So perhaps you have all figured this out already, but I was excited to figure out how to finally neatly get all the data frames, lists, vectors, etc. out of a nested list. It is as easy as nesting calls to the apply family of functions, in the case bel...
Here is some code to run Phylip's contrast application from R and get the output within R to easily manipulate yourself. Importantly, the code is written specifically for trait pairs only as the regular expression work in the code specifically grabs da...
I wrote earlier about some code I wrote for running Phylometa (software to do phylogenetic meta-analysis) from R.I have been concerned about what exactly is the right penalty for including phylogeny in a meta-analysis. E.g.: AIC is calculated from Q in...
Here is an approach for comparing two methods of adjusting branch lengths on trees: bladj in the program Phylocom and a fxn written by Gene Hunt at the Smithsonian.Get the code and example files here: http://wp.me/PRT1F-2vGet phylocom here: http:/...
A while back I posted some messy code to run Phylometa from R, especially useful for processing the output data from Phylometa which is not easily done. The code is still quite messy, but it should work now. I have run the code with tens of different d...
I posted last week a simple function to plot networks using ggplot2 package. Here is version 2. I still need to work on figuring out efficient vertex placement.Changes in version 2:-You have one of three options: use an igraph object, a matrix, or a da...
I have been looking around on the web and have not found anything yet related to using ggplot2 for making graphs/networks. I put together a few functions to make very simple graphs. The bipartite function especially is not ideal, as of course we only w...
In data analysis it is often nice to look at all pairwise combinations of continuous variables in scatterplots. Up until recently, I have used the function splom in the package lattice, but ggplot2 has superior aesthetics, I think anyway.Here a fe...
I have up to recently always done my phenotypic selection analyses in SAS. I finally got some code I think works to do everything SAS would do. Feedback much appreciated!########################Selection analyses#############################install.pac...
A recent survey reported in Science ("Defeating Creationism in the Courtroom, but not in the Classroom"), suggests that high school teachers are not teaching evolution to the fullest extent, say, that grammar is being taught in the English c...
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).
