Opening access to age models through GitHub

As part of PalEON we’ve been working with a lot of chronologies for paleoecological reconstruction (primarily Andria Dawson at UC-Berkeley, myself, Chris Paciorek at UC-Berkeley and Jack Williams at UW-Madison). I’ve mentioned before the incredible importance of chronologies in paleoecological analysis. Plainly speaking, paleoecological analysis means little without an understanding of age.  There are a number of tools that can be used to analyse, display and understand chronological controls and chronologies for paleoecological data. The Cyber4Paleo webinars, part of the EarthCube initiative, have done an excellent job of representing some of the main tools, challenges and advances in understanding and developing chronologies for paleoecological and geological data.  One of the critical issues is that the benchmarks we use to build age models change through time.  Richard Telford did a great job of demonstrating this in a recent post on his (excellent) blog.  These changes, and the diversity of age models out there in the paleo-literature means that tools to semi-automate the generation of chronologies are becoming increasingly important in paleoecological research.

Figure 1.  Why is there a picture of clams with bacon on them associated with this blog post?  Credit: Sheri Wetherell (click image for link)

Figure 1. Why is there a picture of clams with bacon on them associated with this blog post? Credit: Sheri Wetherell (click image for link)

Among the tools available to construct chronologies is a set of R scripts called ‘clam‘ (Blaauw, 2010). This is heavily used software and provides the opportunity to develop age models for paleo-reconstructions from a set of dates along the length of the sedimentary sequence.

One of the minor frustrations I’ve had with this package is that it requires the use of a fixed ‘Cores’ folder. This means that separate projects must either share a common ‘clam’ folder, so that all age modelling happens in the same place, or that the ‘clam’ files need to be moved to a new folder for each new project. Not a big deal, but also not the cleanest.

Working with the rOpenSci folks has really taught me a lot about building and maintaining packages. To me, the obvious solution to repeatedly copying files from one location to the other was to put clam into a package. That way all the infrastructure (except a Cores folder) would be portable. The other nice piece was that this would mean I could work toward a seamless integration with the neotoma package. Making the workflow: “data discovery -> data access -> data analysis -> data publication” more reproducible and easier to achieve.

To this end I talked with Maarten several months ago, started, stopped, started again, and then, just recently, got to a point where I wanted to share the result. ‘clam‘ is now built as an R package. Below is a short vignette that demonstrates the installation and use of clam, along with the neotoma package.


#  Skip these steps if one or more packages are already installed.  
#  For the development packages it's often a good idea to update frequently.

install.packages("devtools")
require(devtools)
install_github("clam", "SimonGoring")
install_github("neotoma", "ropensci")
require(clam)
require(neotoma)

# Use this, and change the directory location to set a new working directory if you want.  We will be creating
# a Cores folder and new files & figures associated with clam.
setwd('.')  

#  This example will use Three Pines Bog, a core published by Diana Gordon as part of her work in Temagami.  It is stored in Neotoma with
#  dataset.id = 7.  I use it pretty often to run things.

threepines <- get_download(7)

#  Now write a clam compatible age file (but make a Cores directory first)
if(!'Cores' %in% list.files(include.dirs=TRUE)){
  dir.create('Cores')
}

write_agefile(download = threepines[[1]], chronology = 1, path = '.', corename = 'ThreePines', cal.prog = 'Clam')

#  Now go look in the 'Cores' directory and you'll see a nicely formatted file.  You can run clam now:
clam('ThreePines', type = 1)

The code for the ‘clam’ function works exactly the same way it works in the manual, except I’ve added a type 6 for Stineman smoothing. In the code above you’ve just generated a fairly straightforward linear model for the core. Congratualtions. I hope you can also see how powerful this workflow can be.

A future step is to do some more code cleaning (you’re welcome to fork or collaborate with me on GitHub), and, hopefully at some point in the future, add the funcitonality of Bacon to this as part of a broader project.

References

Blaauw, M., 2010. Methods and code for ‘classical’ age-modelling of radiocarbon sequences. Quaternary Geochronology 5: 512-518

Student travel support from The Palynological Society

Logo-AASP-Color-Re-Draft-2008This email just came to my inbox, I wanted to share it with the readers.   If you are a student who uses palynology as part of your research please consider membership in The Palynological Society (and, of course the Canadian Association of Palynologists!) and applying for student travel support:

Student Travel Support Other than the Annual Meeting

The Society will entertain applications for student travel support with a deadline of December 1, 2014 for 2015 meetings other than the AASP Annual Meeting. This opportunity allows students to request support for any meeting at which they are presenting their palynological results.

The application should include the following:

  1. one paragraph justification for the request plus a description of the research to be presented (plus the abstract submitted for the presentation, if available)
  2. outline of the requested amount and how the funds would be used
  3. applicant’s email and postal addresses
  4. all of these to be forwarded by the applicant’s advisor who includes a brief explanation of how attendance at this particular meeting will benefit the student.

Application materials should be sent by email to the Chair of the AASP Awards Committee:

Martin Farley at mbfarley [at] sigmaxi.net
Geology, Old Main 213
University of North Carolina at Pembroke

There will be a separate opportunity for travel support to the Annual Meeting, help jointly with the Geological Society of America meeting in Baltimore in mid-2015.

Of note is the upcoming INQUA meeting in Nagoya, Japan (27 July – 2 Aug).  There are some great sessions of interest to a range of Quaternary scientists.

It wasn’t hard to achieve gender balance.

If you aren't aware of this figure by now you should be.  Credit: Moss-Racusin et al. 2012.

If you aren’t aware of this figure by now you should be. Credit: Moss-Racusin et al. 2012.

A couple of weeks ago my colleagues and I submitted a session proposal to ESA (Paleoecological patterns, ecological processes, modeled scenarios: Crossing temporal scales to understand an uncertain future) for the 100th anniversary meeting in Baltimore. I’m very proud of our session proposal.  Along with a great topic (and one dear to my heart) we had a long list of potential speakers, but we had to whittle it down to eight for the actual submission.

The speaker list consists of four male and four female researchers, a mix of early career and established researchers from three continents. It wasn’t hard. We were aware of the problem of gender bias, we thought of people who’s work we respected, who have new and exciting viewpoints, and who we would like to see at ESA.  We didn’t try to shoehorn anybody in with false quotas, we didn’t pick people to force a balance.  We simply picked the best people.

Out of the people we invited only two turned us down.  While much has been said about higher rejection rates from female researchers (here, and here for the counterpoint), both of the people who turned us down were male, so, maybe we’re past that now?

This is the first time I’ve tried to organize a session and I’m very happy with the results (although I may have jinxed myself!).  I think the session will be excellent because we have an excellent speakers list and a great narrative thread through the session, but my point is: It was so easy, there ought to be very little excuse for a skewed gender balance.

PS.  Having now been self-congratulatory about gender I want to raise the fact that this speakers list does not address diversity in toto, which has been and continues to be an issue in ecology and the sciences in general.  Recognizing there’s a problem is the first step to overcoming our unconscious biases.

Upcoming Conferences – Part I: Geological Society of America

Figure 1.  GSA 2014 in beautiful downtown Vancouver!  I listened to them building this convention center every day for months on end, so it had better look nice!

Figure 1. GSA 2014 in beautiful downtown Vancouver! I listened to them building this convention center every day for months on end, so it had better look nice!

Much of the research I do is interdisciplinary. While I often consider myself a paleoecologist, it is just as true that I am a physical geographer, earth scientist, ecologist, geoinformatician and computational biologist, with an order that varies depending on the project at hand. I think Jacquelyn Gill once suggested I call myself a paleobiogeoecoclimatologinformatician, and I honestly think I’m probably forgetting a piece of that.  Anyway, with that in mind I find myself at a variety of conferences each year. I am as much at home at the Botanical Society of America, the American Geophysical Union, or the Geological Society of America‘s annual conferences as I am at the Canadian Association of Palynologist’s meeting. The next meeting for me is this Octobers Geological Society of America meeting in Vancouver BC.

Since Vancouver was home for me while I did my Ph.D, I jumped at the opportunity to present at GSA.  One session in particular was of great interest: Where in the World? Access and Availability to Geoscience Data II. I’ve been involved with the Neotoma Paleoecological Database for a while now, and have been actively working on an R package for the database. In particular I wanted to talk about my experiences at the intersection of Neotoma (the data provider) and PalEON (a data consumer & provider). From my viewpoint both large scale projects have benefitted immensely from the partnership. While the PalEON project is able to get large volumes of data from the Neotoma Database, we have also been able to leverage our connections to begin inputting data into the database, and, because of our particular needs, we have been able to act as a test case for the development of the API, R package, and many of the new upload tools for Neotoma. Much of the success of EarthCube in the near future is going to depend on the ability to gain community trust, and engagement. The partnership between large-scale ecological research and broad community databases provides exactly the kinds of synergies needed to help improve this kind of collaboration, and, ultimately, research success in the future. That talk:

4:30PM: DEVELOPING SYNERGIES BETWEEN LARGE-SCALE RESEARCH AND GEODATABASES: NEOTOMA AND PALEON
Session No. 253
Where in the World? Access and Availability to Geoscience Data II
Vancouver Convention Centre-West 116/117
Tuesday, 21 October 2014: 1:00 PM-5:00 PM

I was also invited by Amy Myrbo to speak about some of our work looking at chronologies in Neotoma. This may seem overly technical, perhaps not particularly ecological, but the way we deal with chronologies in paleoecological data is critically important for modelling past ecosystem changes. Without an accurate understanding of time, it is nearly impossible to make sense of ecological patterns in the past, or to apply them in a meaningful way to modern ecological theory. I’ll talk a bit about the lessons we’ve learned from re-building chronologies in PalEON, particularly some of the great work Andria Dawson has been doing, and how to deal with issues of time when working with large datasets, with specific focus on Neotoma. That talk:

1:00PM: AGE MODELS IN LARGE SCALE SYNTHESIS – DE NOVO OR STATUS QUO?
Session No. 325
Recent Advances in Limnogeology (1:00 – 5:00pm)
Vancouver Convention Centre-West: 213
Wednesday, 22 October 2014

I’m also going to be speaking at the Biodiversity Lunchtime Internal Seminar Series (BLISS) at UBC on Monday, October 20th from noon to 1:00PM, and again for the Biological Sciences Seminar Series at Simon Fraser University on Wednesday October 22 at 3:30PM (as long as the 135 is running on time!).

Lastly, if you are a paleoecologist or palynologist, CAP, the Canadian Association of Palynologists, is having their Annual General Meeting on Wednesday October 22nd at 11:30am at Mahony & Sons, right by the convention. All are welcome, so please come out and join us. Everyone loves meetings!

Ecosystem services have always been with us. Using the past to explore their dynamics.

Figure 1.  Hoping we'll find a proxy for beautiful sunsets.  Image from: BrendelSignature at en.wikipedia

Figure 1. Hoping we’ll find a proxy for beautiful sunsets. Image from: BrendelSignature at en.wikipedia

Clean water, forest products, clean air.  The value of ecosystem services has received a lot of attention in the past several years. In 1997 Robert Costanza and co-authors provided one of the first real valuations of ecosystem services (Costanza et al., 1997), estimating that, at an annual subsidy of ~$33 Trillion, they provide more value to human society than the entire global GNP at the time (~$18 Trillion).  Following Costanza’s paper and the Millennium Ecosystem Assessment (2005) considerable research effort has gone into understanding the extent of ecosystem services around the globe, and at multiple scales, however the widespread application of the term ‘ecosystem service’ has led some to question the consistency with which the term is used (Seppelt et al., 2011).

Regardless, it is clear that ecosystems play a vital role in maintaining critical social functions.  Whether providing clean and safe drinking water, wood for building, or giving us a sense of relief at the sight of a beautiful sunrise, ecosystem services are a fundamental (and often undervalued) component of our well being.  Given this, it is no surprise that we have become keenly interested in projecting changes in valuation of services in the future under changes in land use and as a result of global change.  Joshua Lawler and co-authors (2014) use land use trends to estimate changes in ecosystem services in the continental United States under three different conservation scenarios, but don’t attach value to the shifts.  In Landscape Ecology Monica Turner and co-authors (2013) lay out several key research questions to help resolve our uncertainty about the effects of future change on ecosystem service provisioning.  One of the key research questions in this paper is “How well will understanding of past landscape dynamics and ecosystem services inform the future?“.

The use of paleoecology in understanding ecosystem service function and change is still in its infancy, but John Dearing and co-authors (2012) have provided an excellent road map in their paper “Extending the timescale and range of ecosystem services through paleoenvironmental analyses, exemplified in the lower Yangtze basin”.  Table 1 of the paper provides a long list of ecosystem services and possibly related paleoecological proxies, linking food production to pollen microfossils, fresh water provision to diatom assemblages and air quality regulation to spherical carbonaceous particles, all of which – incidentally- can be found in lake sediment records.

The challenges of using the paleo-record remain, and it is critical that researchers begin to address the methods with which we cross-scales, from the paleo-record to modern ecological time scales, and on to future projections.  Excellent work by McLauchlan et al. (2014) in BioScience is beginning to do just this.  Exploring the ways in which we can integrate paleoeoclogical process into modern ecological theory is critical for understanding the long time-scale processes that ultimately help regulate the provision of ecosystem services.

 References

Costanza, R. et al. 1997. The value of the world’s ecosystem services and natural capital. Nature. 387, 253-260.

Dearing, JA. et al. 2012. Extending the timescale and range of ecosystem services through paleoenvironmental analyses, exemplified in the lower Yangtze basin. Proceedings of the National Academy of Sciences, 109(18), E1111-E1120. [PDF]

McLauchlan, KK. et al. 2014. Reconstructing disturbances and their biogeochemical consequences over multiple timescales. BioScience. [PDF]

Lawler, JJ. et al. 2014. Projected land-use change impacts on ecosystem services in the United States. Proceedings of the National Academy of Sciences, 111(20), 7492-7497. [PDF]

Seppelt, R. et al. 2011. A quantitative review of ecosystem service studies: approaches, shortcomings and the road ahead. Journal of Applied Ecology, 48(3), 630-636. [PDF]

Turner, MG. et al. 2013. Consequences of spatial heterogeneity for ecosystem services in changing forest landscapes: priorities for future research. Landscape ecology, 28(6), 1081-1097. [PDF]

Quaternary Science . . . on Mars . . . three billion years ago.

downwithtime:

Cross-posted from the Open Quaternary blog.

Originally posted on OpenQuaternary Discussions:

For a curious person, one of the great benefits of being a Quaternary researcher is the breadth of research that is relevant to your own research questions.  The recent publication of fifty key questions in paleoecology (Seddon et al., 2014) reflects this breadth, spanning a broad range questions that reflect human needs, biogeophysical processes, ecological processes and a broad range of other issues.  The editorial board of Open Quaternary also reflects this incredible disciplinary breadth.  To me it is clear that the Quaternary sciences is an amalgam of multiple disciplines, and, at the same time, a broadly interdisciplinary pursuit.  To be successful one must maintain deep disciplinary knowledge in a core topic, as well as disciplinary breadth across topics such as ecology, anthropology, geology (and specifically geochronology), and you need a good grounding in statistics and climatology.

One of the things that is not always quite as apparent is the breadth…

View original 700 more words

We’re reading the same paper, but we’re getting different messages.

Earlier I posted about an interesting paper by Jankó and colleagues in Geoforum about similarities and differences in citation patterns between the IPCC and the NIPCC.  It turns out I wasn’t the only one interested in it.

It was pointed out to me that Judith Curry, Watts Up With That and the Heartland Institute have all written posts about the paper.  Their key takeaway message seems to come from the fact that the citations between the two are similar, and that Jankó and co-authors include language that indicates that reflexively dismissing ‘skeptic’ arguments does a disservice to scientific advancement.  This does an injustice to Jankó and colleagues because it misrepresents what I believe is very interesting work into the underpinnings of scientific inquiry, particularly around climate change.  Much of the support Bast and Curry see in the paper comes from a single sentence, associated with a citation from a 2013 paper by Mayanna Lahsen.

My reading of the sentence:

But when we take the contrarian arguments seriously, there is a chance to bring together the differing views and knowledge claims of the disputing ‘interpretive communities’ (Lahsen, 2013b).

Is not to say that we need to accept their arguments as alternate fact, but to say that the reflexive dismissal of contrarian viewpoints limits our ability to engage and understand the contrarian viewpoint.  The paper itself “Anatomy of dissent: A cultural analysis of climate skepticism” certainly shows little support of skepticism. Mayanna Lahsen has done some excellent work understanding climate change denial (skepticism?) from a sociological/anthropological viewpoint.  Indeed, her arguments in the cited reference point more to the fact that scientists need to work harder to engage with skeptics in an effort to avoid cultural backlash.  She is not arguing that skeptics pose acceptable alternative models to anthropogenic climate change.  Take this sentence for “Anatomy of dissent” (the same paper cited by Jankó and colleagues):

To promote their agenda, powerful backlash actors have frequently adopted deceptive strategies to create the fictitious appearance of broad grassroots and scientific support.

Does this in any way suggest that we ought to be taking contrarian arguments seriously because they are valid?  No, we are being asked to take them seriously because by understanding their backgrounds and motivations we can begin to address the causes of backlash against climate science, and move forward toward solutions.

I argued in my last post that just because the IPCC and NIPCC use the same citations, they are not equally acceptable models for global climate and climate change.  Interestingly, just because Bast, Curry and I read the same paper doesn’t mean we came to the same conclusions either.