Monthly Archives: January 2013

More theory papers should have tables like this

From Coulson & Tuljapurkar 2008

From Coulson & Tuljapurkar 2008

1. Coulson, T. & Tuljapurkar, S. The dynamics of a quantitative trait in an age-structured population living in a variable environment. The American Naturalist 172, 599–612 (2008).

R adding ‘X.’ to column names

I received some data recently in an Excel file. I opened it in LibreOffice Calc to have a quick look, saved it as a csv, and (tried) to get down to business in R. But all of my column names were an awful mess. Instead of

SPU_Number  SPU_Name  Long_Site  Site

my column names were prepended with X. and appended with a period, like so:

X.SPU_Number.  X.SPU_Name.  X.Long_Site.  X.Site.

I’d used read.csv(), which uses read.table(). This stackoverflow answer clued me in to the fact that R thought there were special characters at the beginning and end of my column names. I reopened the file in LibreOffice Calc and annoying saw absolutely no special characters at the beginning and end of my column names. But when I opened up the file in a normal text editor I saw that my column names had all been single quoted!

To prevent this from happening to you, make sure you check Edit Filter Settings in the Save As dialogue and then make sure both Save cell content as shown and Quote all text cells are unchecked. Or don’t use LibreOffice Calc – Excel won’t screw up your column names like this.

Calling all students interested in the history of ecology (UPDATE)

The Historical Records Committee of the Ecological Society of America is organizing a poster session on student investigations into ecology’s history. The session description from Dan Song:

Current Student Perspectives On The History Of Ecology

Everyone in ecology and its related fields has, at one point, been a student of ecology. Although it is true that all ecologists are in a state of perpetual learning, students still in school aspiring to be professional researchers hold a special place in the field. Often, students start their research careers by looking into the past (months, decades, centuries) to inspire their own research. While in school student research is still developing and may change; students have not yet lived in the history they are examining. Students are always thinking about how they arrived at their current circumstances as well as projecting their future prospects. Like the skyways connecting buildings in downtown Minneapolis, students serve as the bridges between ecology’s history and its future. This collection of posters presents different historical aspects of ecology that has inspired their own research. We present student perspectives on several key aspects of the field, including ways in which women’s contributions to the field have evolved, through Ruth Patrick’s career, and students’ reflections on the present impact of key figures in ecology, such as E.C. Pielou. In addition to examining pioneering figures the posters also highlight how societal norms, such as gender roles, impacted ecology over time.


If you’re interested in presenting in the session or have any suggestions or ideas, please get in touch with Dan Song at danielssong[at]gmail.

JAN 13 UPDATE: Though ESA typically allows only one presentation per person, presentations in this session aren’t counted [see exemptions] – so you can give a poster in this session and a talk or poster on your other research.

JAN 13 UPDATE: The deadline is tomorrow, Monday, January 14, so get in touch with Dan soon.

JAN 16 UPDATE: While the deadline has passed, you should still contact Dan if you’re a student interested in the history of ecology. If some people are not able to accept their invitations, you might be considered! Also, remember that the general abstract submission deadline for ESA is February 21!

Out of sync – species distributions and people

In a few weeks This week, Charles Menzies will be presenting “Stories of Seals, Abalones, and Strangers” at the Fisheries Seminar Series at UBC, which I’m really looking forward to.  His talk abstract describes environmental destruction of the Gitxaala people’s historical lands

For over two hundred years Gitxaała people have been witness to a fantastical transformation of the lands and seas. Oceans once teeming with marine life have been fished barren. Hillsides along streams have been denuded of trees. Mountains have been drilled into. Waterways have been blocked and diverted. Monstrous windmills are planned for the tops of seaward ridges. Large ships filled with oil and gas are being marshaled soon to descend upon the heart of Gitxaała.

And promises to discuss how the models people like me create affect the Gtxaala:

Despite this transformation Gtxaała maintains a strong attachment to the place. This presentation tells the stories of seals and abalone – important foods and beings within Gitxaała’s world- and the strangers -ḵ’amksiwah- who came and stayed. While models drawn from universalizing sciences appeals to the ḵ’amksiwah, these models tend to create mechanisms more effective at destroying Gitxaała practices then they are in managing so-called resources.

I spend a lot of time thinking about how the distribution of different forest tree species will change as the climate changes. When I think about what climate change means for people, I think about things like how to prepare cities for heavier rainfall or more frequent heat waves, the loss of ecosystem services, resource conflicts, or disrupted agricultural systems. I haven’t spent as much time thinking about the cultural implications of climate change. But reading this talk abstract makes me wonder what species distribution shifts will mean to people whose culture is tied so closely to particular ecosystems. In the past, governments have forcibly removed native peoples from their lands. Now, through climate change, we may be forcibly moving lands away from native peoples. Perhaps there’s a way for our models and predictions about species distributions to be used to prevent or mitigate that.