up - but it is pretty straightforward to write a wrapper function that combines phytools. BM){ lk -f...
blog.phytools.org
Phylogenetic Tools for Comparative Biology: December 2014
http://blog.phytools.org/2014_12_01_archive.html
Phylogenetic Tools for Comparative Biology. Friday, December 26, 2014. Wrapper function to optimize the λ tree transformation for a discrete trait. To an R-sig-phylo query. By posting some code to optimize Pagels λ tree transformation for a discrete character evolving by a continuous-time Markov chain. I did this by writing a very simple wrapper around apes. Function for ancestral character estimation, which also fits this model:. Note that the same model can also be fit using geigers. This latest versio...
