Have you ever wanted to search and fetch barcode data from Bold Systems?I am developing functions to interface with Bold from R. I just started, but hopefully folks will find it useful.The code is at Github here. The two functions are still very buggy,...
We just wrapped up the 2011 iEvoBio meeting. It was awesome! If you didn't go this year or last year, definitely think about going next year.Here is a list of the cool projects that were discussed at the meeting (apologies if I left some out):Vistrails...
The Public Libraries of Science (PLOS) has an API so that developers can create cool tools to access their data (including full text papers!!).Carl Boettiger at UC Davis and I are working on R functions that use the PLoS API. See our code on Githu...
I am writing some functions to acquire data from the OpenStates project, via their API. They have a great support community at Google Groups as well.On its face this post is not obviously about ecology or evolution, but well, our elected represent...
A new paper out in Ecology by Xiao and colleagues (in press, here) compares the use of log-transformation to non-linear regression for analyzing power-laws.They suggest that the error distribution should determine which method performs better. When you...
I am writing a set of functions to search ITIS for taxonomic information (more databases to come) and functions to fetch plant phylogenetic trees from Phylomatic. Code at github.Also, see the examples in the demos folder on the Github site above.
I wrote a simple function for plotting a phylogeny in ggplot2. However, it only handles a 3 species tree right now, as I haven't figured out how to generalize the approach to N species.Any ideas on how to improve this?
I had seen the function idata.frame in plyr before, but not really tested it. Here are a few comparisons of operations on normal data frames and immutable data frames. Immutable data frames don't work with the doBy package, but do work with aggregate i...
With all the packages (and beta stage groups of functions) for comparative phylogenetics in R (tested here: picante, geiger, ape, motmot, Liam Revell's functions), I was simply interested in which functions to use in cases where multiple functions exis...
Treebase is a great resource for phylogenetic trees, and has a nice interface for searching for certain types of trees. However, if you want to simply download a lot of trees for analyses (like that in Davies et al.), then you want to be able to access...
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).
