Keeping up with the literature (in your own lab)

My lab has started blogging about each other’s papers. People in our lab use quite a variety of techniques and have some pretty different research focuses. I love seeing my labmate’s work come together into a cohesive whole and I love digging into new (to me) techniques and ideas. I always learn a lot. In our blogging project, one person takes lead and writes a short summary of the paper and everyone else very briefly answers these questions:

  1. What’s your takeaway from the paper?
  2. What’s the coolest thing about it?
  3. What questions are you left with?

Joane started off the series in January and I followed this month talking about one of her papers.

The Homebrew Series: Inferring Demographic History With ABC, By Joane Elleouet And Sally Aitken

Want to know about the history of the populations you’re studying? Joane Elleouet and Sally Aitken see how far Approximate Bayesian Computation (ABC) and your sequencing method of choice can take you in a new paper in Molecular Ecology Resources. [more]


A long migration

5000 years ago, Native Americans in what is now the southern US created an extraordinary earthwork: Watson Brake took centuries to build and is the oldest mound complex we know about in North America.

We don’t know what it was called or what it meant to its builders; things that happened 5000 years ago are hard to reconstruct. But we try anyway.

While the creators of Watson Brake were mixing their fish bones into the mounds in Louisiana, the eastern edge of the lodgepole pine migration front was crossing the Yukon Plateau 4000 km away. By the time the last handfuls of soil were being packed onto Watson Brake’s 25 foot tall ridges, lodgepole had hit the high, cold teeth of the Selwyn and Pelly Mountain ranges.

Photo by Ed Struzik of Cirque of the Unclimbables (actually in the Mackenzie Mountains to the east of the Selwyns)

The trees couldn’t cross the high mountains, but they followed the Frances River through a pass just 20 km wide to Frances Lake in southeastern Yukon.

Frances Lake with Logan Mountains in the back. From Frances Lake Wilderness Lodge

4000 years ago the vizier to Pharaoh Mentuhotep IV led an expedition to Wadi Hammamat where he gave offerings to Min, a fertility god. A few years later, Mentuhotep was dead, childless, and the vizier was Pharaoh. He probably didn’t kill Mentuhotep, but that was 4000 years ago, so who knows?

About the same time Amenemhat was maybe-but-probably-not thinking about usurping the throne of ancient Egypt, lodgepole pushed out of Frances Lake’s narrow valley. Freed from the confines of the high mountains, lodgepole began a slow march up the the Tintina Trench.

The Tintina trench and its extension, the Northern Rocky Mountain Trench, are a longstanding human travel route and geological marvel. I wonder if the trees followed the people or the people followed the trees?

When the first Roman Emperor died, the eastern edge of the lodgepole migration front rounded the top edge of the Pelly Mountains at Pelly Crossing and sprawled across the eastern portions of the Yukon River watershed, down to meet the western migration front slowly making its way through the valleys of the northern Coast Range.

Pelly Crossing. Bridge not available for use by trees.

But lodgepole kept going up the Tintina Trench, too. Today, they’re are all the way up to Dawson. It’s not clear exactly when they got there, but the Tr’ondëk Hwëch’in have definitely been there longer than lodgepole has.

People move so much faster than trees that we don’t always notice their incredible journeys. But journey they do!

From Strong & Hills in The Holocene, 2013

If you want the details and a discussion of uncertainty around these estimates, check out the paper: Strong, W. L., & Hills, L. V. (2013). Holocene migration of lodgepole pine (Pinus contorta var. latifolia) in southern Yukon, Canada. The Holocene, 23(9), 1340–1349.

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Problems setting root.dir in knitr

RStudio sets the working directory to the project directory, but knitr sets the working directory to the .Rmd file directory. This creates issues when you are sourcing files relative to the project directory in your R markdown file. Specifically, knitr tells you it can’t find those files:

Error in file(filename, "r", encoding = encoding) : 
  cannot open the connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  cannot open file 'home/sus/Documents/research_phd/analysis/phenodata_explore.R': No such file or directory

knitr has an option for dealing with this – root.dir – and Phil Mike Jones even gives a nice little knitr chunk example of using it.

But when I tried it, knitr kept failing to find my file.

```{r "setup", include=FALSE}
opts_knit$set(root.dir = "~/Documents/research_phd/")

It turns out I should have read the documentation more closely.

Knitr’s settings must be set in a chunk before any chunks which rely on those settings to be active. It is recommended to create a knit configuration chunk as the first chunk in a script with cache = FALSE and include = FALSE options set. This chunk must not contain any commands which expect the settings in the configuration chunk to be in effect at the time of execution.

Breaking it into two chunks separating the knitr configuration from the sourcing solved the problem.

```{r "knitr config", cache = FALSE, include=FALSE}
opts_knit$set(root.dir = "~/Documents/research_phd/")

```{r, "setup", echo = FALSE}

Natural history, synthesis papers and the academic caste system | Small Pond Science

Everybody loves natural history. Everybody thinks that we should value natural history more (well, almost everybody), and find a way to value descriptive field biology more in our academic rewards system. I would bet there are more ecologists who hate puppies than ecologists who think that natural history is valued adequately.

Though nearly all of us agree that natural history need to be valued more, if you look at the way we publish and cite and hire and tenure and promote and award scientists, well, we pretty much aren’t valuing it.

We want it to be valued because we all benefit from it. But we all are reluctant to do and publish much of it because we aren’t getting credit for it.

Source: Natural history, synthesis papers and the academic caste system | Small Pond Science

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