[R-sig-ME] Fitting cenexponential family in MCMCglmm

[Jarrod Hadfield]

Hi,

If the lamb is known to have died ymin and ymax should be equal and be the day on which the lamb died. If the lamb was alive at the end it should have 90 in ymin and Inf in ymax. If the lamb was culled it should have the day of culling as ymin and Inf as ymax (assuming the day on which it was culled gives no information on how long it would have lived had it not been culled).

Cheers,

Jarrod


From: R-sig-mixed-models <r-sig-mixed-models-bounces using r-project.org> on behalf of Indrasen Chauhan <indrasenchauhan using gmail.com>
Date: Friday, 2 December 2022 at 12:44
To: r-sig-mixed-models using r-project.org <r-sig-mixed-models using r-project.org>
Subject: [R-sig-ME] Fitting cenexponential family in MCMCglmm
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Dear sirs,

I am estimating the heritability of survival of Malpura sheep from birth to
weaning (90 days), three to six months, six to twelve months and birth to
twelve months for a twenty year data set. The data has a right censored
exponential data as a response variable.

The data have following common structure:

$ itag    : int  2890 2891 2892 2893 2894 2899 2901 2902 2903 2905 ...

 $ stag    : int  2602 2258 2248 2602 2602 2599 2667 2639 2667 2599 ...

 $ dtag    : int  2422 2720 2199 2483 2659 2638 1807 2488 1823 2082 ...

 $ season  : chr  "Winter" "Winter" "Winter" "Winter" ...

 $ sex     : chr  "Female" "Female" "Male" "Male" ...

 $ tyb     : chr  "Single" "Single" "Single" "Single" ...

 $ ewt     : num  26 33.4 31.4 34 29.8 29 28 28.4 34 28.5 ...

 $ bwt     : num  2.6 3.2 3 3.8 2.8 3.4 2.9 2.4 3.2 3 ...

 $ dtd    : chr  "2670" "1966" "444" "1442" ...

 $ cens    : int  0 0 0 0 0 0 0 0 0 0 ...



�itag�, �stag� and �dtag� are the identities of individuals, sire and dam,
respectively. �Season�, �sex�, �tyb� (type of birth), �ewt� (ewe weight at
the time of lambing), and �bwt� (birthweight) are the covariates for the
model. �dtd� (response variable) is the days to survival for the specific
duration of the study, ranging from 1 to 90 days for birth to weaning data.
�cens� is the censoring code. For birth to weaning data, the lambs alive at
the end of weaning (90 days) are recorded as �right censored�, and time of
failure of such lambs is taken as 90 days. Moreover, the lambs which are
removed from the flock before weaning due to reasons other than death
(e.g., culling) are also recorded as �right censored� (in Cox regression).

In mailing lists on MCMCglmm, I have found the following information:

m1<-MCMCglmm (cbind (ymin, ymax) ~1, family="cenexponential", data=dat)

(https://stat.ethz.ch/pipermail/r-sig-mixed-models/2010q4/004933.html)

I am taking example of birth to weaning data.

I have doubts on the following aspects:

(1)    Will the �ymax� be equal to 90 days (days to weaning) or equal to
the maximum number of days an animal survives even after weaning? What
about the information about animals which are still in the flock at the
time of data collection? The data on such animals are right censored in Cox
regression. What to do with data on such animals while estimating
heritability by using MCMCglmm? Will �dtd� contain data (days to survival)
about every animal including the animals which are still in the flock at
the time of data collection or for only the animals which died before the
end of weaning?

(2)    What about the data about the lambs which are removed from the flock
before weaning due to reasons other than death (e.g., culling)?

(3)    How to set up data (�dtd�) for left censored and left truncated
information?

(4)    What to do about censoring code. I could not find any information
about this anywhere for MCMCglmm.


Anticipating response at the earliest.

With kind regards.

--
Dr. Indrasen Chauhan
Scientist, ICAR-IVRI,Mukteshwar
Nainital,Uttarakhand-263138 (INDIA)
Mobile:9461883473,8910856302

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