Quantum Forest

Last night I was helping my wife to fix an MS Word document. The document had been edited by several people, with varying setups, so it was a real mess. Different page sizes (letter and A4), paragraph settings, sections, etc. Making changes at any point of the document created all sort of side effects; for example, content moving to different pages or missing formating when deleting supposedly unrelated sections. At the end, she copied and ‘pasted unformatted’ to another document to be able to fix the document from scratch. The always touted advantage of electronic documents comes down in flames when one needs to resort to such basic fix. Better than typing everything again, but still unacceptable as a proper solution.

In contrast, I have been again enjoying the chance of writing some fairly long documents by myself; that is, with no co-authors. While writing a review paper I can go back to a LaTeX document that I wrote back in 2001. I copied the useful parts–mostly long equations and a couple of paragraphs–and pasted it in my new document. The style will be taken care by the article class (or even the memoir class if I were feeling fancy).

When working in solitary mode I now default to LaTeX. My only change this year was to move from compiling documents with XeLaTeX instead of LaTeX. Reasons? Easy access to my system fonts and full use of unicode, so I can write with whatever characters I prefer. My current setup is documented here.

The only big choice comes to whatever text editing system one prefers. I have done most of my writing during the last two years in TexShop, which is excellent. Nevertheless, I used Aquamacs in a project (just for the sake of it) and there was and old fashion setting that I really liked: automatic flow hard wrapping to a fixed column. This created a neat and easy to read file, which was independent of window size (in contrast to soft wrapping). The drawback is that emacs is a monster program and so much mac-unlike that it is really hard for me to find my way around all the options (and, god, there is an awful lot of options).

My geeky side does enjoy trying editors, and at night time, I tested most of the editors listed in here, from a LaTeX editing viewpoint. My finalists were TexShop, Aquamacs and Textmate. The latter is pure macness and works beautifully; it evens automatically detects documents that require XeLaTeX based on regular expressions. The compilation window is beautiful as well, and it even supports basic code folding for documents (although why folding of sections is not supported is beyond me). The question would be if folding justifies 39 euros… Well, it could be a nice Christmas gift to myself.

P.S. 2008-12-19: I did buy a copy of Textmate, with 15% academic discount.

In these times full of ‘issues’ we need the correct approach to deal with them.

Flight of the Conchords playing ‘Issues (think of it)’.

A friend of mine decided to move on from his job in a large research organization. There are many reasons behind that decision but, at least from the outside, one of them seems to be his unwillingness to cope anymore with management’s stupidity. Another one is the difficulty of working with other members of his ‘team’.

I currently work in a very small department, in a small university. I am the only breeder (of anything) working in the university. On one hand that could be seen as a serious disadvantage: there is a sense of isolation attached to the situation. On the other, it means that ‘we are (I am) small enough to change the world’. I can’t afford wasting time with territorial disputes, I don’t have to agree or disagree with other people. As Herman Hesse said ’solitude is independence’. Another plus, if I want to work with someone else I have to collaborate with people outside my discipline, who are not constrained by tree breeders’ mythologies and superstitions.

There is no replication for this ‘experiment’, so it is hard to generalize any conclusions. Nevertheless, this year that is closing to an end has been one of the most–if not the most– productive of my professional career.

By this time I need a rest, but I am hoping to have an even more productive year in 2009.

A quiet moment in Santiago’s cathedral. Almost five hundred years in the same spot, although it is like ‘my granfather’s axe’: it has been destroyed and rebuilt a few times.

Santiago’s cathedral.

Cathedral

It must be remembered that there is nothing more difficult to plan, more doubtful of success, nor more dangerous to manage, than the creation of a new system. For the initiator has the enmity of all who would profit by the preservation of the old institutions and merely lukewarm defenders in those who would gain by the new ones.—Niccolò Machiavelli, The Prince, Chapter 6.

E debbasi considerare, come non è cosa più difficile a trattare, né più dubia a riuscire, né più pericolosa a maneggiare, che farsi capo ad introdurre nuovi ordini; perché lo introduttore ha per nimici tutti quelli che degli ordini vecchi fanno bene, e ha tepidi defensori tutti quelli che delli ordini nuovi farebbono bene.—Niccolò Machiavelli, Il Principe, Capitolo VI.

A large proportion of my work involves using statistics, mostly analyzing progeny trials or other smaller experimental designs. On terms of statistical techniques, this means generalized linear mixed models (GLMM) with at least one of the random effects with non-independent observations (a pedigree). Variations of the topic include multivariate analyses, longitudinal analyses, spatial analyses. Most of the time the traits are normally distributed, but some times I end up with binary or count traits.

I have checked quite a few books and have some favorites:

• Regression with Graphics: A Second Course in Applied Statistics by Lawrence Hamilton. I have a soft spot for this ‘newbie’ book, which I think presents ideas in a very easy to follow way, always emphasizing understanding the data by using graphics. It is a good beginner’s book.
• Regression Modeling Strategies by Frank Harrell. This is currently my favorite ‘advanced regression modeling’ book. It contains plenty of practical advice, as well as S+/R code examples to fit almost anything. I learned quite a bit on logistic regression from here, and his example modeling probability of surviving the sinking of the Titanic is a classic. I use a simplified version of this example when teaching.
• Experimental Design and Data Analysis for Biologists by Gerry Quinn and Michael Keough. This is one of those ’statistics for biologists’ books, but with a big difference: it assumes that the reader is intelligent. It covers a lot of ground, but always presenting a (relatively) modern approach to design an analysis. It covers statistical power for ecological experiments in a very satisfactory (and clear) way. In my opinion, it is much more useful than Zar’s and Sokal’s ’stats for biologists’ books.
• Data Analysis Using Regression and Multilevel/Hierarchical Models by Andrew Gelman and Jennifer Hill. This book–as Hamilton’s–comes from Social Sciences. It is really enjoyable, has interesting examples and tackle modern approaches, including Bayesian Stats. I am currently trying to read it from cover to cover. If one has some background on stats I would recommend starting with this one, as is quickly becoming one of my favorite books on linear models (my review).
• Matrix Algebra Useful for Statistics (Wiley Series in Probability and Statistics) by Shayle Searle. I have the original hard cover edition and read it from cover to cover during my Ph.D. I think it gives a very good background if one wants to understand what is going on in ANOVA and regression, particularly when trying to figure out statistical software output (my review).
• Linear Models for the Prediction of Animal Breeding Values (Cabi Publishing) by R. (what does the R stand for?) Mrode. I have the first edition, which provides a good–although a bit terse–introduction to BLUP (Best Linear Unbiased Prediction) as used in quantitative genetics models.

I will keep on expanding this list when I remember other titles.

Updated: 2008-11-05.

A beautiful example of compression wood induced by tilting a Pinus radiata tree.

Coffs Harbour Jetty, October 2008, 7 am.

Coffs Harbour Jetty

As far as I know, 2008 has been my most productive year ever from a writing point of view. Besides the blogging and micro-blogging stuff (aka informal public writing), I have worked in lecture notes and I have been writing an inordinate (for me) number of words in research papers. I still hope to submit a couple of more papers this year.

I have written all blog posts using MarsEdit, which is an excellent simple editor. I used MS Word for quite a few papers because I am working with LaTeX-unaware students and colleagues. However, I have also bee using LaTeX for all my lecture notes and a number of long(ish) research papers where I am working mostly by myself.

Until recently, I was using TexShop + LaTeX, but then I discovered XeLaTeX, which added unicode support–so I can write zúñiga in my files–and font management. I can easily access all my fonts in the mac in a fairly simple way. I am documenting the switch in the wiki side of this site.

During some asreml training I re-discovered emacs during Brian’s explanations. I installed Aquamacs (an OS X emacs version), which comes with ESS (emacs speaks statistics) to interface with R and AUCTeX (a LaTeX editing environment) pre-installed. Overall, I am still finding my way within Aquamacs, but the whole system feels very powerful. Now, if I manage to get an asreml version for the mac that would be total bliss.

I just like this poem by Elizabeth Bishop and I am parking it here so I do not lose it. What a contradiction!

The art of losing isn’t hard to master;
so many things seem filled with the intent
to be lost that their loss is no disaster.

Lose something every day. Accept the fluster
of lost door keys, the hour badly spent.
The art of losing isn’t hard to master.

Then practice losing farther, losing faster:
places, and names, and where it was you meant
to travel. None of these will bring disaster.

I lost my mother’s watch. And look! my last, or
next-to-last, of three loved houses went.
The art of losing isn’t hard to master.

I lost two cities, lovely ones. And, vaster,
some realms I owned, two rivers, a continent.
I miss them, but it wasn’t a disaster.

—Even losing you (the joking voice, a gesture
I love) I shan’t have lied. It’s evident
the art of losing’s not too hard to master
though it may look like (Write it!) like disaster.