Informatics
I devote part of my research to the development of tools for managing and analyzing biodiversity data. I want to develop database system that link together specimen information, pictures, DNA sequences. I am also interested to develop analytical tools to test hypothesis on trait evolution.
R
I use R for various tasks: renaming photo file name during field trips, organizing sequence data of the lab, performing statistical analysis, and much more. I publish here some of my scripts that could possibly be useful to someone else.
I use R in combination with Emacs and ESS. If you are new to this, I recommend you start with a « ready-to-install » modified version of Emacs that Vincent Goulet provides. I guarantee that learning how to use Emacs is a wise use of your time.
My R-scripts
The scripts posted here are in the public domain (i.e. you can do whatever you want with them). Feel free to contact me if you have any questions about how to use them or if you have suggestions to improve them. There are some more details in the code.
- rename.jpg.nef: I use this script to rename photos I take in the field. Indeed, I assign a prefix for a given trip and a number that reflects the order in which I took the picture. I wrote this script because when I take pictures in JPG and NEF I want both copies of a given photo to have the same file name.
- autoUpdate: I include this function in my Rprofile so once a week, R checks for updates of the packages I use. It implies that your library is in a folder that belongs to the user. I tested it only on my linux machine, it could work on MacOSX but it doesn’t on Windows.
- table2kml: this function takes a tab delimited file of latitude/longitude coordinates and returns a (very basic) KML file that can be opened in Google Earth
- mergeFilesInFolder: this functions allows you to merge files from sub-folders in a single folder.
More to come
phylobase
I have been contributing to the development of the package phylobase. Phylobase aims to provide basic functionalities to handle phylogenetic trees and data associated with them. Developers can then have a common tool-kit to manipulate phylogenetic data in R. They can then focus on the development of new methods rather than re-coding basic functions. End-users can use methods from different packages without having to worry about data compatibility.
You can phylobase from CRAN by typing directly in R:
install.packages("phylobase", repos="http://R-Forge.R-project.org")
Phylobase is still in beta stage which means that there is still room for improvements. Don’t hesitate to send comments or suggestions to the developer mailing list.