Sweave (bash) shell script II

Fixed buglet with --noquiet, -nq option. Fixed version is available here. I will not post this version to CRAN, not yet.

Sweave (bash) shell script

My Sweave.sh (bash) shell script eases the compilation of Sweave (link1, link2) file to Postscript or PDF format i.e. Sweave --> LaTeX --> Postscript/PDF. Although, this seems an easy task, it can get quite involved, since there are many ways and glitches on how to compile LaTeX (LaTeX web page, Wikipedia) source file. For example:

• LaTeX --> PS via texi2dvi or latex and dvips and then ps2pdf for PS --> PDF,
  
• LaTeX --> PDF via texi2pdf or pdflatex.
  

Until now Sweave.sh worked only with Sweave source files i.e. a mix of LaTeX and R code. Today I have modified it in such a way so that it can also work with LaTeX file only. Now I can easily type

Sweave.sh --noweave -otld file.tex

to compile file.tex to PDF and open it directly in default PDF previewer. New version will be posted on CRAN. For the impatient I uploaded the script to my webpage.

See also:

• Using Sweave with LyX
• Computer Algebra System (CAS) in LyX via Ryacas

Course: Design and Economics of Animal Breeding Strategies

John P Gibson and Jack C M Dekkers put on the web course notes for the course

Design and Economics of Animal Breeding Strategies

Two new chicken breeds for welfare friendly market

UK market will get two breeds that target welfare friendly market. Everything for the buyer! Original news.

Honey bee genetics

This post is for keeping track of writings about genetics & breeding in honey bee. Btw. Germany has BLUP evaluation for bees - link.

First some slovenian honey bee sites:

• Honey bee organization in Slovenia
• Museum
  

Some notes on genetics in bees from Germany:

• Zucht und Genetik der Honigbiene
• Entwicklung von geeigneten Zuchtwertschätzmodellen für die Honigbiene
• Selektion von varroatoleranten Honigbienen unter Nutzung drohnenbrütiger Arbeitsbienen
• Anwendung molekulargenetischer Methoden in der Zucht auf Varroatoleranz
• Berechnung von Erblichkeiten und genetischen Beziehungen zwischen Eigenschaften der Honigbiene

Some relevant papers:

• 1950 INBREEDING AND HOMOZYGOSIS IN BEES
• 1950 MATING SYSTEMS IN HONEY BEES
• 1990 On the relative importance of queens and workers to honey production
• 1990 Heritabilities for several colony traits in the honeybee (Apis mellifera carnica)
• 1991 Genetic correlations among several colony characters in the honey bee (Hymenoptera : apidae) taking queen and worker effects into account
• 1991 Selection for high and low, colony weight gain in the honey bee, Apis mellifera, using selected queens and random males
• 1992 Five years of bi-directional genetic selection for honey bees resistant and susceptible to Varroa jacobsoni
• 1999 Schätzung von Populationsparametern für die Toleranz der Honigbiene (Apis mellifera carnica) gegenüber Varroa jacobsoni Oudemans
• 1999 Selecting honey bees for resistance to Varroa jacobsoni
• 2000 Heritability of the Varroa-specific hygienic behaviour in honey bees (Hymenoptera: Apidae)
• 2007 Genetic evaluation in the honey bee considering queen and worker effects - A BLUP-Animal Model approach

On genomic matrices:

• 1985 Efficient selection rules to increase non-linear merit: application in mate selection - they say "The genomic tabular method can also be adapted to non-diploid individuals (e.g. bees are diploid or haploid)", they also give a recursive form to get gametic matrix
• 1993 Analysing gametic variation with an animal model
• 2002 Inverse of gametic relationship matrix

Genome stuff:

• Honey bee genome project
• SNP data
• Honey Bee Genome Publication and Press Portal
  


• beeBase

Razno:

• Sex-gene problem: Insights into honey bee sex gene could bring sweet success in breeding

Free classic music

Do you like to listen to some classic music while working with the computer? Try:

http://www.beethoven.com

P.S. Works smoothly also with my Ubunut Linux setup

Firefox extensions

I use the following Firefox extensions:

• GooglePreview - nice preview of search hits
• Gmail Space - use Gmail as a web disk
• FireFTP - FTP client in FF
  
• Foxmarks - sync bookmarks between various computers
• PDF download - decide what to do when you click on PDF download
• Download Statusbar - see downloads in the statusbar
  
• Add bookmark here - put bookmark where you want
• Next please - open next page of search hits
• ForecastFox - weather
• Firebug - web devel
• Web developer - web devel
• ieTab - open in IE tab
• FirefoxView - open in FF
• JSView - view JS and CSS files
  
• View source chart - should be clear
  

Unilever and McDonalds change to free-range eggs

From WorldPoultry.net ...

Heritability estimates are dependent on the model

I frequently realize that heritability estimate is dependent on the model used for the estimation. I have in mind mixed/hierachical/multilevel model. You can play with adding or removing "fixed" effects as noted by Wilson, but you can also play with adding or removing "random" effects or even moving effects between "fixed" and "random" set of effects.

Bob's comment on Hill et al. Data and Theory Point to Mainly Additive Genetic Variance for Complex Traits

Bob has blogged about recent paper by Hill et al. in PLOS about variance components of genetic variance of complex (quantitative) traits. He argues that things are not so simple as Hill et al. state.

Opening farm subsidies to public scrutiny

Mariann Fischer Boel has blogged about opening farm subsisides to public in detail on the internet by the end of April next year. More ...

My webpage

I decided to move my (now old) webpage to Google pages. I did this move, since I find editing Google pages very easy and slick. However, file handling is quite limited. You can easily upload any file you want, but you can not create folders and there is a disk quota. Therefore, I decided to use Scribd for file sharing. Scribd offers unlimited storage for free and is also very easy and slick to use. I have started to migrate all my writings and talks to Scribd and made link on writings page.

Course and Workshop on Whole Genome Association and Genomic Selection

International postgraduate course and workshop

Whole Genome Association and Genomic Selection

September 1-8, 2008, in Salzburg, Austria

http://www.nas.boku.ac.at/12100.html

Use of genotype probabilities in selection on PrP genotype in sheep

I have finished paper on use of genotype probabilities in selection on PrP genotype in sheep. PrP genotype is one of the main factors for susceptibility to scrapie in sheep. Here is the link to the last version of the paper. And the abstract:

PrP genotype probabilities for ungenotyped animals of Jezersko-Solcava sheep breed were calculated. Data consisted of 10,429 animals among which 3,669 had PrP genotype data. There were 2,673 live ungenotyped animals. Five PrP haplotypes were present with the following frequencies: ARR 0.174, AHQ 0.074, ARH 0.083, ARQ 0.632, and VRQ 0.037. All 15 PrP genotypes were found. Iterative allelic peeling with incomplete penetrance model as implemented in GenoProb program was used for calculation of PrP genotype probabilities. There were only some additional PrP genotype and NSP type identifications with high probability. Main reasons for a low number of additional identifications can be attributed to large number of haplotypes with moderate frequencies, incomplete penetrance model, uniform prior, and inherently pedigree and genotype data structure. Incomplete penetrance model caused inflation of small probabilities but has proved to be very useful for field data where conflicting data rise due to pedigree of genotype errors. Novel parameters (maximal NSP type, average NSP type and its variance and accuracy) are proposed that make use of PrP genotype probabilities and can facilitate selection for scrapie resistance. Parameters were derived with emphasis on practical implementation of selection schemes based on NSP types. Maximal NSP type can be used to infer maximal potential scrapie susceptibility of individual ungenotyped animals as well as for whole flocks. Average NSP type makes full use of all PrP genotype probabilities and is the most useful and practical parameter for selection on NSP type and therefore PrP genotype. In addition, accuracy of average NSP type should also be used as selection criteria in order to assess the variability of average NSP type.

Populacijska genetika in selekcija domačih živali

Pred časom sem že postavil spletno stran za objavo gradiva za vaje pri predmetu populacijska genetika in selekcija domačih živali. Spletna stran se nahaja na mojih spletnih straneh pri Google-u:

http://gregor.gorjanc.googlepages.com/popgen

Danes smo si s študenti ogledali en praktičen in zanimiv primer, kako lahko vplivamo na letni genetski napredek. Ja, primer sem povzel po knjigi "Understanding Animal Breeding" od Bourdon-a. Sicer bolj uporabljamo "zeleno" knjigo "Introduction to Quantitative Genetics" od Falconer-ja. Za zaključek pa še povezava do prispevka o tem avtorju in njegovi knjigi.

Alternativa kastriranju prašičev pitancev

Chicory roots can replace castration
http://www.agrsci.org/ny_navigation/nyheder/nyheder/chicory_roots_can_replace_castration

Good news for male pigs – castration not necessary
http://www.agrsci.org/ny_navigation/nyheder/nyheder/good_news_for_male_pigs_castration_not_necessary

Uspešnost selekcije mlečnega goveda v ZDA itd.

G. E. Shook
Major Advances in Determining Appropriate Selection Goals
http://jds.fass.org/cgi/content/full/89/4/1349

Vpliv seksiranega semena na rejo mlečnega goveda

De Vries in sod. (2008) so raziskali možni vpliv seksiranega semana na rejo mlečnega goveda.

Exploring the Impact of Sexed Semen on the Structure of the Dairy Industry
http://jds.fass.org/cgi/content/full/91/2/847

Histogram v živo

Hardy-Weinberg

Hardy, Weinberg and Language Impediments
http://www.genetics.org/cgi/content/full/152/3/821

PrP allele (haplotype) and genotye frequencies in sheep II

I wrote about better display of PrP haplotype and genotype frequencies in last post. I have proposed a set of histograms instead of a table. However, parallel plot (R example 1, R example 2, random web article) is even better. Here is my attempt to use it on data compiled by Lühken et al. (2008):

• parallel plot of allele (haplotype) frequencies
• parallel plot of genotype frequencies

There is still room for improvement of the plot i.e. axis, ticks, ... For example, I would prefer to have 0-100 % scale on y axis. Anyway, the idea of parallel plot for haplotype/genotype frequencies in case of many haplotypes/genotypes should be clear. Here is also the data and R code to produce the plots.

PrP allele (haplotype) and genotye frequencies in sheep

Lühken et al. (2008) published estimates of PrP allele (haplotype) and genotye frequencies in for 56 sheep breeds in Europe and Middle East. They made a huge one-page table with all the numbers. Gosh, it is hard to read that table! There is to much info. It would be much better if they would plot this data. Well, I did and I think it is much more informative. I just copied their table into a spreadsheet and used R to do the plotting

• plot of allele (haplotype) frequencies
• plot of genotype frequencies

Browse Happy

http://browsehappy.com

Some hot animal science from Wageningen

Animal Science Group at Wageningen has a nice newsletter with hot news in animal science. Here is a list of link to newsletters:

• Newsletter 7
• Newsletter 6
• Newsletter 5
• Newsletter 4
• Newsletter 3
• Newsletter 2
• Newsletter 1
  

One more statistical package

I just came across another statistical package - aML.

Genetic diversity in human

There is a nice review paper "Going the distance: human population genetics in a clinal world" by Handley et al. They have a nice picture of earth globe with routes of colonization and genetic diversity. If you have access to Trends in genetics, these two links are very informative:

• globe picture
• relationship between genetic distance and distance
  

Lessons learned from the dog genome

Wayne and Ostrander wrote a paper "Lessons learned from the dog genome". Here is their abstract: "Extensive genetic resources and a high-quality genome sequence position the dog as an important model species for understanding genome evolution, population genetics and genes underlying complex phenotypic traits. Newly developed genomic resources have expanded our understanding of canine evolutionary history and dog origins. Domestication involved genetic contributions from multiple populations of gray wolves probably through backcrossing. More recently, the advent of controlled breeding practices has segregated genetic variability into distinct dog breeds that possess specific phenotypic traits. Consequently, genome-wide association and selective sweep scans now allow the discovery of genes underlying breed-specific characteristics. The dog is finally emerging as a novel resource for studying the genetic basis of complex traits, including behavior".

Progress in mapping sheep genome

http://www.engormix.com/e_news_view.asp?news=12256&AREA=OVI

LaTeX and Windows

Two pages (one static web page and blog post linking to the first) with LaTeX and Windows comparison:

• http://www.johndcook.com/blog/2008/04/03/microsoft-word-and-latex/
• http://www.ifs.hr/~mpinter/miktex.html

I think that blog spot is very relevant!