Contents of the ASReml Cookbook:
- Obtaining ASReml and its manual
- Using a decent text editor
- Using ASReml in a mac
- Take me to the recipes!
- Improving the cookbook
- Citing or referencing the cookbook
The cookbook is also available as a Single Page, which makes easier to print it as a single document.
ASReml is a very powerful statistical software developed by Arthur Gilmour from New South Wales Agriculture, with support from an international team of leading statisticians. It is specifically designed for fitting mixed models for large datasets, with unmatched model flexibility and high speed. It is far faster than SAS, S-Plus and similar software. I have a few reasons why I think that ASReml is the best software for genetic evaluation.
ASReml’s manual is the source of all knowledge, with over 200 pages. That is a bit of an overstatement, but it is certainly exhaustive and sometimes daunting. One of the problems when you start using ASReml is how do I start? How do I setup my models the way I used to in SAS / Genstat / DFREML / etc? I have trees, no animals, what do I do? I have spent a long time learning how to fit models with the software, and I have I decided to make some of the information available in this site, in case it can be of some use for you.
How do I obtain ASReml?
ASReml is now a commercial product. Trial (30 days) versions can be obtained from VSN’s International web site. The page Obtaining AS Reml provides full instructions for getting the software and the manual.
Using a decent text editor
To run an ASReml job you need to write an ASReml command file (the file with a .as extension). Hence, one of the first things you should get is a decent text editor. If you work in MS Windows you already now that Notepad is hopeless, and probably you do not want to spend any money. There are plenty of free or shareware editors around, but I recommend using Context, which is a free ‘ASREml aware’ programming text editor. There are a few instructions to Setup Context for ASReml use.
Can I use ASReml in my mac?
ASReml is supported natively in Windows and a few variants of Unix that do not include OS X (see Obtaining AS Reml for more details). However, there are two ways of running ASReml on Intel-based Apple computers (Macbook, Macbook Pro, Mac Pro and new mac minis and imacs):
- Use Bootcamp to boot your mac in one of the operating systems supported by ASReml. For example, you could boot using Windows XP and the mac would essentially be a windows machine. Now, why would you want to commit such a crime?
- Use a virtualization machine, for example Parallels, to have multiple operating systems running on your mac. In this case there is a windows containing a session of Windows (or Linux, or whatever) running inside OS-X. This is how I run ASReml in my Macbook Pro.
I have tried this only with the Windows version of ASReml, but I assume that it would work the same with the Unix versions. If you go for the second option be aware that you will require plenty of RAM; essentially you will be running two operating systems at once. With 1GB my system felt sluggish but with 1.5GB and higher it worked quite well.
Here is what you are really looking for! Below there are recipes to run the following types of analyses:
- Job Anatomy
- Basic structure
- Equation model description
- Univariate Analysis including:
- Some basic models
- Equivalent models
- Clonal data
- Multiple site, single trait
- Covariance Structures
- Multivariate Analysis:
- Single site, multiple traits
- Two sites, single trait treated as multivariate
- Estimating Heritability:
- Functions of variance components and .pin files
- Genetic correlations
- This section is in preparation and is incomplete
- Longitudinal Analysis:
- Longitudinal analysis in ASReml
- Random regression models
- Spatial Analysis
- Spatial analysis in ASReml
- Spatial analysis for irregularly spaced trees
- Data Tips
- Truncating the dataset
- Univariate to multivariate format
- Starting values: the apocryphal Dutch method
- Simulations Using SAS
- Simulations Using Python
- General Resources
- Other ASReml sites
- Race classification
- General information produced by the CRC-SPF
- Cooking Recipes, including some real recipes to avoid hunger while running ASReml
- Home made pizza dough and toppings
- Beef with plum sauce and Chinese greens
- Smoked chicken and cream pasta
The cookbook also includes interesting replies to ASReml discussion group posts. Note: I have not necessarily used or checked the advice:
- How do I fit Generalised Models?
- Binomial and Poisson models
- Problems with this type of analyses
- Problems Overlapping Design Matrices in genetic models
- More coming soon.
Improving the cookbook
Feel free to Contact Me if you have any suggestions about material that should be included here or, even better, if you have some code examples that you would like to share. If you have any problems reading these pages see the colophon.
Citing or referencing the cookbook
If the ASReml Cookbook was useful for your analyses, you may cite it in the following way:
- Author. (Date of publication, use last modified date). Title. Retrieved date of access, from URL. For example:
- Apiolaza, L.A. (February 2006). ASReml cookbook. Retrieved 18 February 2006, from http://uncronopio.org/ASReml/.
Copyright (1997–2007) by Luis Apiolaza, some rights are reserved.