Ecology

Here is one of the talks by Thomas Brouquet, and see the rest here. Thomas Broquet by mez_en_video

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: workflow tool, awesome project by Claudio Silva Commplish: purpose is to use via API’s, not with the web UI Phylopic: a database of life-form silouhettes, including an API for remote access, sweet! Gloome MappingLife: awesome geographic/etc data visualization interace on the web SuiteSMA: visualizating multiple alignments treeBASE: R interface to treebase, by Carl Boettiger VertNet: database for vertebrate natural history collections RevBayes: revamp of MrBayes, with GUI, etc. Phenoscape Knowledge Base Peter Midford lightning talk: talked about matching taxonomic and genetic data BiSciCol: biological science collections tracker Ontogrator TNRS: taxonomic name resolution service Barcode of Life data systems, and remote access Moorea Biocode Project Microbial LTER’s data BirdVis: interactive bird data visualization (Claudio Silva in collaboration with Cornell Lab of Ornithology) Crowdlabs: I think the site is down right now, another project by Claudio Silva Phycas: Bayesian phylogenetics, can you just call this from R? RIP MrBayes!!!! replaced by RevBayes (see 9 above) Slides of presentations will be at Slideshare (not all presentations up yet) A birds of a feather group I was involved in proposed an idea (TOL-o-matic) like Phylomatic, but of broader scope, for easy access and submission of trees, and perhaps even social (think just pushing a ‘SHARE’ button within PAUP, RevBayes, or other phylogenetics software)! Synopses of Birds of a Feather discussion groups: http://piratepad.net/iEvoBio11-BoF-reportouts

A post over at the Phased blog (http://www.nasw.org/users/mslong/) highlights a recent paper in PLoS One by Robert Warren et al. Similar results were obtained in a 2007 Ecology Letters paper by Nekola and Brown, who showed that abundance distributions found in ecology are similar to those found for scientific citations, Eastern North American precipitation, among other things. A similar argument was made by Nee et al. in 1991 (in the journal PRSL-B). The author of the blog appears to agree with the outcome of the Warren et al. study. ...

[UPDATE: i remade the maps in green, hope that helps…] A recent survey reported in Science (“Defeating Creationism in the Courtroom, but not in the Classroom”) found that biology teachers in high school do not often accept the basis of their discipline, as do teachers in other disciplines, and thus may not teach evolution appropriately. Read more here: New York Times. I took a little time to play with the data provided online along with the Science article. The data is available on the Science website along with the article, and the dataset I read into R is unchanged from the original. The states abbreviations file is here (as a .xls). Here goes: ...

I recently gathered fish harvest data from the U.S. National Oceanic and Atmospheric Administarion (NOAA), which I downloaded from Infochimps. The data is fish harvest by weight and value, by species for 21 years, from 1985 to 2005. Here is a link to a google document of the data I used below. I had to do some minor pocessing in Excel first; thus the link to this data. https://spreadsheets.google.com/ccc?key=0Aq6aW8n11tS_dFRySXQzYkppLXFaU2F5aC04d19ZS0E&hl=en Get the original data from Infochimps here http://infochimps.com/datasets/domestic-fish-and-shellfish-catch-value-and-price-by-species-198 ...

Another grad student and I tried recently to make a contribution to our understanding of the relationship between ecological network structure (e.g., nestedness) and community structure (e.g., evenness)… …Alas, I had no luck making new insights. However, I am providing the code used for this failed attempt in hopes that someone may find it useful. This is very basic code. It was roughly based off of the paper by Bluthgen et al. 2008 Ecology (here). In my code the number of interactions is set to 600, and there are 30 plant species, and 10 animal species. This assumes they share the same abundance distributions and sigma values. ...

Anthony Ives, of University of Wisconsin-Madison, and Matthew Helmus of the Xishuangbanna Tropical Botanical Garden, present a new statistical method for analyzing phylogenetic community structure in an early view paper in Ecological Monographs. See the abstract here. Up to now, most phylogenetic community structure papers have calculated metrics and used randomization tests to determine if observed metrics are different from random. The approach of Ives and Helmus fits models to observed data, instead of calculating single metrics. ...

Here is some code to run Phylometa from R. Phylometa is a program that conducts phylogenetic meta-analyses. The great advantage of the approach below is that you can easily run Phylometa from R, and manipulate the output from Phylometa in R. Phylometa was created by Marc Lajeunesse at University of South Florida, and is described in his 2009 AmNat paper. Phylometa can be downloaded free here. Save phylometa_fxn.R (get here) to your working directory. Then use the block of code below to call the functions within phylometa_fxn.R. ...

I am starting this blog not because I am a seasoned code writer, but because I am learning how to use R specifically for ecology and evolution, and figured many others might have the same questions I have. If I find cool solutions I will post them here for all to view, criticize, improve, etc.