Wednesday, August 31, 2011

rnpn: An R interface for the National Phenology Network

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The team at rOpenSci and I have been working on a wrapper for the USA National Phenology Network API. The following is a demo of some of the current possibilities. We will have more functions down the road. Get the publicly available code, and contribute, at Github here. If you try this out look at the Description file for the required R packages to run rnpn. Let us know at Github (here) or at our website, or in the comments below, or on twitter (@rOpenSci), what use cases you would like to see with the rnpn package.

Method and demo of each:
Get observations for species by day
From the documentation: "This function will return a list of species, containing all the dates which observations were made about the species, and a count of the number of such observations made on that date."

#### Note, the data below is truncated for blogging brevity...
> getobsspbyday(c(1, 2), '2008-01-01', '2011-12-31') # Searched for species 1 and 2 from Jan 1, 2008 to Dec 31, 2011
          date count   species
1   2009-03-08     2 species 1
2   2009-03-15     1 species 1
3   2009-03-22     1 species 1
4   2009-03-24     1 species 1
5   2009-03-26     1 species 1
6   2009-04-17     1 species 1
7   2009-04-24     1 species 1
8   2009-05-12     1 species 1
9   2009-05-20     1 species 1
10  2009-11-24     1 species 1
11  2009-12-07     1 species 1
12  2010-01-18     1 species 1
13  2010-01-23     1 species 1
62  2011-05-29     1 species 1
63  2011-06-27     1 species 1
64  2011-06-30     2 species 1
65  2009-03-17     1 species 2
66  2009-04-03     3 species 2
67  2009-04-05     3 species 2
68  2009-04-10     3 species 2
69  2009-04-17     3 species 2

Get individuals at specific stations
From the documentation: "This function returns all of the individuals at a series of stations."

> getindsatstations(c(507, 523)) # Searched for any individuals at stations 507 and 523
   individual_id individual_name species_id kingdom
1           1200         dogwood         12 Plantae
2           1197    purple lilac         36 Plantae
3           1193         white t         38 Plantae
4           3569     forsythia-1         73 Plantae
5           1206            jack        150 Plantae
6           1199      trout lily        161 Plantae
7           1198           dandy        189 Plantae
8           1192           red t        192 Plantae
9           1710    common lilac         36 Plantae
10          1711  common lilac 2         36 Plantae
11          1712       dandelion        189 Plantae

Get individuals of species at stations
From the documentation: "This function will return a list of all the individuals, which are members of a species, among  any number of stations."

> getindspatstations(35, c(60, 259), 2009)  # Search for individuals of species 35 at stations 60 and 259 in year 2009
  individual_id individual_name number_observations
1          1715            west                   5
2          1716            east                   5

Get observation associated with particular observation
From the documentation: "This function will return the comment associated with a particular observation."

> getobscomm(1938) # The observation for observation number 1938
[1] "some lower branches are bare"

Monday, August 22, 2011

Tenure track position in systematics at the University of Vermont

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There is an awesome position opening up for an assistant professor in systematics at the University of Vermont. Below is the announcement, and see the original post at the Distributed Ecology blog. Why is this related to R? One can do a lot of systematics work in R, including retrieving scientific collections data through an upcoming package handshaking with VertNet (part of the rOpenSci project), managing large data sets, retrieval of GenBank data through the ape package (see fxn read.genbank), phylogenetic reconstruction and analysis, and more. So I am sure a systematist with R ninja skills will surely have a head up on the rest of the field. 

Assistant Professor in Systematics

Department of Biology
University of Vermont
Burlington, Vermont

The Department of Biology of the University of Vermont seeks applications for a tenure- track Assistant Professor position in Systematics and Evolutionary Biology of arthropods, especially insects. The position will be open in the fall of 2012. The successful candidate will have expertise in classical and molecular systematics, including analysis of complex data sets. Candidates pursuing phylogenomics and innovative methods in bioinformatics in combination with taxonomy are especially encouraged to apply. Department information at:

All applicants are expected to: 1) hold a Ph.D. degree in relevant disciplines and have two or more years of postdoctoral experience; 2) develop a competitively funded research program; 3) teach undergraduate courses (chosen from among general biology, evolution, systematic entomology, and others in the candidate's expertise); 4) teach, mentor and advise undergraduate and graduate students; and 5) oversee a natural history collection of historic significance.

Candidates must apply online: On left see "Search Postings" then find "Biology" under "HCM Department" then posting 0040090 (first posting). Sorry, but we cannot supply the direct link because it will time out.

Attach a cover letter with a statement of research focus and teaching interests (one document), a curriculum vitae, representative publications, and the contact information of three references.

Review of applications will begin on September 15, 2011, and will continue until the position is filled. Questions and up to three additional publications may be directed to Dr. Jos. J. Schall:

The University of Vermont recently identified several "Spires of Excellence" in which it will strategically focus institutional investments and growth over the next several years. One spire associated with the position is Complex Systems. Candidates whose research interests align with this spire are especially encouraged to apply
The University seeks faculty who can contribute to the diversity and excellence of the academic community through their research, teaching, and/or service. Applicants are requested to include in their cover letter information about how they will further this goal. The University of Vermont is an Affirmative Action/Equal Opportunity employer. The Department is committed to increasing faculty diversity and welcomes applications from women, underrepresented ethnic, racial and cultural groups, and from people with disabilities.

Friday, August 12, 2011

Thursday at #ESA11

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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:

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.

    Thursday, August 11, 2011

    Wednesday at #ESA11

    Recology has moved, go to

    Interesting talks/posters:

    • Ethan White's poster describing was of course awesome given my interest in getting data into the hands of ecologists over at 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, August 8, 2011

      Monday at #ESA11

      Recology has moved, go to

      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 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.

      • 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. 

      (#ESA11) rOpenSci: a collaborative effort to develop R-based tools for facilitating Open Science

      Recology has moved, go to

      Our development team would like to announce the launch of rOpenSci. As the title states, this project aims to create R packages to make open science more available to researchers.

      What this means is that we seek to connect researchers using R with as much open data as possible, mainly through APIs. There are a number of R packages that already do this (e.g., infochimpstwitteR), but we are making more packages, e.g., for MendeleyPLoS Journals, and taxonomic sources (ITISEOLTNRSPhylomaticUBio).

      Importantly, we are creating a package called rOpenSci, which aims to integrate functions from packages for individual open data sources.

      If you are somewhat interested, follow our progress on our website, on Twitter, or contact us. If you are really^2 interested you could go to Github and contribute. If  you are really^3 interested, join our development team.