A week in office

Based on this blog you might think that nothing really significant has happened in the first months of this year. Well, I can tell you the truth: nothing really significant has happened. People are mostly just sitting in their offices doing whatever small things are part of their research work. But maybe even the ordinary can be worth reporting - once.

Monday. Rain and snow. I spent the morning making figures for the next manuscript. In the afternoon I browsed through one biometrics book wondering if I need to include some kind of statistical test to confirm that my results are what they look like. Rest of the day was mainly putting the results to paper, one page more was finished. Highlight of the day: final program of the physense-seminar was announced.

Tuesday. The proofs of a recently accepted laser manuscript (codename: motolaser) arrived for checking and final corrections. Most of the day was spent in this job. I also managed to add a few more paragraphs to the yesterdays work before leaving to the sunny spring day outside. Highlight of the day: hopefully this really was the end of the motolaser project, something that started already in fall 2006 and has required a remarkable amount of time and patience since then – while being really funny at times.

Wednesday. Continuing with the manuscript. I decided that one of the figures needs more points, which meant a significant workload for my computer during the morning. In the afternoon I continued writing, and managed to finish early versions of both results and discussion sections. Highlight of the day: an interesting discussion about one particular pine tree growing more than 200 km away.

Thursday. Wrote abstract to the article and spent rest of the day reading once again those same old, vague articles to confirm that I had cited them correctly. Highlight of the day: lunch break.

Friday. Another sunny but quite boring day. More checking of references and clarifying the unclear parts of the manuscript. Happily all this was finished by the end of the day so the paper was more or less ready to move forward. Highlight of the day: closing the pc for weekend.

Cajanus tube demystified

One of the questions I keep on hearing is: what is the Cajanus tube and how it is used? Actually it is all very simple, but in scientific articles there is never enough space to describe everything comprehensively. So hopefully this will make things clearer.

At least in this case one image tells more than tens of words, so this is how the Cajanus tube looks like:

As you see, it is little like a periscope, but it is used for looking upwards. The balancing system at the top keeps the tube leveled, and the user looks vertically through the tube that has a small mirror (placed at 45 degrees angle) at the bottom and a crosshair at the top. The whole system is usually placed on a supportive staff. This allows the measurer to define exactly whether some point is covered by the canopy. It can be used for measuring crown radiuses or canopy cover. In canopy cover estimation the standard method is to establish some transects in the study plot, and then measure the percentage of the transect covered by the crowns.

The Cajanus tube has already a long history. It was designed by Werner Cajanus, who was the first professor in forest inventory in Finland, already in the 1910’s for use in crown radius measurements. Risto Sarvas showed how it can be used for canopy cover measurements in the 50’s, but after that I have not found any Finnish publications until LAI detectives. Actually nobody of our forest inventory staff here in Joensuu had even seen a Cajanus tube before I borrowed the one in the picture from Metla’s Suonenjoki research station.

The final question of an interested reader should now be “where to get one?” As far as I know, nobody makes these anymore. There is one fairly similar commercial version called the GRS densitometer, but it is nowhere as useful as the Cajanus tube, because it has no self-leveling system (the user must use the in-built leveling bubbles to keep it vertical). So the remaining option is to build one with your own hands – for example plywood and mirror can be used for the tube, and the leveling system can be made of some screws and iron bars. Or maybe an average researcher should just find someone handier to do the job…

America, America

December was an exciting month for me. Matti and I spent a week visiting Ranga Myneni's group at Boston University (BU) and another week in San Francisco participating in the fall meeting of the American Geophysical Union (AGU). I had been looking forward to the trip for quite a while - it would be nice to meet friends at BU (I was a visiting scholar there three years ago) and to go to a conference to get some new and fresh ideas. And of course, to see the way Americans prepare for Christmas (and all the other wintery holidays)...

Boston greeted us with wind and cold weather. Places looked pretty much the same as three years ago. I guess the biggest change was the new ticket system in the "T" (subway) and a Chinese extension to the campus food court. During our stay there, we had a very interesting discussion about p-theory and multi-angular data with Yuri and Mitch, and learned about the global greening and time trend research Sangram, Arindam and Ranga were working on. Sometimes even short, brief conversations can serve as a basis for starting something new. And hearing somebody else explain the thing you are working on, but with words different from those that you usually yourself use, can really help get a new perspective.

The AGU meeting in San Francisco was huge with about 15 000 participants and dozens of parallel sessions. For me, the most interesting part was a session dedicated to looking 50 years back and 50 years in to the future of Earth Observation missions. The session differed from the usual technical sessions; scientists who had worked some 30 years in the field talked about their experiences and thoughts for the future. My own contribution to the meeting was a poster presentation on estimation of photon recollision probability from multi-angular, hyperspectral data in the session "Remote Sensing of Land Surface Properties, Patterns, and Processes". The poster session was not as busy as I had hoped for, but to look for the positive side, nearly all the hand-outs I had prepared disappeared from my poster stand during the day.

Nights out in San Francisco were spent running around the city. Lots to see... the Sun setting in the Pacific Ocean, old cable cars, the Golden Gate Bridge, lazy California sea lions at Pier 39, the crooked Lombard street, busy Chinatown, Castro and Haight-Ashbury. Overall, the trip to "America" was a success, and my book shelves now have 10 kg's more books than before the trip! And for some mysterious reason, my jeans have shrunk.

San Francisco streets.

The beta regression

Sorry folks, but this post is (for once) almost purely scientific, and does not include anything about eating or drinking. The reason for this is that the article with which I worked for most of last spring has now been published, and as I think that most of you won’t probably bother to read it, I decided to write something about it into this blog. If advertising would not work, so much time and money would not be spent on it…

The aim of my PhD project is to develop and compare different methods for estimating forest canopy cover. As accurate field measurements of cover percent are quite slow, one alternative is to use statistical model to predict it from easily measurable forest variables. This issue had been around since my master’s thesis, where my first attempts to model the cover with simple linear regressions were made with a data collected near Metla’s research station in Suonenjoki. The results were relatively good, but linear regression models just don’t function very well in modelling percentages: no scientist wants to see percentages that are negative or larger than 100%. In addition, the old models did not function nearly as well when more data were included, so there was still a lot of work to be done when I started the process in early 2007.

I spent some time studying the different modelling techniques: logistic regression, nonlinear curves and generalized linear models, to see if any of these would function better with this kind of data. Nothing very useful appeared, until I found this lecture material by Juha Heikkinen. There was a hint: Juha suggested using the beta distribution in modelling proportions. Fine, but how? Luckily, nowadays there is always one to ask: Google. After some surfing I discovered that there was an R library called betareg, which was just the thing I was looking for: the beta regression was both simple and suitable for this kind of problem. Another interesting thing was that even though a lot of statistics are used in forest science, I could not find any earlier forest-related studies where this technique would have been used, only something related to psychology. So maybe this paper would have something “new” after all.

What remained then was the tough job of curve fitting. In this case it meant writing numerous R-scripts to handle the data, testing the different model shapes, and fixing the small bugs in the library. I tested many different model shapes with not too good results, as the correlations were heavily nonlinear. In the end I decided to use cubic functions to make the polynomials flexible enough, but fortunately the beta regression’s logistic link function would take care of extrapolation problems. As the analysis was done, what remained was the writing of the manuscript, which was finished in May. The manuscript was then offered to Silva Fennica, and after some revisions it was accepted for publication. And now, here it is, and it is time for new challenges.

The Coffee & Cake Ceremony

Yesterday it was once again time for one of our group's traditions: the coffee and cake ceremony. The ceremony takes place every time one of us publishes a paper: the first author takes all the members of the group (who are in town) as well as the co-authors to a café to enjoy a piece of cake and coffee. The ceremony has been extended to cover also other situations: it's called the coffee&cake&cognac ceremony when we receive scientific awards or funding (or something like that) and it's the dinner&wine ceremony when something Really Big happens.

Yesterday, it was Pola's turn (she published a paper), and she took us (Janne, Matti and me) to Fazer in the afternoon. For me it meant a very short day at work since I gave a lecture in the morning and had to prepare the following day's lecture in basically no time before rushing downtown to the café...

While enjoying the cakes we had our daily chance to catch up on all the more or less scientific gossip. Who's done what, who's heard what...

Chilli-chocolate cake - excellent!

Hurtigruten again...

Lauri forgot to mention our latest experiment (carried out during the Hurtigruten trip): does a PhD degree correlate positively with success in card games?

NORSEN-meeting at Hurtigruten, 1.-3.11.2007

Even forest science is mostly office work - the field work is most often outsourced to students or specially educated forestry professionals. Practically the only variety to daily computer routines comes from different conference and meeting trips. So when I heard that there would be a possibility to attend the NORSEN-meeting arranged in Troms, Northern Norway, and the legendary coastal steamer Hurtigruten, I was of course quite eager to go, expecting to learn a little what all that field work last summer had been about, discuss with others, and just have a good time seeing new places and landscapes. Only the 13 hours travel time per direction from Joensuu was something that I did not look forward to. Especially when the route was through Helsinki and Oslo, which seemed slightly irrational from my perspective.

So in the evening of the first travelling day our group - me, Matti, Miina, Pekka, Pola, Terhikki and Juha - were sitting in the auditorium listening a presentation by a local satellite company that uses radar data e.g. to detect oil spills in the Arctic Ocean. After the unforgettable lutefisk dinner we moved to the ship - MS Trollfjorden, which was a moderate shock for someone not used to luxurious travelling… And as the morning brightened and the snowy peaks of Lofoten became visible, it became clear that the yesterdays journey had already paid off.

The meeting itself was also worth listening to. The NORSEN coalition included a number of different participants sharing an interest of using satellite data in environmental monitoring, and to me it was interesting to hear what is remote sensing outside forest sector. Usually it is seems to be much simpler… But after some hours as tiredness began to take over, you could almost imagine being on any university seminar (at least when the room was not swaying to and fro) - until you stepped out of the auditorium and saw the new surroundings. Wow! Lofoten and Hurtigruten are worth the praise they are given. Or maybe we were just lucky, as there was no rain during the whole trip…

In the Friday evening we left the ship in Svolvaer, local governmental center, and after a few hours waiting boarded another, slightly older ship that was heading back north. Next day was free, so there was plenty of time for enjoying the scenery (even sun appeared!), meals (especially dessert!) and some scientific speculations (how do you measure LAI if the trees are covered by snow?). At sunset we were back in Troms, and I’d guess many of us would like to return to Hurtigruten some day. At least as a well-off pensioner, like most of the passengers.

And then things started to go wrong: darkness, chilling wind under the cold sky, crowded restaurants, a terrible movie (that I skipped at the cost of chilling wind), burnt pizzas and slow service, smoky airport hotel, delayed flights, airport bus taking an unusual route back in Joensuu… Well, nothing disastrous actually, but when I once more began to focus on revising a laser manuscript in my room at the university next morning, the ordinary days of the new week did not seem too bad after all.

Official part


Cruising


Hotel yard, sunday morning