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This page was updated on 2012-12-16 (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. Posts in my blog, this is where I update most frequently. It covers more advanced uses and comparisons with other software.
  2. Very basic usage.
  3. Specifying model equations.
  4. Univariate analysis, including basic equivalent models, diallels, clonal trials and multiple-site as single trait.
  5. Extracting results like variance components, fixed and random effects, etc, from the fitted model.
  6. Covariance structures.
  7. Multiple environments.

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.

Other resources

  1. The official ASReml-R reference manual (PDF file) at VSN international.
  2. The mixed-models-on-TAP website. This site, by the ASReml crowd, aims to introduce people to the analysis of mixed models. Most content is still under construction.
  3. Updates and beta (some times more like alpha) versions of ASReml-r are posted in mixed-models-on-tap and in austatgen (now deprecated although keeps on getting updated).
  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.