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8/07/2006

After playing for a little while, view
I managed to connect my Macbook Pro to the internet using my mobile phone via bluetooth. I have a small Samsung ZV10 and my service provider is Vodafone New Zealand. The steps are quite simple:

  • Click the bluetooth icon in the topbar and select ‘setup bluetooth device…’.
  • Check that the phone is running bluetooth and that is discoverable (Under settings, practitioner
    connectivity).
  • Select mobile phone in the list of available devices.
  • The computer will search and—we hope—find your mobile phone.
  • The computer will generate a numeric passkey that has to be keyed in and accepted in the phone.
  • Select ‘Access the Internet with your phone’s data connection’ in the next menu.
  • The settings to connect to Vodafone in New Zealand are:
    • username: vodafone.
    • password: vodafone.
    • GPRS CID string: *99#
    • Modem script: Vodafone VC701SI

This explanation is based on the excellent—and illustrated—version by Pukupi.

After using the Macbook Pro for a few more weeks, this
I have been settling on my final software selection:

  • Quicksilver: which is a great launcher and keeps learning about my preferences. Additional plugins installed: del.icio.us, help dictionary, firefox and iphoto.
  • Office: well, I do exchange a lot of documents with colleagues and friends that use the Windows version. In general works quite well, although compatibility is not perfect. My main issues have been spreadsheets containing lots of VBA or embedded Activex controls and compressed graphics in PowerPoint, which show that puzzling ‘QuickTime and a TIFF/JPEG decompressor are required to view this picture’ message. In addition, Microsoft has not released a Universal binary for Office, and will not do it until they have the next version available, whenever that is.
  • Thunderbird: after trying Mail.app and Entourage, my experience was disappointment with how unreliable Mail.app was (missing emails and crappy IMAP support) and found Entourage too big and clunky.
  • Firefox and Camino: Firefox is a great browser, but it feels a bit un-Macintosh. Camino uses the same engine, but with a nicer interface. I like the ability of closing the tabs just next to their names (a la Safari). However, it does not have (yet) incremental search, which is something that I love in Firefox (PS 2006-06-29. It is possible to have a close button in the tabs of Firefox through the use of the Tab X add-on. PS 2006-06-30. Bob Cantoni points out ‘to close Firefox tabs, just middle-click on the tab to close it; i.e., click the scroll wheel’).
  • R: a great cross-platform (and free) statistical software. I do most exploratory analysis using it, and only go to SAS, using Parallels (see below), when strictly necessary for working with other people.
  • Parallels: allows running windows and I currently use it only to run SAS. It still feels a bit slow, but for writing and prototyping SAS code is good enough. I bought the pre-release copy at US$50.
  • Copywrite: I normally become very easily distracted when using a word processor to write. All the options, fonts and formats become a real nightmare. Enter Copywrite, which is a simple writer’s editor. It allows only basic formatting, so it is very good for the first couple of drafts.
  • Devonthink: after reading Merlin Mann’s comment on 43 folders, I decided to give it a try. I am quite tempted to use it in a continuous basis. It is a good brain dump, where I can put all odds and ends that I normally loose. The current version still has some bugs and missing features, like that the full screen editor works only for plain text and that changing the colours of text may have effects on other parts of the program. Anyway, searching and connecting notes seems to work quite well. I still think that Copywrite’s full screen editor is much better and less distractive. PS 2006-06-30: I have decided to wait until the next version before buying Devonthink: still too buggy for my taste.
  • Writeroom: I just started testing this great full screen writing system. Just write there, no need to save. If I want something a bit more complex, I can type using Markdown and convert it to HTML using Humane.Text service. PS 2006-06-30. Jers Novel Writer is another writing program that supports full screen mode and that deserves a try.
  • TeXShop a highly polished LaTeX distribution, that I am using for writing lectures notes for STAT220 (Biometry I).

Sharing printers in a mixed network

I can not remember another time when I have been using so many computers in such a regular basis. My main work machine is Mastropiero1 (Macbook Pro 15”), although there is an exception for simulation work, where I use Nutcracker (a.k.a. Black Box, a generic 3GHz, Windows XP machine, which just happens not to be beige). In addition, at home I also use Happy Meal2, a Power PC Mac Mini that acts as back up and has the printer connected. Last—and certainly least—I keep Beige Box (a generic 1GHz Windows XP machine) still functional at home, just in case we need some extra simulation capability when time is not an issue.

Last weekend, we bought another cheap windows laptop for Plus Tree, our consulting arm. It is a Compaq Presario V2000, temporarily named Lucrezia Borgia3.

Given that the printer is attached to Happy Meal and that we some times need to access it from either Mastropiero or Lucrezia Borgia using wi-fi, we:

  • Shared the printer (using System Preferences, Sharing), which works for any Mac computer in the network, including Mastropiero.
  • Allowed access from Windows machines—like Lucrezia Borgia—installing Bonjour for Windows, which has a handy ‘Bonjour Printer Wizard’. Use the Wizard and the printer is now available to Windows too. Piece of cake!

Incidentally, after using the Compaq laptop for a while, I can say that it feels as warm as the Macbook Pro on the top surface. The exception is the part above the function keys in the MBP, which is bloody hot.

P.S. 2006-06-30. Welcome to 43 folders’ readers. Five hundred visits in two days; not bad for a small sidebar link.

1 Homage to the (in)famous composer so many times presented by Les Luthiers (and English article in Wikipedia).

2 Its volume is actually a bit smaller than a MacDonald’s Happy Meal box.

3 Obvious reference to this Renaissance woman.

It has been a log time without writing about research. New country, click new city, unhealthy new job. In addition, thumb
consulting and professional service. Last but not least, family and friends come first: the end result is very little time to blog and even less for writing about research.

So, what am I doing at the moment? Simple, trying to figure out areas where I am not hitting diminishing returns too quickly. For example, estimating two hundred variance components is too rich, if we can do the job with ten. The practical return from all the additional works tends to zero: we are not making much of a difference. So, what’s the point? Yes, I can publish that, but who cares?

From a practical point of view, the real issue for me is on what is affecting competitiveness in a big way. Forestry is a long term endeavour, and the longer the rotation the higher the risk. From that point of view, extending rotation because radiata pine wood quality is not good enough borders on the stupid. Doh, of course is crappy wood; answers:

  1. Use something else or is there life beyond radiata pine?
  2. Select and breed for trees that have decent (I do not mean good) quality.

So, what are my current obsessions?

  • Profitable shorter rotations. What are the limiting factors (hint: crappy wood quality, small size pieces and scale of the operations) to make this happen?.
  • Very early selection of adequate trees. Notice emphasis: selection does not to be perfect to be useful. Adequate selections at age two is much better than good selections at age ten years.
  • Why do trees grow the way they do in wood properties? Why do trees choose different strategies that have such dramatic differences in wood quality?
  • Rapid turn-over breeding strategies. Are we still taking fifteen years for a breeding cycle? It is 2006! Can’t we do any better?

There is an obvious quantitative void in my obsessions, I know. But I am going back to attempting to understand some basic processes before I embark in more number cruncing. Despite of this, I am also interested (but not obsessed) in the following problems:

  • Simulation of breeding strategies. I have a project working on this topic starting in October this year.
  • Mate allocation and population structure. Trying to show that we can get rid of sublines and other artificial groupings when using sensible mating policies.
  • Large scale genetic evaluation: how simple is simple enough? My way to help having frequent genetic evaluations.

What else? I am involved in a couple of three projects with students, dealing with wood quality, breeding or both. I have a new Ph.D. student starting in August on the interaction of economics and breeding. Ah, I almost forgot: there is a large number of lectures coming my way, better look busy…

Filed in genetics, research No Comments

Current obsessions

21/03/2006

I have slightly changed the focus of my attention during the last month or so. My current obsessions are:

  • Optimisation of breeding programs, diagnosis for which I am learning to use AMPL, with Fritz’s help. I will need to create and format some data to include in some simulations analysed by AMPL and I think I will use Python to prototype them. If I run in to speed bottlenecks I will reimplement numerically intensive processes in either C++ or Fortran 95.
  • Genetics of wood properties. After some early forages on wood properties—which finished when Carolyn changed jobs—I am back at it. John has been very welcoming and we are trying to put a couple of projects together. We should have some early results by mid next year.

There are a few bits and pieces that do not fall in these two broad areas, but they will converge pretty soon.

Family-wise

Working with Marcela and Orlando in the veggie patch. I have never had much of a green thumb, but I am really trying. We sowed coriander, parsley and chervil, and planted bok choi, onions, dill, lemon balm and capsicum. Apart from the capsicum seedlings that are struggling (a drainage problem is my guess) everything is doing fine.

Marcela and Orlando checking worm farm

Marcela’s worm farm is the old-new addition. We used to have a worm farm in Australia, but due to quarantine issues, we decided to leave it there. So we needed to get a new one plus order the first batch of worms by mail.

Filed in gardening, genetics, miscellanea, photos, research, statistics No Comments

Done with the bloody paper!

10/11/2004

I finally completed (and submitted to Silvae Genetica) the manuscript for ‘Genetic variation of physical and chemical wood properties of Eucalyptus globulus‘. This is not my first or last paper (it is publication 25), melanoma but it took such a long time that it deserves a special mention. The project was plagued with problems and delays that, stomach although did not affect the final quality of the data, made data analysis and writing the manuscript a real pain in the back.

By the way, Silvae Genetica looks like a very old fashioned 1800s journal. I always associate the image of a very old German worker printing the journal in a damp basement. Nevertheless, it is almost compulsory reading for tree breeders and the publisher seems now keen to give it a facelift.

When writing papers I use either a combination of MS Word and Endnote (a reference manager) or LaTeX in its MiKTeX incarnation with TexnicCenter as a text editor. I use the latter combination for large documents, like convoluted course notes. This time I chose Word but did not have a ‘Silvae Genetica style’ for Endnote, which is necessary to format the citations in the text. I created a style that works for journal articles, books, book chapters and conference proceedings, which you can download from here.

I do not expect to see the manuscript for around three months. By then I should receive comments (I hope positive) from the referees.

Filed in forestry, genetics, research, software, writing 2 Comments

Away in Melbourne

6/12/2003

This week I spent three days in medstore 148.262504&sspn=1.23713,2.966309&ie=UTF8&z=16&om=1″ title=’nomap’>Melbourne, attending a meeting of the Research Working Group on Forest Modelling and Information Systems (RWG2). It was my first experience in this group, having participated in meetings of RWG1 and RWG7 in the past. One of the nice things of working in a new area is that there is no sense of respect for the ‘big names’. There is no ‘they were my lecturers’ or ‘I have read their papers’, so meetings and relationships are much freer and relaxed.

People were very nice and welcoming, and I was able to put faces to names like Cris Brack (Australian National University), Ian Ferguson (University of Melbourne), Chris Goulding (New Zealand Forest Research), Valerie LeMay (University of British Columbia) and Jerry Vanclay (Southern Cross University). There were many other ’small names’ (including mine) and we have quite a bit of fun and exchanged lots of ideas. Thanks guys!

I always have lots of fun presenting and this time was no exception, talking about spatial models for modelling mammal browsing in plantations. This is one of my current pet topics (pun intended), I mean spatial models, not only for browsing, and I hope to have something in publishable form soon.

Filed in environment, forestry, geocoded, research, statistics No Comments

Notes from the bush

25/10/2003

I was conducting some preliminary analysis of regeneration data: counts of seedlings in a series of plots. The distribution was certainly non-normal, diagnosis with a strong ‘Poisson look’, doctor so I went for a generalised linear model with a Poisson family and a log link. Lately, plague I’ve been running analysis in parallel using Splus and Genstat. I was quite surprised with the results: the coefficients of the model were different but the predicted values were identical. After meditating about the wonders of statistical software (read #@$) for a while, I did remember about the default Helmert contrasts in Splus. In Helmert contrasts, the jth linear combination is the difference between the j+1st and the average of the first j levels. However, most statistical software (including Genstat and SAS) reports the results using Treatment contrasts.

Note to self: use treatment contrasts as default, so results from Splus are comparable with the ones obtained with other software. Change the defaults using the following code:

options(contrasts = c(factor="contr.treatment",
+ ordered="contr.poly"))

help
148.267365&spn=0.588701, find 1.246948&z=10&om=0″>Scamander, Tasmania

I spent a few days based in Scamander, North Eastern Tasmania. The drive up North with Rebecca and Andrew was quite pleasant; only three hours and we reached the first stopover. Note: this was written last Tuesday, but there was no way to connect to internet from the hotel.

In the last couple of months I came across two papers about the analysis of progeny trials that require some comment: one on diallels and one on clonal data. Both of them expand on the tricks and contortions required to run those analysis using SAS, specifically using proc mixed and proc iml.

I was quite surprised about the transformation of computational limitations of a specific piece of software (namely SAS) into research papers. Both problems can be tackled in one line of model specification in ASReml. Potentially, one could write a macro in MSWord for BLUP analyses, but is it worth doing it? So what is going on? It seems that being provincial and sticking to old school models pays on terms of boosting publication records. Please guys, just visit the ASReml cookbook and get a life!

Filed in geocoded, research, statistics No Comments

The publication game

17/10/2003

Several years ago, symptoms I think it was 1996, pills I was given a copy of A Ph.D. is not enough: a guide to survival in science (link to Amazon), which is an easy to read and entertaining book. Not that the information contained in it is groundbreaking (it should be of most use to some extreme nerds), but there are a few things that I still remember. For example, a fundamental principle, in preparing a talk, is never overestimate your audience and the concept of publon, the minimum publishable unit.

Publication is a funny game, because in most academic institutions is one of the basic components of the survival system (by the way, this is not my case). Because of this, the publon (quantum of publication) is dominant in scientific literature. A set of publons, a series of short papers, looks much better in your curriculum than the odd juicy paper. Unfortunately, that puts a lot of stress in the publication system, with thousands of journals trying to cope with the influx of tens of thousands of papers each year.

Journals take quite a long time to review the manuscripts, and we end up with not so interesting papers that take a long time to be published. Biometrics has an interesting document entitled Review times in statistical journals: Tilting at windmills? (PDF file) by Raymond J. Carroll, discussing strategies for Associate Editors and Referees with the aim to reduce publication time. In summary, editors should reject some papers without any additional review, while reviewers should focus in content rather than in correcting spelling or suggesting useless changes to the manuscript. Using this approach in forestry journals would make my life easier: I wouldn’t waste time reading manuscripts that will never be published and publication would be much more expeditious.

In summary, pushing for fewer and juicier papers, and streamlining the publication process would certainly benefit researchers.

Filed in research, writing No Comments