My talk on doing phylogenetics in R

Recology has moved, go to http://recology.info/2011/11/my-talk-on-doing-phylogenetics-in-r

I gave a talk today on doing very basic phylogenetics in R, including getting sequence data, aligning sequence data, plotting trees, doing trait evolution stuff, etc.

Please comment if you have code for doing bayesian phylogenetic inference in R.  I know phyloch has function mrbayes, but can't get it to work...

Phylogenetics in R

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My little presentation on getting web data through R

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With examples from rOpenSci R packages. p.s. I am no expert at this...
Web data from R

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R talk on regular expressions (regex)

Recology has moved, go to http://recology.info/2011/10/r-talk-on-regular-expressions-regex

Regular expressions are a powerful in any language to manipulate, search, etc. data.

For example:

> fruit <- c("apple", "banana", "pear", "pineapple")
> fruit
[1] "apple"     "banana"    "pear"      "pineapple"

> grep("a", fruit) # there is an "a" in each of the words
[1] 1 2 3 4
> 
> strsplit("a string", "s") # strsplit splits the string on the "s"
[[1]]
[1] "a "    "tring"

R base has many functions for regular expressions, see slide 9 of Ed's talk below.  The package stringr, created by Hadley Wickham, is a nice alternative that wraps the base regex functions for easier use. I highly recommend stringr.


Ed Goodwin, the coordinator of the Houston R Users group, gave a presentation to the group last night on regular expressions in R. It was a great talk, and he is allowing me to post his talk here.

Enjoy!  And thanks for sharing Ed!

regex-presentation_ed_goodwin

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R tutorial on visualizations/graphics

Recology has moved, go to http://recology.info/2011/09/r-tutorial-on-visualizationsgraphics

Rolf Lohaus, a Huxley postdoctoral fellow here in the EEB dept at Rice University, gave our R course a talk on basic visualizations in R this morning.

Enjoy!

"Ten Simple Rules for OA Publishers" talk by Philip Bourne

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Ten Simple Rules for Open Access Publishers

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@drewconway interview on @DataNoBorders at the Strata conference

Recology has moved, go to http://recology.info/2011/09/drewconway-interview-on-datanoborders

The O'Reilly Media Strata Summit has many interviews on YouTube (just search YouTube for it)

Drew Conway is the author of a R packages, including infochimps, an R wrapper to the Infochimps API service.

The YouTube video:

Open science talk by Carl Boettiger

Recology has moved, go to http://recology.info/2011/09/open-science-talk-by-carl-boettiger

Carl Boettiger gave a talk on the topic of open science to incoming UC Davis graduate students.

Here is the audio: http://www.archive.org/details/ThingsIWishIKnewThreeYearsAgo-ByTheDavisOpenScienceGroup&reCache=1

Here are the slides: http://hazelnusse.github.com/DOS_WOW2011/#title-slide

My take on an R introduction talk

Recology has moved, go to http://recology.info/2011/09/my-take-on-r-introduction-talk

UPDATE: I put in an R tutorial as a Github gist below.


Here is a short intro R talk I gave today...for what it's worth...

R Introduction

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FigShare Talk

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FigShare - I very much like this idea of a place to put your data online that is NOT published. Dryad is a nice place for datastes linked with published papers, but there isn't really a place for datasets that perhaps did not make the cut for a published paper, and if known to the scientific community, could potentially help resolve the "file-drawer" effect in meta-analyses. (wow, run on sentence)

 
"Figshare - Why don't you publish all your research?" Mark Hahnel Imperial College London from London Biogeeks on Vimeo.

Jonathan Eisen on the Fourth Domain and Open Science

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Stalking the Fourth Domain with Jonathan Eisen, Ph D from mendelspod on Vimeo.

Thursday at #ESA11

Recology has moved, go to http://recology.info/2011/08/thursday-at-esa11

Interesting talks/posters:

Richard Lankau presented research on trade-offs and competitive ability. He suggests that during range expansion selection for increased intraspecific competitive ability in older populations leads to loss of traits for interspecific competitive traits due to trade-offs between these traits.


Ellner emphatically states that rapid evolution DOES matter for ecological responses, and longer-term evolutionary patterns as well. [His paper on the talk he was giving came out prior to his talk, which he pointed out, good form sir]


Lauren Sullivan gave an interesting talk on bottom up and top down effects on plant reproduction in one site of a huge network of sites doing similar nutrient and herbivory manipulations around the globe - NutNet (go here: http://nutnet.science.oregonstate.edu/).


Laura Prugh shows in California that the engineering effects (i.e., the mounds that they make) of giant kangaroo rats are more important for the associated food web than the species interaction effects (the proxy used was just density of rats).


Kristy Deiner suggests that chironomids are more phylogenetic similar in lakes with stocked fish relative to fishless lakes, in high elevation lakes in the Sierra Nevada. She used barcode data to generate her phylogeny of chironomids. If you have barcode data and want to search BOLD Systems site, one option is doing it from R using rbold, a package under development at rOpenSci (code at Github).


Jessica Gurevitch presented a large working group's methods/approach to a set of reviews on invasion biology. We didn't get to see a lot of results from this work, but I personally was glad to see her explaining to a packed room the utility of meta-analysis, and comparing to the medical field in which meta-analysis is sort of the gold standard by which to draw conclusions.


Following Jessica, Jason Fridley told us about the Evolutionary Imbalance Hypothesis (EIH) (see my notes here). He posed the problem of, when two biotas come together, what determines which species are retained in this new community and which species are left out. He listed a litany of traits/responses to measure to get at this problem, but suggested that with a little bit of "desktop ecology", we could simply ask: Is the invasability of X region related to the phylogenetic diversity of that region? In three destination regions (Eastern Deciduous Forests, Mediterranean California, and the Czech Republic) out of four there was a positive relationship between proportion of invasive plant species in a source region and the phylogenetic diversity of the source regions.

Wednesday at #ESA11

Recology has moved, go to http://recology.info/2011/08/wednesday-at-esa11

Interesting talks/posters:

• Ethan White's poster describing EcologicalData.org was of course awesome given my interest in getting data into the hands of ecologists over at rOpenSci.org. Ethan also has software you can download on your machine to get the datasets you want easily - EcoData Retriever. [rOpenSci will try to take advantage of their work and allow you to call the retriever from R]
• Carl Boettiger's talk was awesome. He explained how we need better tools to be able to predict collapses using early warning signals. He developed a way to estimate the statistical distribution of probabilities of system collapse. 
• Jennifer Dunne: Explained how she put together an ancient network from Germany. Bravo. 
• Carlos Melian explained his model of network buildup that starts from individuals, allows speciation, and other evolutionary processes. 
• Rachel Winfree told us that in two sets of mutualistic plant-pollinator networks in New Jersey and California, that the least connected pollinator species were the most likely to be lost from the network with increasing agricultural intensity. 
• Dan Cariveau suggests that pollination crop services can be stabilized even with increasing agriculture intensity if in fact pollinator species respond in different ways. That is, some pollinators may decrease in abundance with increasing ag intensity, while other species may increase - retaining overall pollination services to crops.

Monday at #ESA11

Recology has moved, go to http://recology.info/2011/08/monday-at-esa11

Monday was a good day at ESA in Austin. There were a few topics I promised to report on in my blogging/tweeting.


...focused on open source data. Carly Strasser's presentation on guidelines for data management was awesome (including other talks in the symposium on Creating Effective Data Management Plans for Ecological Research). Although this was a good session, I can't help but wish that they had hammered home the need for open science more. Oh well. Also, they talked a lot about how, and not a lot of why we should properly curate data. Still, a good session. One issue Carly and I talked about was tracking code in versioning systems such as Github. There doesn't seem to be a culture of versioning code for analyses/simulations in ecology. But when we get there...it will be easier to share/track/collaborate on  code.

...used R software. David Jennings talked about a meta-analysis asking if phylogenetic distance influences competition strength in pairwise experiments. David used the metafor package in R to do his meta-analysis. Good form sir.

...did cool science. Matt Helmus presented a great talk on phylogenetic species area curves (likely using R, or Matlab maybe?).


p.s. We launched rOpenSci today.


Oddities:

• The Tilman effect - Tilman's talk was so packed it looked like there was a line waiting to get into a trendy bar. Here's a picture (credit: Jaime Ashander). Bigger room next time anyone? 
• Wiley came out with an open source journal called Ecology and Evolution. This brings them to 3 open source journals (the other two are in other fields). We (rOpenSci) will attempt to hand-shake with these journals. 
• The vegetarian lunch option was surprisingly good. Nice. 

Blogging/tweeting from #ESA11

Recology has moved, go to http://recology.info/2011/07/bloggingtweeting-from-esa11

I will be blogging about the upcoming Ecological Society of America meeting in Austin, TX. I will focus on discussing talks/posters that:

1. Have taken a cool approach to using data, or
2. Have focused on open science/data, or
3. Done something cool with R software, or
4. Are just exciting in general

I will also tweet throughout the meeting from @recology_ (yes the underscore is part of the name, recology was already taken). 

The hashtag for the meeting this year is #ESA11

Models in Evolutionary Ecology seminar, organized by Timothee Poisot

Recology has moved, go to http://recology.info/2011/07/models-in-evolutionary-ecology-seminar

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



Thomas Broquet by mez_en_video