Without beliefs

22/09/2009

I am re-reading Stephen Batchelor’s ‘Buddhism without beliefs’, pills which I first read in 1999. I still think that the following paragraph captures really well my own position:

An agnostic Buddhist eschews atheism as much as theism, and is as reluctant to regard the universe as devoid of meaning as endowed with meaning. For to deny either God or meaning is simply the antithesis of affirming them. Yet such an agnostic stance is not based on disinterest. It is founded on a passionate recognition that I do not know. It confronts the enormity of having been born instead of reaching for the consolation of a belief.

Simple: I do not know.

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Godspeed Norman

14/09/2009

Norman Borlaug–the ‘father of the Green Revolution’–just died§. I raise my glass for a breeder who did make a difference.

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Default to R

8/09/2009

Last March§ I posted an explanation of the issues behind getting R accepted in our School for teaching statistics.

At School level, weight loss I needed to spend substantial time compiling information to prove that R could satisfy my colleagues’ statistical needs. Good selling points were lme4, information pills lattice/ggplot and pointing my most statistically inclined colleagues to CRAN. Another important issue was the ability to have a GUI (Rcmdr) that could be adapted to our specific needs. We will develop an extra menu item to fit non-linear models for growth models used in forestry. Our School has now adopted R as the default software for teaching any statistical content during the four years of the curriculum.

At the university level, my questions to the department of Mathematics and Statistics sparkled a lot of internal discussion, which resulted in R being adopted as the standard software for some of the second year courses (it was already the standard for most courses in 3rd and 4th year). The decision was not unanimous, particularly because for statisticians knowing SAS is one of those ‘must be in the CV’ skills, but they went for change. The second year courses are offered across colleges, which makes the change very far reaching. These changes will also imply that in the near future many computers in the university will come with R preinstalled.

It is nice to see interesting changes once in a while.

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Around Japan

20/08/2009

I will keep updating this post with the itinerary.

Monday 17: trip from Christchurch to Auckland, seek then from Auckland to Narita International Airporthemorrhoids 140.366993&sspn=0.08176,0.151062&ie=UTF8&ll=35.7727,140.388279&spn=0.681899,1.208496&z=10″>§. Nice 767 plane. This was followed by a car ride from Narita to Hitachi§.

Tuesday 18: visiting progeny trials around Hitachi, quick tour at Tree Breeding Center and first presentation on GxE interaction. Banquet as the guest of honor.

Wednesday 19: visiting another progeny trial and seed orchard for ‘low pollen’ Sugi varieties. Drive to Tsukuba§ and presentation on breeding objectives broadcasted by internet. Drive to Narita, plane from Narita to New Chitose Airport§ (Hokkaido), train to Sapporo§.

Thursday 20: progeny trials, clonal trials and seed orchards around Sapporo, Hokkaido.

GoingOutInSapporo.jpg

Sapporo’s restaurant district.

Friday 21: visit silvicultural trials. Presentation about very early screening for wood quality in Sapporo. Banquet with people attending the presentation.

Saturday 22: train from Sapporo to Chitose, flight from Chitose to Kansai airport§ (Osaka), train from Kansai to Kyoto§, subway to hotel. Visit to market, some shopping and washing my clothes.

Yoko.jpg

Yoko, our friendly waitress/theology student starts bringing the food. Nice restaurant in Kyoto.

Sunday 23: Free day. Temples galore in Kyoto: Higashi Honganji, Nishi Honganji, Sanjūsangen-dō.

Tuesday 25: Presentation in Kyoto on very early screening for wood quality. Flight from Kyoto to Kumamoto (Kyūshū)§.

Prayers.jpg

Prayers.

Wednesday 26: last presentation in Kumamoto on very early screening for wood quality (free at last!). Banquet with 15 people.

Thursday 27: Drive from Kumamoto to Miyazaki§. Visited CP progeny trial and several silvicultural experiments on the way. Flight from Miyazaki to Haneda Airport, Tokyo.

japan_circle_mapper.gif

Another 22,000 kilometers in two weeks. This does not consider cars, trains and buses.

Friday 28: Going around Tokyo looking for presents and suffering the heat. It is a big, large, enormous city. Train to Narita airport and 7 pm Air New Zealand flight to Auckland, where I arrived the next day.

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Note to self on terminal

13/08/2009

Sometimes I change a few defaults but then I forget how I did it. First, seek showing all hidden files (both in Finder and Terminal) is easy. Just type in Terminal the following commands:

defaults write com.apple.finder AppleShowAllFiles TRUE
killall Finder

The second line kills all instances of finder and restart them. The other issue is to activate color display (for directories, binary files, etc) in Terminal, which implies adding the following lines to one’s profile by using:

echo "export CLICOLOR=1
export LSCOLORS=exfxcxdxbxegedabagacad" >> .profile

man ls describes options for tweaking the color scheme.

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Space invaders

11/08/2009

Jellyfish (Blue background)

Jellyfish in Newport’s Aquarium (Oregon).

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Catching up

2/08/2009

I have been traveling, search well, we have been traveling and this has left little time to post. Now recovering from a small surgery I can have a peek at the wonders of the interwebs and check what these times passes as news.

In a first approach nothing really important happened. That’s right, besides the odd celebrity dying, the ups and downs of the world economy and the typical storms in a glass of water of the tech industry, there was nothing to catch my eye. In a second approach, same thing, and this was a relief because it supports the sempiternal suspicion: most of the things that we believe are important are not. Taking a little bit of distance, of perspective, smoothes things out, the single details (for which we live or die) become a continuum and we start seeing trends. Take too long and trends become useless, because we can’t use them (trends have inbuilt ‘best before’ dates). Take too many snapshots and we drown in noise.

This time the pause was granted by air travel, driving, accommodation with spotty wireless coverage, red tape, friends with luddite dial-up connection (in 2009!) and too many things happening to take time off in front of a computer.

The first two weeks I was based in Ames§, Iowa (go Cyclons!), which felt like going to a different planet. It was hot and humid (particularly coming from winter in Christchurch), flat and with majestic storms. Two tornado warnings in two weeks, friendly people and research teams doing amazing things. When I visit a place I always ask myself ‘Could I live here?’ (and I have lived in many cities in five countries) and the answer was ‘I don’t know’. On one side it is too flat, with too few forests, too hot in summer and too cold in winter. On the other, people were nice and they were doing very interesting, meaningful work.

The next three weeks I was based in Corvallis§, Oregon, which was similar to parts of Chile, Tasmania and New Zealand. It looked familiar and we have very good friends in Corvallis. The question again ‘Could I live here?’ had a similar answer: the landscape, climate and people are good. However, I did not click with the university and its research. Maybe it was an anticlimax because it came after Iowa State and Pioneer—working with crops—to deal with trees, which move much more slowly.

I think that there is an issue of attitudes: in agriculture (working with crops or animals) one can feel the pulse, the drivers with more immediacy. Trees provide too much time to look for excuses and why things do not seem to work OK. In some issues it is a lot harder to make changes in forestry, although from another point of view one has too convince fewer people: there are fewer players.

But I digress, the most important point is perspective. Talking with a researcher in Iowa I pointed out ‘I’ve been away from genetics for a while, things have moved on and I do not have the time to catch up with everything that has happened. Therefore, I have ignored everything else but X and Y.’ It is a bet, but an informed one (I hope) and we will see how things pan out in the next couple of years.

It was good to be away for a while. It is good to be back as well.

Hiking with friends

Hiking in Oregon with old friends.

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Back in Christchurch

28/07/2009

gcmapUS.gif

After five weeks and over 30, ed
buy 000 km of moving around.

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Using R for genetic analyses

11/06/2009

As some people know, visit I have been using asreml for genetic analyses for quite a few years and even keep the ASReml Cookbook§. I was quite happy to see the development of asreml-R, ed a package that makes available most of ASReml’s functionality from R. This made my life easier: I still use plain-vanilla ASReml for very big jobs, but I can access a much more comprehensive statistical system for fairly substantial jobs.

One of my main problems with asreml-R is that is not available for OSX (mac). Yes, I can dualboot or use a virtual box, but both options are a bit of a pain. I rather use my computer with its primary operating system and no strange overheads. I have requested several times to have a mac version. It seems that the code can be compiled without problems, but it is the license management software that is not available for the mac.

I then started looking for options to run genetic analyses. nlme was designed around hierarchical models and fitting experimental designs did not feel right. lme4 is looking good and the main issue was around fitting pedigrees, a matter at least partially solved by the pedigreemm package. I then came across the MCMCglmm§ package, which has some nice features: it makes Bayesian analyses accessible, ready support for pedigrees and a syntax not that different from asreml-R.

After playing with the MCMCglmm library, I found that I could not use pedigrees with parents acting both as males and females. I modified the code (line 26 of inverseA.R) to print a warning rather than to stop and the compiled the library again. Voila! it is working (the beauty of having access to the source).


R CMD INSTALL /Users/lap44/Downloads/MCMCglmm --library=/Users/lap44/Library/R/2.9/library

By the way, ASReml is still my primary tool at the moment, but I enjoy having good alternatives.

Filed in genetics, mac, software, statistics 2 Comments

Slide

1/06/2009

Slide

It is a long way down the slide. Auckland Zooapoplectic 174.72049&spn=0.002635,0.003782&t=h&z=18″>§.

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