Re: [Fwd: asreml]

Hi,
It would really help to include th.as file or relevant parts that declare the terms in the model, particularly T1, time and animal?

Animal should be declared with !p if you want to get the genetic variance, permanent environment variance and temporary environment variance.

>One potential issue is that some individuals are present
>in both time periods, but I can't see why this should cause
>singularities.

Also, can you provide a clear picture of your design?
In particular, what is the connectivity between the two time points?
Your statement suggests that there are very few animals that connect time points. If so, then that really, truly messes up repeatability models and models with covariance between time points.

I think that you would be better off treating the two time points as different traits with a genetic covariance but no residual covariance. This is essentially what the first model is doing but without any structures, it is difficult to see this.

Bruce

---- Original message ----
>Date: Tue, 6 Feb 2007 14:08:32 +1100
>From: arthur.gilmour_at_DPI.NSW.GOV.AU
>Subject: Re: [Fwd: asreml]
>To: ASREML-L_at_AGRIC.NSW.GOV.AU
>
>Dear
>
>re:
>
>I'm fitting a model with an animal effect and a permanent environment
>effect. Individuals are spread over two time periods and I want to
>test whether a model with time specific animal and PE effects is
>better than a model where both periods are treated equally. For
>univariate models this is fine:
>
>
>T1 ~ mu time !r at(time,1).animal at(time,2).animal at(time,
>1).identity at(time,2).identity
>
>versus
>
>T1 ~ mu time !r animal identity
>
>
>
>Comments:
>
>1. The univariate models reported assume repeated measures
>2. The comparison across time assumes no genetic links between times.
>Otherwise,
>it would be better to include a correlation.
>3. Also, if you are allowing different genetic and PE variances, it would
>be better
>to also allow different residual variances.
>
>Consequently, my version of the first model might end up being
>
>T1 ~ mu time !r time.animal time.identity !uni(time,2) !GU
>0 0 2
>time.animal 2
>time 0 US !GP # assuming genetic links, else DIAG
>.1 .01 .1
>animal 0 AINV
>
>time.identity 2
>time 0 DIAG .1 .1 !GP
>identity
>
>===========================
>You further wrote
>If I fit a multivariate model either the animal or the PE effects are
>flagged as singular depending on which order the terms are fitted. I
>am confident that these parameters can be estimated from the data
>because a) all (3) traits have the same pattern of missing data so if
>the univariate model is idenitifiable the multivariate model should
>be and b) I can fit a multivariate model for each time period
>separately by generating two data sets and all model parameters are
>estimated. One potential issue is that some individuals are present
>in both time periods, but I can't see why this should cause
>singularities.
>
>The most likely cause is that ASReml may not associate the A inverse with
>the Tr.time.animal term
>when written as a G structure unless it is explicity declared in the
>appropriate fashion (see eaxample above).
>
>My attempt at your model is
>
>T1 T2 T3 ~ Trait time Tr.time !r Tr.time.animal Tr.time.identity
>2 2 2
>zzz # Insert number of records at time 1 after sorting the data
>Trait 0 US !GP
>6*0
>
>zzz # Insert number of records at time 2 after sorting the data
>Trait 0 US !GP
>6*0
>
>Tr.time.animal 3
>Trait 0 US !GP
>6*0
>time 0 CORUH !GPPF
>.1 1 1
>animal 0 AINV
>
>Tr.time.identity 3
>Trait 0 US !GP
>6*0
>time 0 CORUH !GPPF
>.1 1 1
>identity
>
>
>This is a fairly sophisticated model, so may need better starting values
>than I've given.
>If you only have a little bit of data, it may be too sophisticated for
>your data.
>But, according to my understanding of your email, this is what you are
>moving towards.
>
>May you know Jesus Christ and His blessing in 2007,
>
>Arthur Gilmour, His servant .
>
>PS My Mixed Model Regression Mapping paper is now available at
>http://dx.doi.org/10.1016/j.csda.2006.12.031
>
>Profile: http://www.dpi.nsw.gov.au/reader/17263
>Personal website: http://www.cargovale.com.au/
>
>mailto:Arthur.Gilmour_at_dpi.nsw.gov.au, arthur_at_cargovale.com.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
>
>ASREML 2 is now available from http://www.VSNi.co.uk/products/asreml
>The ASReml discussion group is at ASREML-L_at_dpi.nsw.gov.au
>To join it, mailto:arthur.gilmour_at_dpi.nsw.gov.au
>Cookbook: http://uncronopio.org/ASReml
>
>Proposed travel:
>ASReml workshop (Forestry) 16-18 April Tasmania
>Biom Brch meet 2-4 May
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>AAABG 24-26 September Armidale
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Received on Sat Feb 06 2007 - 08:55:14 EST