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This page was updated on 2010-04-24 (NZST) and is tagged asreml, statistics, software.

asreml-r cookbook

Since I run all my non-genetic statistical analyses in R and created the asreml cookbook in 2001, I thought it would be useful to 'translate' the cookbook to asreml-r, the R package version of asreml.

I see this document as providing an entry point to R for traditional asreml users and to asreml for traditional R users (used to nlme or lme4).

The translation effort is relatively recent, so these pages are in a state of disarray. Another difference is that I discovered that there were several users outside tree breeding—mostly animal and crop breeders—that were using the cookbook as a 'quick start', so I will try to cover a few things outside tree breeding. In addition, we have the crowd applying quantitative genetics to study natural populations and evolution; incidentally, we used asreml to study the genetics of personality of squid around 2005-2006 (see my publication [27]).

If you see this document (both structure and content) changing often take it as good news; that would mean that I am busy typing stuff. The notation of asreml-r is relatively new to me, so I need to rediscover how to do things in this new beast.

Recipes

  1. Very basic usage.
  2. Specifying model equations.
  3. Univariate analysis, including basic equivalent models, diallels and clonal trials.
  4. Extracting results like variance components, fixed and random effects, etc, from the fitted model.
  5. Covariance structures.
  6. Multiple environments.

Other resources

  1. The official asreml-r reference manual (PDF file) at VSN international.
  2. Updates and beta (some times more like alpha) versions of asreml-r are posted in austatgen.
  3. Installation instructions for Linux, OS X and Windows are here
  4. The R wiki contains a brief and clear tutorial written by Kevin on fitting a linear model with asreml-r.
  5. The Wild Animal Modeling Wiki (WAMWiki, Isn't that a cool name?) contains tutorials for several programs, including asreml-r. Those tutorials support a good review paper (available in the site) on applications of animal model BLUP in ecology.
  6. A 2007 presentation (PDF 1.9 MB) by David Butler on 'Asreml-R: an R package for mixed models using residual maximum likelihood'. It provides a broad overview of asreml-r syntax and capabilities.
  7. The asreml-on-TAP website (currently under construction).

Getting help

If you are stuck preparing your analysis, please ask the question(s) in the asreml forum. I barely have time to run my own analyses; I cannot provide direct help on asreml.