[Basta-users] Monthly capture history; 0 birth or death information

[Fernando Colchero]

Hi Ken,

  Sorry (again) for the late reply. I attached a code to simulate BaSTA like data for a Gompertz model, let me know if this helps. 

   About the interpretation of the parameters, here is a summary:

   exp(a0) + c + exp(b0) provides the baseline mortality at age x, commonly it is dominated by exp(a0) + c. The parameter a1 is always preceded by a negative sign and it controls the speed at which infant mortality declines. The b1 parameter controls the speed at which adult mortality increases, so it can give you a measure of the ageing rate. Let me know if this clarifies a bit.

Best,

   Fernando

Fernando Colchero
Associate Professor
Department of Mathematics and Computer Science
Max-Planck Odense Center on the Biodemography of Aging

Tlf.               +45 65 50 23 24
Email           colchero at imada.sdu.dk <mailto:colchero at imada.sdu.dk>
Web             www.sdu.dk/staff/colchero <http://www.sdu.dk/staff/colchero>
Pers. web    www.colchero.com <http://www.sdu.dk/staff/colchero>
Adr.              Campusvej 55, 5230, Odense, Dk

University of Southern Denmark

> On 27 Feb 2018, at 18:49, Ken Honeycutt <rkenhoneycutt at gmail.com> wrote:
> 
> Fernando,
> 
> Thanks for your response and for sending along the latest BaSTA version, especially the bit about using "recaptTrans." I tried that and it worked well. 
> 
> I do have a couple more questions.
>  
> First, is your R-code to simulate populations (as in your 2012 J of Animal Ecology paper) publicly available somewhere? I'm thinking simulating populations would help with confidence in my results.
> 
> Second, I'm having a little trouble interpreting the meanings of parameters from the Gompertz bathtub model (I believe there are alpha0, alpha1, beta0, beta1, and c). I see these are described mathematically in the BaSTA MME supporting information, but I'm having trouble visualizing the meanings. Specifically, I'm wondering at what values would these parameters represent a bathtub shape for mortality.
> 
> Thanks,
> Ken
> 
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> On Sat, Feb 24, 2018 at 12:58 AM, Fernando Colchero <colchero at imada.sdu.dk <mailto:colchero at imada.sdu.dk>> wrote:
> Hi Ken,
> 
>    Sorry for the late reply. You can use months, just bearing in mind that the parameters correspond then to the distribution of ages at death in months, not in years. There is an argument that you can use for the recapture probability changes during the months you didn’t sample, which is “recaptTrans”. That argument takes a vector of times during which recapture probabilities have changed. 
> 
>    About the lack of information on birth and death, in principle BaSTA can handle it, but of course, the less information, the higher the uncertainty in the estimation. We have tested the package on datasets without birth and death information and it works, but your setup is quite particular… Please let us know if you need more assistance. Also, I would recommend that you install the latest version of BaSTA. It is not in cran, but you can donwnload it from:
> 
>   https://github.com/fercol/BaSTA/blob/master/latestBuild/BaSTA_1.9.5.tar.gz <https://github.com/fercol/BaSTA/blob/master/latestBuild/BaSTA_1.9.5.tar.gz>
> 
> Best,
> 
> Fernando
> _________________________________
> 
> Fernando Colchero
> Associate Professor
> Department of Mathematics and Computer Science
> Biodemography Unit
> 
> Tlf.              +45 65 50 23 24 <tel:+45%2065%2050%2023%2024>
> Email          colchero at imada.sdu.dk <mailto:colchero at imada.sdu.dk>
> Web            www.sdu.dk/staff/colchero <http://www.sdu.dk/staff/colchero>
> Pers. web   www.colchero.com <http://www.sdu.dk/staff/colchero>
> Adr.             Campusvej 55, 5230, Odense, Dk <https://maps.google.com/?q=Campusvej+55,+5230,+Odense,+Dk&entry=gmail&source=g>
> 
> University of Southern Denmark
> _________________________________
> 
> 
> 
> 
>> On 23 Feb 2018, at 22:36, Ken Honeycutt <rkenhoneycutt at gmail.com <mailto:rkenhoneycutt at gmail.com>> wrote:
>> 
>> Hi BaSTA users,
>> 
>> I just noticed the partial capture history I posted for example did not appear as I expected; and the text continues after many many rows of 0s and 1s. Here's the capture history again in csv. Hopefully this is better.
>> 
>> Thanks,
>> Ken
>> 
>> ID,Birth,Death,6,7,8,9,...,17,18,19,20
>> 1,0,0,1,0,1,0,0,0,1,1,1
>> 2,0,0,0,1,0,0,0,0,0,1,0
>> 3,0,0,1,0,1,0,0,0,0,0,1
>> 4,0,0,0,1,0,0,0,0,1,0,1
>> …,0,0,1,0,1,0,0,0,0,1,1
>> 1544,0,0,0,1,0,0,0,0,0,1,0
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> 

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