From: Peter Adam <peter.j.adam_at_GMAIL.COM>

Date: Wed, 18 Jun 2008 02:39:38 -0700

Date: Wed, 18 Jun 2008 02:39:38 -0700

Dear Auther and others:

I am working on bivariate analysis using tree (or animal) model

and in a puzzle about the R structure. In my data, trait A was

measured at sites 2-3-4, and trait B was measured at sites 1-3-4.

I would like to fit heterogeneous residual variances for different

sites. I therefore set the covariances to 0 for sites 1 and 2,

and also fix the variances to 0 for the combinations of site and

trait without data.

I first tried the following code:

!PART 1

trait_a trait_b ~ Trait Tr.site !r Tr.site.rep Tr.tree Tr.site.fam

4 2 3

1200 0 IDEN

Trait 0 US 0.1E-7 0.0 0.6748 !GFFU

1221 0 IDEN

Trait 0 US 0.8250 0.0 0.1E-7 !GUFF

3519 0 IDEN

Trait 0 US 0.8242 0.2106 0.5981

3507 0 IDEN

Trait 0 US 0.8286 0.2127 0.6065

......

and it worked as I expected:

Covariance/Variance/Correlation Matrix UnStructured Residual

0.1000E-07 0.000

0.000 0.6741

Covariance/Variance/Correlation Matrix UnStructured Residual

0.8353 0.000

0.000 0.1000E-07

Covariance/Variance/Correlation Matrix UnStructured Residual

0.8245 -0.1306

-0.9180E-01 0.5996

Covariance/Variance/Correlation Matrix UnStructured Residual

0.8289 -0.7723E-01

-0.5487E-01 0.6090

Then I changed the residual variance for trait A at site 1 from

0.1E-7 to 0.0.

!PART 2

trait_a trait_b ~ Trait Tr.site !r Tr.site.rep Tr.tree Tr.site.fam

4 2 3

1200 0 IDEN

Trait 0 US 0.0 0.0 0.6748 !GFFU

1221 0 IDEN

Trait 0 US 0.8250 0.0 0.1E-7 !GUFF

3519 0 IDEN

Trait 0 US 0.8242 0.2106 0.5981

3507 0 IDEN

Trait 0 US 0.8286 0.2127 0.6065

......

I noticed that instead of fixing it to 0, ASReml filled the first

variance with a non-zero value (0.3885):

Covariance/Variance/Correlation Matrix UnStructured Residual

0.3885 0.000

0.000 0.6741

Covariance/Variance/Correlation Matrix UnStructured Residual

0.8353 0.000

0.000 0.1000E-07

Covariance/Variance/Correlation Matrix UnStructured Residual

0.8245 -0.1306

-0.9180E-01 0.5996

Covariance/Variance/Correlation Matrix UnStructured Residual

0.8289 -0.7723E-01

-0.5487E-01 0.6090

I further changed the another 0.1E-7 to 0 as well, and ASReml failed

with the message: "REQUIRE !ASUV qualifier for this R structure". The

error message changed to "Error structures are wrong size" once I used

!ASUV qualifier (and added !f mv in the model as well).

So, how does ASReml treat 0s in R structure? What is the real

difference between 0 and a very small number like 0.1E-7? Why 0s are

ok for covariances but not for variances?

Thanks!

Peter Adam

Received on Fri Jun 18 2008 - 02:39:38 EST

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