Re: Asreml for phenotypic plasticity

From: <arthur.gilmour_at_DPI.NSW.GOV.AU>
Date: Thu, 30 Mar 2006 17:34:09 +1100

Dear Mellissa

I agree with Brian.
Try the following coding to allow a correlation between slope and

PD ~ mu AGE sCONES !r !{ newid CONES.newid !} DAM YR Byear
0 0 1

newid 2
2 0 US !GP
0.001 0.01
newid 0

The analysis will be on the GAMMA scale so the variance components are
relative rather than absolute.

The .sln file should have an intercept and slope for each 'newid'

You have defined AGE as a FACTOR with !A which is likely to have its
levels in an unnatural order.

I imaging making CONES a factor and interacting it with newid might just
generate a term equivalent to the residual
unless there are multiple observations for an individual with the same
value for CONES

The F-statitics do relate to Wald tests. ASReml2 will often be able to
calculate the residual degrees of freedom
to complete the F-test but ASReml1.1 cannot.

I'm unclear what your are plotting from the .yht file. Residual vs Fitted
I would not expect to see a relationship unless you have a pedigree on
in which case it would be an artefact of the model.

 Check out
for my personal greetings and update.

I thank God for His mercy through Jesus Christ.

Arthur Gilmour PhD
Principal Research Scientist (Biometrics)
NSW Department of Primary Industries
Orange Agricultural Institute, Forest Rd, ORANGE, 2800, AUSTRALIA

fax: 02 6391 3899; 02 6391 3922 Australia +61
telephone work: 02 6391 3815; home: 02 6364 3288; mobile: 0438 251 426
The ASReml discussion group is at
To join it,

Proposed travel:
ASReml workshop CSIRO 16-18 May
[IBC Quebec 16-21 July 2006]
WCGALP8 13-18 Aug Brazil
You wrote:
Hi all,
I am trying to analyse variation in phenotypic plasticity using Asreml. I
multiple measurements of parturition date for ~270 females, and I am using
interaction between food abundance (CONES) and individual identity as the
of the reaction norm (i.e. CONES.newid). I find I get quite different
in the asr file if I used standardised cones (centred on zero). Should
this be
the case?

Also, I find I have only one estimated effect size for CONES in the sln
although AGE (also a fixed effect) has an effect size for each age
Would making CONES a factor change this?

I would also like to know how the analysis of variance presented in the
asr file
relates to Wald stats (if it does!). Can I use this to compare models with
different fixed effects?

Finally, I find no significant variation in phenotypic plasticity - but
when I
plot the values from the yht file for the best-fitting model, it looks as
though there is significant variation. Can anyone suggest why this would

My job file is as follows:
 newid !P #identity of individual
 YR !A #year of parturition
 AGE !A #age of individual
 CONES #measure of food abundance
 PD #parturition date in Julian days
 DAM !P #identity of individual's mother
 sCONES #standardised cone number
 sAGE #standardised age of individual
 Byear !A #birthyear of individual
PD ~ mu AGE sCONES !r newid DAM CONES.newid YR Byear
1 1 5 !STEP 0.001
0 0 IDEN 382

newid 1
newid 0 IDV 56

DAM 0 IDV 21

CONES.newid 2

YR 1
YR 0 IDV 21

Byear 1
Byear 0 IDV 21 #!GP

Thanks in advance for any suggestions.

This message is intended for the addressee named and may contain
confidential information. If you are not the intended recipient or
received it in error, please delete the message and notify sender. Views
expressed are those of the individual sender and are not necessarily the
views of their organisation.
Received on Tue Mar 30 2006 - 17:34:09 EST

This webpage is part of the ASReml-l discussion list archives 2004-2010. More information on ASReml can be found at the VSN website. This discussion list is now deprecated - please use the VSN forum for discussion on ASReml. (These online archives were generated using the hypermail package.)