[ECOLOG-L] MSc/PhD Position
MSc or PhD position: The ecology and evolution of non-transitive competition and its effect on biodiversity An NSERC-funded graduate student position (MSc or PhD) is available in the Department of Biological Sciences at the University of Lethbridge (Alberta, Canada). The student will be co-supervised by Rob Laird of the University of Lethbridge and Brandon Schamp of Algoma University (Sault Ste Marie, Ontario, Canada). The focus of the project is non-transitive competition (as in the game Rock-Paper-Scissors) and its potential to promote the maintenance of biodiversity via indirect facilitation. The project will include some combination of lab work, field work, and mathematical/computer modeling -- ideally all three! Our previous empirical work has examined coexistence in plant and invertebrate communities, but we welcome applicants interested in working on other systems as well. Interested candidates should visit our web pages for details and previous publications (http://people.uleth.ca/~robert.laird/http://people.uleth.ca/%7Erobert.laird/, http://people.auc.ca/schamp/) and send us an email including your CV and a brief statement of your research experience and interests. Dr. Brandon Schamp (brandon.sch...@algomau.camailto:brandon.sch...@algomau.ca) Dr. Robert Laird (robert.la...@uleth.camailto:robert.la...@uleth.ca)
Re: [ECOLOG-L] Making Species Co-Occurrence Matrix
Andy, Jane,
If speed is an issue or you are working with larger problems than the
example Andy used, then we can exploit other tools in R to get the same
answer as Andy's spp.cooc() function, but much more efficiently, using a
matrix multiplication:
Here's Andy's example and my version with some timings:
## Set a random seed
set.seed(123)
## dummy data
sppXsite - matrix(rpois(15,0.5),nrow=3)
colnames(sppXsite) - paste(spp,1:5,sep=)
rownames(sppXsite) - paste(site,1:3,sep=)
sppXsite# here's what it looks like
# now make a function to compute the co-occurrence matrix
spp.cooc - function(matrx) {
# first we make a list of all the sites where each spp is found
site.list - apply(matrx,2,function(x) which(x 0))
# then we see which spp are found at the same sites
sapply(site.list,function(x1)
{
sapply(site.list,function(x2) 1*any(x2 %in% x1))
})
# the result is returned in a symmetrical matrix of dimension
# equal to the number of spp
}
## And my version
spp.cooc2 - function(mat) {
ncol - NCOL(mat)
res - matrix(as.numeric((t(mat) %*% mat) 0), ncol = ncol)
rownames(res) - colnames(res) - colnames(mat)
return(res)
}
all.equal(spp.cooc(sppXsite), spp.cooc2(sppXsite)) ## TRUE!
## Timings
system.time(replicate(1000, spp.cooc(sppXsite)))
system.time(replicate(1000, spp.cooc2(sppXsite)))
system.time(replicate(1000, spp.cooc(sppXsite)))
user system elapsed
0.728 0.004 0.733
system.time(replicate(1000, spp.cooc2(sppXsite)))
user system elapsed
0.067 0.000 0.068
## larger problem
set.seed(123)
sites - 100
species - 50
sppXsite.big - matrix(rpois(sites * species, 0.5), nrow=sites)
colnames(sppXsite.big) - paste(spp, seq_len(species), sep=)
rownames(sppXsite.big) - paste(site, seq_len(sites), sep=)
## Timings
## Note the first line below takes ~40 seconds on my fast PC
system.time(replicate(1000, spp.cooc(sppXsite.big)))
system.time(replicate(1000, spp.cooc2(sppXsite.big)))
## Timings
system.time(replicate(1000, spp.cooc(sppXsite.big)))
user system elapsed
41.049 0.043 41.244
system.time(replicate(1000, spp.cooc2(sppXsite.big)))
user system elapsed
0.423 0.037 0.468
If speed or size of problem is not an issue then either works just well
enough.
I don't think we have anything like this in Vegan, but happy to be
corrected if we do. If we don't, I'll chat with Jari and see about
adding it to the package.
All the best,
G
On Fri, 2010-08-27 at 12:41 -0400, Andy Rominger wrote:
Hi Jane,
I think someone may have asked something similar on the r-sig-eco email list
(which is a good resource in general:
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology)
I think the answer may have been there there's a function in the vegan
package for R (http://cran.r-project.org/web/packages/vegan/index.html).
But it would be pretty simple to write something up in R. Here's one way of
doing it (if I'm correct in my interpretation of a co-occurrence matrix!).
The actual function (called `spp.cooc') is really only 2 lines long--the
code just looks longer from making up example data and adding in the
comments.
Hope this might do the trick for you! Note that in it's current form you
would have to give the function a matrix or data.frame of ONLY NUMBERS in
which species are columns and sites are rows. This could be changed by
manipulating the MARGIN argument of the apply command below, i.e., site.list
- apply(matrx,1,...)
Hope this helps--
Andy
# make some example data
sppXsite - matrix(rpois(15,0.5),nrow=3)
colnames(sppXsite) - paste(spp,1:5,sep=)
rownames(sppXsite) - paste(site,1:3,sep=)
sppXsite# here's what it looks like
# now make a function to compute the co-occurrence matrix
spp.cooc - function(matrx) {
# first we make a list of all the sites where each spp is found
site.list - apply(matrx,2,function(x) which(x 0))
# then we see which spp are found at the same sites
sapply(site.list,function(x1)
{
sapply(site.list,function(x2) 1*any(x2 %in% x1))
})
# the result is returned in a symmetrical matrix of dimension
# equal to the number of spp
}
# here's how it works
co.matrix - spp.cooc(sppXsite)
co.matrix
On Fri, Aug 27, 2010 at 12:46 AM, Jane Shevtsov jane@gmail.com wrote:
Is there a fast way to make a species co-occurrence matrix given a
site-species matrix or lists of species found at each site? I'm
looking for a spreadsheet or database method (preferably OpenOffice)
or R function.
Thanks,
Jane
--
-
Jane Shevtsov
Ecology Ph.D. candidate, University of Georgia
co-founder, www.worldbeyondborders.org
Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes
The whole person must have both the humility to nurture the
Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream
of Spaceflight
--
[ECOLOG-L] AGU session on earth-system stewardship
Here's a reminder from Rob Jackson that abstracts are due tomorrow! Original Message Subject:AGU session on earth-system stewardship Date: Wed, 01 Sep 2010 07:58:52 -0400 From: Rob Jackson Dear Colleagues, Terry Chapin, Jen Harden, and I have organized a joint ESA/AGU Biogeosciences session on Scientific Foundations for Earth-System stewardship for the fall AGU meeting in San Francisco (see below). Confirmed speakers in the session include Inez Fung, Chris Field, Bill Schlesinger, and Dennis Lettenmaier. Please submit your work to the session and pass along this message to others who might be interested. Abstracts are due tomorrow, Thursday September 2nd. Thanks! Rob Jackson 919-660-7408 http://www.biology.duke.edu/jackson Biogeosciences Session, AGU Fall Meeting 2010 /Scientific Foundations for Earth System Stewardship/ Human activities have exceeded or are close to exceeding safe boundaries for many aspects of the environment, including climate, nitrogen inputs to ecosystems, and biodiversity loss. Potential loss of permafrost with global warming and the loss of tropical diversity are just two examples of environmental tipping points that may soon be crossed. This session on global planetaryEarth System stewardship focuses on how sound geophysical biophysical science and knowledge from other disciplines can be combined to provide environmental solutions. In addition to the above examples, potential topics include resilience of the coupled Earth System, geophysical threats to life on Earth, geoengineering and climate management, and socio-ecological feedbacks to the environment. The session is part of a series of joint activities between the American Geophysical Union and the Ecological Society of America. Convener Information: Robert B. Jackson, jack...@duke.edu, 919-660-7408; Department of Biology and Nicholas School of the Environment, Box 90338, Duke University, Durham, NC 27708 Jennifer W. Harden, jhar...@usgs.gov, 650-329-4949; U.S. Geological Survey, 345 Middlefield Rd, ms 962, Menlo Park, CA 94025 F. Stuart Chapin, terry.cha...@alaska.edu, 907.474.7922; Department of Biology and Wildlife Institute of Arctic Biology, University of Alaska, Fairbanks, Alaska, 99775 Index Terms: 0400 Biogeosciences; 1600 Global Change; 4800 Oceanography: Biological And Chemical; 0315 Biosphere/Atmosphere Interactions Original Message Ends
[ECOLOG-L] federal Sage Grouse monitoring protocol
I am looking for federal protocol on lek surveys for Sage Grouse. I am sure the USFWS and BLM must have something, but haven't found any on the internet. If you know a link or have a pdf please send along. Thanks in advance, David Anderson
[ECOLOG-L] SCUBA diving for a good cause
Dear Ecolog community,If you are doing any recreational scuba diving in Florida between now and early October, you have a chance to participate in a research project on the goliath grouper spawning aggregations.Here is how:http://www.teamorca.org/cfiles/goliath.cfmwhile consulting this link, you can also join Team ORCA (email list, facebook) mission to save the oceans, and get special news about marine ecosystems near you, our monthly e-newsletter and more.For an excellent goliath grouper scuba diving article, you can read issue 17 of the Underwater Journal, with great photography from Walt Stearns. It includes diving recommendations to see the spawning aggregations.Download issue 17 herehttp://www.underwaterjournal.com/Thanks for your help[apologies for cross-postings] Sarah Frias-Torres, Ph.D. Postdoctoral Scholar Schmidt Research Vessel Institute Postdoctoral Fellowhttp://independent.academia.edu/SarahFriasTorresOcean Research Conservation Association 1420 Seaway Drive, 2nd Floor Fort Pierce, Florida 34949 USA http://www.teamorca.org
Re: [ECOLOG-L] Making Species Co-Occurrence Matrix
Hi Gavin,
Thanks! For just getting the data into R, speed isn't an issue, but it
could be important for null model analysis. But is it possible to make
this function correspond to my version that changed any() to sum() in
order to make the co-occurrence matrix say how many times the species
co-occurred?
Thanks,
Jane
On Wed, Sep 1, 2010 at 4:49 AM, Gavin Simpson gavin.simp...@ucl.ac.uk wrote:
Andy, Jane,
If speed is an issue or you are working with larger problems than the
example Andy used, then we can exploit other tools in R to get the same
answer as Andy's spp.cooc() function, but much more efficiently, using a
matrix multiplication:
Here's Andy's example and my version with some timings:
## Set a random seed
set.seed(123)
## dummy data
sppXsite - matrix(rpois(15,0.5),nrow=3)
colnames(sppXsite) - paste(spp,1:5,sep=)
rownames(sppXsite) - paste(site,1:3,sep=)
sppXsite # here's what it looks like
# now make a function to compute the co-occurrence matrix
spp.cooc - function(matrx) {
# first we make a list of all the sites where each spp is found
site.list - apply(matrx,2,function(x) which(x 0))
# then we see which spp are found at the same sites
sapply(site.list,function(x1)
{
sapply(site.list,function(x2) 1*any(x2 %in% x1))
})
# the result is returned in a symmetrical matrix of dimension
# equal to the number of spp
}
## And my version
spp.cooc2 - function(mat) {
ncol - NCOL(mat)
res - matrix(as.numeric((t(mat) %*% mat) 0), ncol = ncol)
rownames(res) - colnames(res) - colnames(mat)
return(res)
}
all.equal(spp.cooc(sppXsite), spp.cooc2(sppXsite)) ## TRUE!
## Timings
system.time(replicate(1000, spp.cooc(sppXsite)))
system.time(replicate(1000, spp.cooc2(sppXsite)))
system.time(replicate(1000, spp.cooc(sppXsite)))
user system elapsed
0.728 0.004 0.733
system.time(replicate(1000, spp.cooc2(sppXsite)))
user system elapsed
0.067 0.000 0.068
## larger problem
set.seed(123)
sites - 100
species - 50
sppXsite.big - matrix(rpois(sites * species, 0.5), nrow=sites)
colnames(sppXsite.big) - paste(spp, seq_len(species), sep=)
rownames(sppXsite.big) - paste(site, seq_len(sites), sep=)
## Timings
## Note the first line below takes ~40 seconds on my fast PC
system.time(replicate(1000, spp.cooc(sppXsite.big)))
system.time(replicate(1000, spp.cooc2(sppXsite.big)))
## Timings
system.time(replicate(1000, spp.cooc(sppXsite.big)))
user system elapsed
41.049 0.043 41.244
system.time(replicate(1000, spp.cooc2(sppXsite.big)))
user system elapsed
0.423 0.037 0.468
If speed or size of problem is not an issue then either works just well
enough.
I don't think we have anything like this in Vegan, but happy to be
corrected if we do. If we don't, I'll chat with Jari and see about
adding it to the package.
All the best,
G
On Fri, 2010-08-27 at 12:41 -0400, Andy Rominger wrote:
Hi Jane,
I think someone may have asked something similar on the r-sig-eco email list
(which is a good resource in general:
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology)
I think the answer may have been there there's a function in the vegan
package for R (http://cran.r-project.org/web/packages/vegan/index.html).
But it would be pretty simple to write something up in R. Here's one way of
doing it (if I'm correct in my interpretation of a co-occurrence matrix!).
The actual function (called `spp.cooc') is really only 2 lines long--the
code just looks longer from making up example data and adding in the
comments.
Hope this might do the trick for you! Note that in it's current form you
would have to give the function a matrix or data.frame of ONLY NUMBERS in
which species are columns and sites are rows. This could be changed by
manipulating the MARGIN argument of the apply command below, i.e., site.list
- apply(matrx,1,...)
Hope this helps--
Andy
# make some example data
sppXsite - matrix(rpois(15,0.5),nrow=3)
colnames(sppXsite) - paste(spp,1:5,sep=)
rownames(sppXsite) - paste(site,1:3,sep=)
sppXsite # here's what it looks like
# now make a function to compute the co-occurrence matrix
spp.cooc - function(matrx) {
# first we make a list of all the sites where each spp is found
site.list - apply(matrx,2,function(x) which(x 0))
# then we see which spp are found at the same sites
sapply(site.list,function(x1)
{
sapply(site.list,function(x2) 1*any(x2 %in% x1))
})
# the result is returned in a symmetrical matrix of dimension
# equal to the number of spp
}
# here's how it works
co.matrix - spp.cooc(sppXsite)
co.matrix
On Fri, Aug 27, 2010 at 12:46 AM, Jane Shevtsov jane@gmail.com wrote:
Is there a fast way to make a species co-occurrence matrix given a
site-species matrix or lists of species found at each site? I'm
looking for a spreadsheet or database
[ECOLOG-L] post doc opportunity
Dear Colleague, Please post the job announcement listed below. Thank you! Regards, Wil Wollheim Post-Doctoral Opportunity: Modeling Arctic Stream Biogeochemistry - The University of New Hampshire seeks a highly motivated postdoctoral scientist who will address research questions regarding arctic stream biogeochemical processes, the influence of the hyporheic zone, responses to changing seasonality, and consequences for nutrient fluxes at river network scales. The successful candidate will be expected to develop, apply, and evaluate models to address these questions. Modeling will focus on the seasonally dynamic role of the hyporheic zone, a critical area of biogeochemical activity that is expected to change as the arctic climate warms. Initial model development will be at the reach scale, with ultimate translation to the network scale. A background in mathematics and hydrology or other environmental science is essential. The successful candidate must have strong quantitative skills, preferably with a programming background (including MATLAB or R). This modeling effort is part of a larger collaborative science team that includes researchers from multiple institutions taking field measurements and conducting experiments in a number of arctic streams located on the north slope of Alaska. The position is focused on modeling, but the successful candidate will also be expected to participate in seasonal field campaigns at Toolik Lake, Alaska during spring, summer, and fall conditions. Position is available immediately and will remain open until filled. Applicants should send a curriculum vitae, statement of research interests, and contact information for three references to Dr. Wilfred Wollheim (wil.wollh...@unh.edu ). --- Wilfred M. Wollheim Research Assistant Professor Co-Director,Water Systems Analysis Group Complex Systems Research Center Institute for the Study of Earth, Oceans and Space University of New Hampshire 211 Morse Hall Durham, NH 03824 603-862-0812 (office) 603-862-0587 (fax) --
[ECOLOG-L] PhD Research Assistantship aquatic and avian ecology
Ph.D. Research Assistantship in avian and aquatic ecology. Project involves both experimental and sampling approaches to address questions about controls on wading bird aquatic prey animals and their habitat in the Everglades. Candidate will be exposed to multidisciplinary research program as well as the application of science into one of the nations most comprehensive ecosystem restoration projects. MS degree and experience in avian ecology, wetland ecology, aquatic ecology, or wildlife science is required. The ability to work effectively at remote wetland field sites is essential, as is the ability to work well in teams. Candidate must have evidence of the ability to publish the results of scientific studies. Strong statistical analytical skills are also favorable. Expected start date is January 2011. Graduate stipend is $20,000/year with tuition waiver. The degree is through the Integrative Biology PhD Program at Florida Atlantic University. Applications must be received by October 18, 2010. Send via email, a CV, pdf of transcripts, GRE scores (unofficial copy will suffice), names and contact information for 3 references, and a letter of interest to: Dr. Dale Gawlik, Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431-0991. dgaw...@fau.edu, 561-297-.
[ECOLOG-L] SEEDSNet career fair
You are invited to share information about your programs and opportunities with our diverse and dynamic SEEDS students. The mission of ESA's award-winning SEEDS program is to advance the ecology profession through opportunities that stimulate and nurture underrepresented student to not only participate in ecology, but to lead. Our ESA SEEDS Diversity in Ecology Graduate School and Career Fair is a great way to connect with our talented undergraduate and graduate students. Our next opportunity to exhibit will be a virtual career fair on SEEDSNet during the week of November 15th. Exhibitors will receive up to eight hours of live chat time to interact with students over the course of the week, a listserve-wide mailing of your opportunity in SEEDS Marketplace, and a three month promotion on SEEDSNet and the SEEDS homepage. Register by Sept. 30th and we will give you a 50% off recession rate discount - $250 for universities, government, and non profits, and $500 for corporations. You can find more information and register here http://www.esa.org/seeds/opportunities/career.php. Or contact Melissa Armstrong directly with questions at meli...@esa.orgmailto:meli...@esa.org.
[ECOLOG-L] ReRev
Is your university using ReRev? http://rerev.com/facilities.html Sustainability exercise: UNT students helping power rec center DENTON (UNT), Texas -- The University of North Texas is converting the Pohl Recreation Center into one of the largest human power plants in the country by capturing the kinetic energy produced by exercise machines and converting it into electricity. The 36 elliptical machines that are included in the project are fitted with a device from ReRev, a Florida company that developed the system, which feeds electricity produced by each machine into the recreation center's power grid. ReRev says during a typical 30-minute workout, each machine produces 50 watt hours of clean, carbon-free electricity, enough to power a compact fluorescent light bulb for 2.5 hours or a laptop computer for an hour. UNT has a vast array of sustainability programs under way on campus and this project underscores our commitment to saving energy, said Laura Klein, senior associate director of recreational sports at UNT. It's a great educational opportunity for our students, faculty and staff. This system provides a lesson in sustainability and energy use. As they work out, they'll be thinking of the energy they're producing and perhaps it will influence them to consider sustainability in their daily lives. A monitor will be set up near the ellipticals that will indicate the amount of electricity being produced, giving users a clear picture of how much energy is being saved. Students are huge proponents of renewable energy projects and the ReRev system gives them a chance to participate while getting a good workout, Klein said. Students are very aware of sustainability and the need to find alternate, clean power sources, which bodes well for our future because they will be the ones who will be leading those efforts in a very short time. ReRev captures and diverts the kinetic energy produced by exercise and given off as heat. Instead, ReRev's system converts it into alternating current that's used in the recreation center's power grid. That converted electricity is fed directly into the building's electrical supply, lowering the buildings overall use by a small amount. Because each of the elliptical machines normally dissipates heat into the room, the system also means slightly lower air conditioning costs. We're not going to power the building from these machines, but we are generating clean electricity and helping educate students. The real value of the system is both in showing how much work it takes to make electricity as well as the lesson in making buildings more sustainable, Klein said. Approximately 20 universities in the U.S. are using the ReRev system. Alexandra Ponette-González, Ph.D. NSF Postdoctoral Fellow Department of Geography and the Environment University of Texas at Austin -- Department of Geography University of North Texas (Fall 2011) -- Alexandra Ponette-González, Ph.D. NSF Postdoctoral Fellow Department of Geography and the Environment University of Texas at Austin
