BibTeX and Google Scholar

at 25 January 2008

Preference settings on different websites should be checked regularly. As an example, Google adds functionality to their sites continuously, and you can easily miss the improvement. I found out yesterday that Google Scholar has a time-saving option for LaTeX-users. The references can be exported in BibTeX format. Of course, maybe I am the last to know, but I will describe the procedure anyhow.

To add the link to the BibTeX-code, you simple vist the Google Scholar page. Next to the Search button there is link to Scholar Preferences. If you click that link you can see the list of options. At the bottom, you find the option Show links to import citations into. Just select it and you have added the functionality to Google Scholar. Of course, you can also select other export formats, such as Endnote or Refman.

Another option is the Library Links option. Currently, I have a link to, but it seems that it should be possible to add our local library. Does anybody know how to do it?

Hi everybody

at 03 December 2007

Most of you have probably seen me around the halls by now. My name is Jared O'Connell and I started with the Statistics & Decision Analysis group two weeks ago.

My background is Applied Statistics and Computer Science, which were my majors at the University of Western Australia. After finishing my bachelor's degree, I worked for three years at a government science body, the CSIRO, performing satellite imagery analysis (link). This work involved the analysis of large amounts of data using classification, robust regression, HMMs and parallel computing to make it all run fast enough!

I now will be working within the ILSORM project, looking at the relationship between progesterone, activity levels and reproductive status in cows. I look forward to working with you all.

Course in Generalized Linear Models with Biological Applications

at 30 November 2007

In spring 2008 (start: 25. February) our reserach group offers a course in generalized linear models with biological applications.

The course introduces the modeling (regression analysis) of non-normal observations as for example counts and proportions. Methods to handle correlated observations will also be introduced. The lectures are accompanied by computing exercises using the statistical package ‘R’. Due to its versatility and graphical capacities it has something to offer even to the experienced SAS user.

The course is open to everyone with basic statistical knowledge. The course is free of charge for PhD students. It is also free for students and employees affiliated to Aarhus University. The course is approved as a PhD course (10 ECTS points) at Aarhus University.

For additional information please check the course homepage

Best regards

Ulrich Halekoh

New versions of Windows Live Writer and JabRef

at 20 November 2007

Lars has previously blogged about Windows Live Writer and JabRef. Both programs have now been updated. Visit Writer Zone: Windows Live Writer: Out of Beta or the JabRef page at SourceForge to download the new versions.

How to reconfigure a keyboard

at 15 November 2007

Recently we held an the introductory R-course. In R you need to use the tilde (~) sign often. Everytime you specify a statistical formula, you write something like:

Y ~ Treatment + X

One of the participants had a keyboard on her (italian) laptop that had no '~' sign. As one of the participants could remember, that is no problem. You simply type the ASCII-code of '~' (126) on the numeric keypad while you hold down the 'Alt' key. And of course, on a laptop without a numeric keyboard you simply find the blue 'fn' key and the blue 'num lock' key and push them down simultaneously, then you type the ASCII code with the Alt key pressed, and then the blue 'fn' key and the blue 'num lock' key again. (If you forget the final part, 5t 5s act4a33y n4 *r6b3e0, s60e 6f the 2eys are s50*3y re*3aced w5th n40bers, oops - I meant to say, it is actually no problem, some of the keys are simply replaced with numbers).

The R-Help list had some discussion concerning this problem in 2004, where the solution above was suggested.

However, the satisfactory solution is to remap the keyboard. Microsoft has a utility program for doing this. You may download it from the Microsoft Keyboard Layout Creator. For Windows XP you probably need the old version (1.3), while Vista users can use version 1.4.

The instructions in the help menu are easy to follow. I'll just show a couple of screen dumps. First of all I load an existing keyboard via the File | Load existing keyboard option. I choose the Danish keyboard. The program then shows an image of the existing keyboard layout.

By selecting the different shift states, you may see the key mapping in the corresponding states. As an example, the AltGr shift state below.

In fact I have already changed the keyboard mapping. As you an see the keyboard now shows a '~' sign corresponding to the 'N' key. In order to obtain this mapping I simply clicked on the key in the screen image. A popup window allowed me to type the '~'-sign and he redefinition was made. (If your keyboard does not have the '~' sign you need to use the trick with the numeric keyboard and Alt 126 as described above).

Finally, you choose Project| Build DLL and setup Package, as described in Help file of the program. This produces an msi-file that can be executed and your new keyboard is installed.

So now I have a keyboard that produces a a tilde sign when I press AltGr+N. In contrast to the existing one (next to the Enter key in the right hand side) this one is not a dead key. I do not need to wait for another keypress to see the '~'sign.

Another option is to use e.g. AutoHotkey.

How to import SAS data set into R

at 07 November 2007

The import of data into R is still a bit complicated if the original data are stored in the SAS-data format. Though solutions have existed for a long time, see e.g. the R-documentation concerning Importing from other statistical systems, it is complicated to use these facilities. They are based on functions which need to call the SAS-program from R. The settings for doing this do not always correspond to the settings on the computers we use.

I have written a short note/web-page with focus on the export problem from the SAS point of view. The note compares three different intermediate formats: csv, xls and xport format.

In normal use, the route via the xls format seems best. Data are exported via SAS code similar to:

libname sasdata "C:/SASImport";
libname out Excel
data out.rimporttest;
set sasdata.rimporttest;

and imported into R via the read.xls command in the xlsReadWrite package.

Further detail in the note, which also includes R-functions. The note is also available as a pdf-file

AMORPH – Agricultural practise – mobility, availability and retention of phosphorus in soils

at 08 August 2007

The project will focus on the potentially mobile dissolved and colloidal P covering a broad range of agricultural soil types and tyr to investigate how aspects of agricultural practices influence the potential P mobility.

Our group will mainly be involved in analysing the plant available P (Olsen P) in order to describe how the plant available P depends on explanatory variables.

The project is lead by Gitte Rubæk (Department of Agroecology and environment)

NLES4 – Nitrogen Leaching from agricultural fields

The purpose of the project is to improve the existing NLES3 model for prediction of nitrogen leaching under different growing conditions

Our group will be responsible for the statistical analyses of leaching recorded in trials and on private farms.

The project is lead by Uffe Jørgensen (Department of Agroecology and environment)

IMPACT – Impacts and adoption to climate change in cropping systems

The purpose of the project is to analyse likely impacts of climate change on arable cropping systems in Denmark with particular reference to drop quality, N cycling, nitrate leaching and changes in occurrence of pests and diseases.

Our group will mainly be involved in the analyses of existing long term trial in order to evaluate the effect of climate on crop yield.

The project is lead by Jørgen E. Olesen (Department of Agroecology and environment)

Wink screensnapshot software

at 18 June 2007

Wink ( is a free software to catch screen-shots.

Main features:

  1. three modi: 1) take single screen shots 2) take shots at each mouse OR key action 3) take at real time. You can change between these modi in a session.
  2. You can choose to record a specific window only (for example slices) or the whole screen.
  3. You can edit the final screenshots: add voice, add text elements.
  4. You can interleave different sessions.
  5. The final formal is an adobe Flash swf-file, which is started via an html file. Any user is able to download Flash from Adobe.

Two commerical alternatives are camtasisa (microsoft about 300 dollar) and captivate (adobe about 600 dollar).

Captive seems to be more like wink, as it allows to take individual snapshots. It has the addtitional freature to allow interative learning facilitites as quizzies etc.

See for a comparison of both: