[Basta-users] out$lifetable errors

[Owen Jones]

When it is called from within the basta function, MakeLifeTable subsets the data to only include those individuals that are born within the study period.

You can run MakeLifeTable *after* basta has run, on the out$Xq matrix.

e.g. MakeLifeTable(out$Xq[1,])

In the case where you make all birth dates within the study period, and the error messages are not produced, a life table will be produced.

out$lifeTable (note the upper case T in table - you had a typo in your code).


Cheers,
Owen



On 7 Nov 2011, at 11:45, Cliff Cunningham wrote:

> Dear Fernando and Owen,
> 
> 	I get the "NULL" when I type
> out$lifetable
> 
> even  when I make all the birthdates at 1979 (within the time of the study), though these errors disappear:
> 
>>> .Warning messages:
>>> 1: In max(DeathAges, na.rm = TRUE) :
>>>   no non-missing arguments to max; returning -Inf
>>> 2: In max(wa) : no non-missing arguments to max; returning -Inf
>>> 3: In MakeLifeTable(x, ax = 0.5, n = 1) : NAs introduced by coercion
> 
> 
> 
> 	On the very bright side I was able to calculate a great life table by hand that made perfect sense when I used
> 
> out$Xq
> 
> 	to output all the ages at death.  This gave exactly the qx's I was expecting (since this example had 100% recapture rate, just to test the output).  
> 
> 	So its not that it wasn't calculating the ages at death.
> 	
> 	All the best!
> 
>    	Cliff Cunningham
> 
> 
>         Professor
> 	Biology Department
>     	Duke University
>         130 Science Drive
> 	Durham NC 27708
> 	Phone 919-660-7356
> 
> http://www.biology.duke.edu/cunningham
> 
> 
> 
> 
> On Nov 7, 2011, at 11:23 AM, Colchero, Fernando wrote:
> 
>> Dear Cliff,
>> 
>>    Were all birth times in 1978? If that's the case, then the life table cannot be constructed because it uses non-truncated individuals (i.e. only those that were born during the study). Still, we do have a bug, since the model should report that more explicitly. We'll try to fix it as soon as possible.
>> 
>>    Best,
>> 
>>    Fernando
>> 
>> ______________________________________________
>>  
>> Fernando Colchero
>> 
>> Max Planck Institute for Demographic Research
>> Konrad Zuse Str. 1, 18057, Rostock, Germany
>> Tel:  +49 (0) 381 2081 113
>> Fax: +49 (0) 381 2081 529
>> E-mail: Colchero at demogr.mpg.de
>> ______________________________________________
>> 
>> 
>> 
>> 
>> 
>> On Nov 7, 2011, at 11:03 AM, Cliff Cunningham wrote:
>> 
>>> Dear BaSTa,
>>> 	After several runs I have typed  out$lifetable and got the following
>>> 
>>> > out$lifetable
>>> NULL
>>> 
>>> 	I should report I got several warning messages (see bottom) when I ran the following: 
>>> Survival parameters converged appropriately. 
>>> DIC was calculated
>>> .Warning messages:
>>> 1: In max(DeathAges, na.rm = TRUE) :
>>>   no non-missing arguments to max; returning -Inf
>>> 2: In max(wa) : no non-missing arguments to max; returning -Inf
>>> 3: In MakeLifeTable(x, ax = 0.5, n = 1) : NAs introduced by coercion
>>> 
>>> 
>>> My code was as follows, 
>>> 
>>> out <- basta(object = Males.dat$newData, studyStart = 1979, studyEnd = 1982, burnin=1000 ,niter=10000, nsim=4, parallel=TRUE, ncpus=4)
>>> 
>>> 	In this one I had all the birthdays at 1978, and first captures in 1979.
>>> 
>>> 
>>> 
>>> 
>>> Here are the errors from the 
>>> Multiple simulations finished.
>>> Total MCMC computing time: 3.91 minutes
>>> 
>>> Thanks so much!!
>>> 
>>>    	Cliff Cunningham
>>> 
>>> 
>>>         Professor
>>> 	Biology Department
>>>     	Duke University
>>>         130 Science Drive
>>> 	Durham NC 27708
>>> 	Phone 919-660-7356
>>> 
>>> http://www.biology.duke.edu/cunningham
>>> 
>>> 
>>> 
>>> 
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> 
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