# Re: Survival analysis using random regression

From: Arthur Gilmour <arthur.gilmour_at_CARGOVALE.COM.AU>
Date: Fri, 16 Oct 2009 21:35:37 +1100

Dear Jose

I suspect there are several forms of survival analysis.
I understand in your case that each individual is represented by 52
lines of data and survival switches from 1 to 0 somewheerre through the
period of 52 days.

Do you have a reasonable number of families (= dams I gather)

Assuming you have a good number of individuals,
I would probably start by looking at the overall profile of survival
Some kind of sigmoid curve is more likely is it not.

Then I would add ID to the model since this represents just a mean
shift. Then add dam to see if there is a genetic component to the
individual vasriation.

Only if you have a lot of individuals and families would I attempt the
change of slope at the genetic level.

See below

On Fri, 2009-10-16 at 01:19 +0100, jozzeman wrote:
> Hi,
>
> I'm trying to analyse survival data using a random regression model,
> but I have some problems interpreting the results. The data structure
> in the data file is as follows:
>
> ID father mother GDP1 Tank GDP2 day SR
> A440 1 3 0.8 1 0.2 1 1
> A440 1 3 0.8 1 0.2 2 1
> A440 1 3 0.8 1 0.2 3 0
> : : : : : : : :
> : : : : : : : :
> A440 1 3 0.8 2 0.2 52 0
> B550 1 3 0.5 2 0.4 1 1
> B550 1 3 0.5 2 0.4 2 1
>
>
>
>
> Reading the data is as follows:
>
> Survival analysis
> ID !P
> father
> mother
> GDP1 !m-9.9 # average daily gain before challenge to disease
> Tank # 2 levels
> GDP2 !m-9.9 # average daily gain after challenge to disease
> day # days of challenge tests (from 1 to 52)
> SR # survival score at a given day (1 or 0 depending if individual
> is alive or dead in a specific day)
> sr2.txt !ALPHA !REPEAT
> sr2.txt !NODISPLAY !MVINCLUDE !SKIP 1 !maxiter=500
>
> I started fitting the follow model:
>
> SR ~mu pol(day,1)*Tank !r pol(day,1).mother !f mv

For this to work, 'mother' should be a 'FACTOR'.
but I think the model needs ide(ID) first.

> 0 1 1

This shuld be
0 0 1
>
> pol(day,1).mother 2
> pol(day,1) 0 US .1 .01 1 !GP
> mother
>
> I am interested in estimating the genetic variance of the family (full
> sibs) this is why I am including only the random effect associated
> with mother effect.
>
> Am I in the right way?
See above
> See above
>
> Can I use !BINOMIAL and !LOGIT qualifiers in the model in order to
> take account the binary nature of the trait?
>
YES but I would concentrate on a plausible model on the 0,1 scale first.

> How can I estimate heritabilities for SR?
>
Lets get the model sorted, and sensible from a genetic perspective
first. Then it should be clearer.

> How can I fit a multivariate analysis for estimating the genetic
> correlation between SR and GDP2?
>
> I would appreciate very much any suggestions or comments about the
> coding for the analysis.
>
>
>
>
>
>
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>
>
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```--
Best Wishes,
Arthur Gilmour
School of Computing and Mathematics
Charles Sturt University
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Received on Sat Oct 16 2009 - 21:35:37 EST

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