Re: Asreml for phenotypic plasticity

Dear Asremlers

The values I get in the .sln file seem very small, whether or not I use a random
regression - are the values in the .sln file residuals from the fixed effects?
(e.g. I would expect an intercept of ~150, but the intercepts are more in the
range of 0.3362+-4.366).

Melissa Gunn
University of Sheffield

> Dear Mellissa
>
> I agree with Brian.
> Try the following coding to allow a correlation between slope and
> intercept:
>
> PD ~ mu AGE sCONES !r !{ newid CONES.newid !} DAM YR Byear
> 0 0 1
>
> newid 2
> 2 0 US !GP
> 0.2
> 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
> value??
> I would not expect to see a relationship unless you have a pedigree on
> newid
> in which case it would be an artefact of the model.
>
> Check out http://www.cargovale.com.au/
> for my personal greetings and update.
>
>
> I thank God for His mercy through Jesus Christ.
>
> Arthur Gilmour PhD
> mailto:Arthur.Gilmour_at_dpi.nsw.gov.au
> 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
>
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>
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> <><><><><><><><><><><><><><><><><><><><><><><><><>
> You wrote:
> Hi all,
> I am trying to analyse variation in phenotypic plasticity using Asreml. I
> have
> multiple measurements of parturition date for ~270 females, and I am using
> the
> interaction between food abundance (CONES) and individual identity as the
> slope
> of the reaction norm (i.e. CONES.newid). I find I get quite different
> answers
> 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
> file,
> although AGE (also a fixed effect) has an effect size for each age
> presented.
> 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
> be?
>
>
> 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
> !MVREMOVE !MAXIT 1000
> 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 1
> DAM 0 IDV 21
>
> CONES.newid 2
> CONES 0 US !GP
> 1.5
> newid
>
> YR 1
> YR 0 IDV 21
>
> Byear 1
> Byear 0 IDV 21 #!GP
>
> Thanks in advance for any suggestions.
> Melissa
>
>
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Received on Sat Apr 03 2006 - 12:19:16 EST