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Probabilistic Coupling

Environmental Modelling & Software has just published my work on a new technique for coupling models: Probabilistic Coupling. My thoughts on coupled models had been percolating for a couple years, before a session at the International Conference on Conservation Biology in 2013 offered me a chance to try it out.

Probabilistic coupling has three main goals:

  • Allowing models to be coupled without distortionary feedback
  • Allowing multiple models to inform the same variable
  • Allowing models to be coupled with different scales

With these three features, the very nature and approach of coupling models can change. Current model coupling requires carefully connecting models together, plugging inputs into outputs, and then recalibrating to recover realistic behavior again. Instead, this allows for what I call “Agglomerated Modeling”, where models are thrown together into a bucket and almost magically sort themselves out.

The code for the model is available within the OpenWorld framework, as the coupling example.

Torch passing

A friend: “The big story in the world this week is… the inevitable passing of the torch. We will witness the beginning of a new era this week, I feel.”

Naturally, he was only using the French election (NYT: “The result was a full-throated rebuke of France’s traditional mainstream parties, setting the country on an uncertain path”) in jest to refer to something completely unrelated, but it gave me a thought. Much as I love some parts of globalization and the Post-WWII international institution, this is a passing of the torch. And that uncertain recipient of the torch– maybe populist, maybe bigoted, maybe urban, technophilic, and progressive– that recipient is us.

Every generation seems surprised when the torch is passed in their lifetime, but it cannot be otherwise.

LJ blasted about its 18th birthday, of which I had apparently been part 13.55 years, and posted 473 times. I guess it was time to move on.

Next stop: London

My time at UC Berkeley is drawing shut, and for the past 4 months I have been pursuing my own eclectic version of the academic job market. I find myself squarely between economics, geophysics, and data science, with disconnected bits to show from a tough-to-articulate whole. But I have also been fortunate to have strong supporters, who appreciate whatever it is that I do. With their help, the job search has treated me well, and forced me to decide between excellent and incomparable alternatives. So, this is a post of victory!

Each of my five fly-out interviews required distinct presentations, across them covering papers on fisheries, coffee, and climate, a teaching talk on thermoeconomics, and a pitch for a new sustainability program. I interviewed at science, economics, and interdiscplinary departments, and got the support of the faculty at every one. Flame and I just finished a revisitation of the top US options, to decide on our new home.

But across professional fit, cultural metabolism, Flame’s opportunities, and the politrumpal climate, we realized that the best choice was none of them: I am taking a 100% research assistant professorship at the Grantham Research Institute on Climate Change and the Environment at the London School of Economics! LSE is in the heart of London, which is also home to Flame’s nonprofit.

There I can look forward to a huge pool of potential collaborators, including two from my PhD program. LSE straddles the divide between the US academic world, where I will be able to keep my collaborations alive, and the European world of modeling and proaction that I have always been drawn to. The advertised position was for “Growth and the Environment”, which I’m all about. And connecting science with policy is part of the job, with a team at hand specifically for this purpose.

I move there at the beginning of 2018. Between now and then, I have 4 more months at Berkeley, and in July I start a mini-postdoc-#2 at the University of Chicago.

I can’t wait to set up in a new continent, and hope you all come to visit!

All work and play, Day 5

Another back-dated day from the Balkans Trip, originally at http://johanna.existencia.org/.

It was gloriously sunny, the perfect day to explore the town of Mostar on my own.  I got lost and then found again, crossed five bridges (in both directions), read a book and composed several post cards.  I did not, however, consume my required 3 espresso-based drinks.

James fastidiously programmed away save a lunch and dinner break where we enjoyed waterfront dining and fantastic Italian-inspired food, respectively.

In the hours between sunset and pitch black, we explored Počitelj, an Ottoman Empire fortress with an incredible amphitheater, sizable mosques and steep staircases. Attempting photos in the dark proved fruitless, so we ventured back to Mostar and enjoyed a very good dinner at Restaurant Schumann. I suggest if you in town, you take the mile plus walk to this harbor of home-made pasta, breads and local charm.  No tourists.

One culinary observation: we always get the “basic” bread when we sit down (part of the 2 euro per person cover charge). Other diners get some version of a grilled thick pita bread.  I’ve asked for the local bread, and then received a side of cold, deflated pita.  Moreover, when I request garlic (another of my daily requirements), I get whole, raw cloves, which I do my best to macerate with a butter knife. More words to learn.

Tomorrow, we will mobilize to Dubrovnik, where our plans and expectations of Croatia await.

I ❤ small towns, Day 4

Another back-dated day from the Balkans Trip, originally at http://johanna.existencia.org/.

Today, we decided to go to Bosnia. The drive from Montenegro to Bosnia provided stunning views of the bay, snowcapped mountains, vocal yacks, and sacks of potatoes for sale by the side of the road. We took the long way ‘round, with the prettiest of views (cue song lyrics), following the serpentine shore of the Bay of Kotor. The bay narrows into a strait, flowing into an upper bay, with an island monastery sitting at its mouth. All around the bay are jutting cliffs, with terracotta roofs in isolated hamlets. We climbed through strings of tunnels and Old-Western style homesteads, before coming to the vineyards of Bosnia.

Crossing the border was pretty easy, with no bribes needed. The green card we purchased through the rental car agency seemed to do the trick. We approached the tiny town of Mostar (which I still want to call monster…) three hours later.

Mostar pulls at heart strings with its picturesque bridges and stone-lined streets.  To seal the deal on its delights, our boutique hotels provides unlimited cookies for James.  By driving through the vertical and tiny streets—as we saw on a sign earlier— “you risk your life”. But now settled, we plan to stay two nights so that tomorrow can be spent with my purchasing of hand painted decorative items (Turkish style) and James making climate models (computer style).  We are both helping the world, I reckon.

This evening we strolled along the dividing river, where locals were watching football and filling time during the “low” season.  Observation: men and women seem to run in separate groups.  Not in the forcibly gender segregated way we saw in Egypt, but far from the coed peer groups you get in the US.

I love that wifi is available virtually everywhere here, so if any on you darling readers have an iPhone, it’s free to message and facetime me, and I would love that tomorrow (Note the 5 hour time difference ahead of EST).

Chiseled features, Day 3

Another back-dated day from the Balkans Trip, originally at http://johanna.existencia.org/.

It’s Wednesday so we must be in another country…

We flew to Tivat, Montenegro and rented a car (with limited challenge but moderate wait for the car to arrive) from now through Sunday. Our first stop is the picturesque Bay of Kotor. It was drizzly and cold when we arrived, but we left the car safely (if expensively) at a car park and ventured into the walled city on foot to find our centrally-located hotel in the winding streets.

Kotor is a city covered in beautiful white and tan stone: the streets are tiled, the water drains are carved, the churches and homes are built of huge, sturdy blocks. Shops and caffes sprout shingle signs, carefully branded for the onrush of tourists that will arrive by yacht in May. The mountain rises with water-sculpted towers, looming imposingly behind the city, with the city wall snaking along its highest ridges.   Montenegro feels like a more cloistered Greece; they also use the Euro but seem to resent it.

As the light waned, James thought it would be a great idea to explore the step mountain—on foot. When I protested, he conceded that we could drive. At a 70 degree slope, we were greeted by 25 hair pin turns. I backed down—from several cars—and then out–when it became pitch black and the Bay sneered bellow, reflecting the schizophrenic headlights of cars that took the curves at 100 kph.

We decided to find our way back on safer roads, and selected the Stari Mlini (http://www.starimlini.com/) for dinner. Named for the working water wheel on the far side of the Bay, we enjoyed stunning salads, clay-oven-prepared eggplant and local octopus. The dining room was warmed by a fire and we were the sole “seasonal” dinners at 8pm. The chardonnay made 50 km away was not unpleasant.

Back in the car, we zoomed to the hotel so James could do some calls (translate: be on the computer for the next 4 hours) while I explored the night life in town. I sampled the local rose and red wines, and for young grapes, they outshine VA productions. I happened upon a Bollywood style music video production underway, where the singers were dressed as jesters and Princess Jasmine. The taping concluded with some well positioned fireworks that illuminated the fortress walls. I also passed the youth hostel, where I head a smattering of German and a sole American voice complaining about Adweek and LA.

Tomorrow, we plan to enjoy the free breakfast and then head to Mostar, Bosnia, and perhaps reconsider the treacherous drive into the hills of the Adriatic coast.

NB: A note on the format of these blogs: I write steam of conscious observations then James edits for accuracy (i.e. spelling of locations) and adds alliterative adages (self-explanatory and excruciating). Please submit your comments, c/o the Internet to us.

Sad to leave Novi Sad, Day 2

Another back-dated day from the Balkans Trip!

Happy Pi Day!

Goal: consume as many Serbian pies as possible today.

We started at a lovely coffee shop providing extensive chemistry lessons on coffee composition and bean varietal. James had a Nutella croissant, which he counts as pie number one of the day.

Took a bus 1.5 hours to the northwest of Belgrade to the darling town of Novi Sad where we had a fantastic meal at Fish & Zelenish (http://www.fishizelenis.com/), feasting on baked feta, sizable salads and salmon tar-tar above an open kitchen. They gifted us a cookbook/menu and regional salt. No pie was consumed, but we somehow were not feeling deprived. It was definitely the best meal we’ve had so far.

We wandered the dense old town, of tiled streets and artist resalers. Found a swanky hotel to take some work meetings/calls and make arrangements for tomorrow. Amended plan includes flying into Tivat, Montenegro and renting a car to explore the coast. Why Tivat? Oh, tickets are only €60, compared to €250 flights or 12 hour buses to go half the distance.

Dinner was a very late, with an overpriced excursion to the Opera/restaurant. Sitting in a plush overhead booth, with a silent bell tassel to call the waiter, we order ambergine with raw garlic and baked goats (cheese). Alas, after hours, the music was recorded and the kitchen too early shuttered.

The day in numbers:

  • Pies consumed: 0.314
  • Ratio of time on train to time on bus to cover the dame distance: 1.8 to 1
  • (Took the bus to Novi Sad, and the train back. The price was the same, time spent was not).
  • Jewish historical sites visited: 2
  • Post cards sent: 3
  • Bread products sampled: 6
  • Churches seen: 14
  • Enclosed spaces with smoking: 100% minus Fish & Zelenish.

Science and language

One of the rolling banners at last year’s meeting of the American Geophysical Union had a scantly-clad woman and the words “This is what most people think of as a ‘model’”. See, scientists have a communications problem. It’s insidious, and you forget how people use words and then feel attacked when you have to change how you speak.

I have a highly-educated editor working with me on the coffee and climate change report, and she got caught up on a word I use daily: “coefficient”. For me, a coefficient is just a kind of model parameter. I replaced all the uses of “coefficient” with “parameter”, but I simultaneously felt like it dumbed out an important distinction and wondered if “parameter” was still not dumbed down enough.

AGU has a small team trying to help scientists communicate better. I think they are still trying to figure out how to help those of us who want their help. I went to their session on bridging the science-policy divide, and they spent a half hour explaining that we have two houses of congress. Nonetheless, it is a start, and they sent us home with communication toolkits on USB. One gem stood out in particular:

So I will try to reduce the ignorance and political distortions of my devious communication plots, until I can flip the zodiac on this good response loop. Wish me luck.

Tropict: A clearer depiction of the tropics

Tropict is a set of python and R scripts that adjust the globe to make land masses in the tropics fill up more visual real estate. It does this by exploiting the ways continents naturally “fit into” each other, splicing out wide areas of empty ocean and nestling the continents closer together.

All Tropict scripts are designed to show the region between 30°S and 30°N. In an equirectangular projection, that looks like this:

original

It is almost impossible to see what is happening on land: the oceans dominate. By removing open ocean and applying the Gall-Peters projection, we get a clearer picture:

version4

There’s even a nice spot for a legend in the lower-left! Whether for convenience or lack of time, the tools I’ve made to allow you to make these maps are divided between R and Python. Here’s a handy guide for which tool to use:

decisions

(1) Supported image formats are listed in the Pillow documentation.
(2) A TSR file is a Tropict Shapefile Reinterpretation file, and includes the longitudinal shifts for each hemisphere.

Let’s say you find yourself with a NetCDF file in need of Tropiction, called bio-2.nc4. It’s already clipped to between 30°S and 30°N. The first step is to call splice_grid.py to create a Tropicted NetCDF:

python ../splice_grid.py subjects/bio-2.nc4 ../bio-2b.nc4

But that NetCDF doesn’t show country boundaries. To show country boundaries, you can follow the example for using draw_map.R:

library(ncdf4)
library(RColorBrewer)

## Open the Tropicted NetCDF
database <- nc_open("bio-2b.nc4")
## Extract one variable
map <- ncvar_get(database, "change")

## Identify the range of values there
maxmap <- max(abs(map), na.rm=T)

## Set up colors centered on 0
colors <- rev(brewer.pal(11,"RdYlBu"))
breaks <- seq(-maxmap, maxmap, length.out=12)

## Draw the NetCDF image as a background
splicerImage(map, colors, breaks=breaks)
## Add country boundaries
addMap(border="#00000060")
## Add seams where Tropict knits the map together
addSeams(col="#00000040")

Here’s an example of the final result, for a bit of my coffee work:

arabica-futureb

For more details, check out the documentation at the GitHub page!

And just for fun, here were two previous attempts of re-hashing the globe:

version1

I admit that moving Australia and Hawaii into the India Ocean was over-zealous, but they fill up the space so well!

version3

Here I can still use the slick division between Indonesian and Papua New Guinea and Hawaii fits right on the edge, but Australia gets split in two.

Enjoy the tropics!

Redrawing boundaries for the GCP

The Global Climate Prospectus will describe impacts across the globe, at high resolution. That means choosing administrative regions that people care about, and representing impacts within countries. However, choosing relevant regions is tough work. We want to represent more regions where there are more people, but we also want to have more regions where spatial climate variability will produce different impacts.

We now have an intelligent way to do just that, presented this week at the meeting of the American Geophysical Union. It is generalizable, allowing the relative role of population, area, climate, and other factors to be adjusted while making hard decisions about what administrative units to combine.  See the poster here.

Below is the successive agglomeration of regions in the United States, balancing the effects of population, area, temperature and precipitation ranges, and compactness. The map progresses from 200 regions to ten.

animation

Across the globe, some countries are maintained at the resolution of their highest available administrative unit, while others are subjected to high levels of agglomeration.

world-24k

The tool is generalizable, and able to take any mechanism for proposing regions and scoring them. That means that it can also be used outside of the GCP, and we welcome anyone who wants to construct regions appropriate for their analysis to contact us.

algorithm