[Basta-users] juvenile survival

[Fernando Colchero]

Hi Luisa,

   Quick question, which version of BaSTA are you using? There is a new version at https://github.com/fercol/basta2.0 that uses an improve method to construct the life table (based on product limit estimators). It also allows using the model on census data as well. Unfortunately, BaSTA is temporarily off CRAN due to some issues when checking the package on some platforms, which do not affect functionality, but they need to be solved. You can still find version 1.9.5 in https://github.com/fercol/BaSTA.

   About your project, you can certainly change the time units to months and then interpret the results as such. Still, I don’t think that’s going to solve your problem. If I understand correctly, you know the time of birth of all the individuals, and then, after releasing them, you don’t see them until they are about 2 years old, isn’t it?
I believe that what you are doing of conditioning your analysis to a minimum age of 2 is correct. In that case, BaSTA uses a constant mortality function for all ages up to that minimum age, and then the model you chose from that age onwards. Still, the life table is built for all ages. I suspect that maybe the model is having a hard time with the 0 recapture probabilities between ages 0 and 2. Could you send me a subset of the data so I can run some tests?

Best,

  Fernando

-----------------------------------------------------
Fernando Colchero
Associate Professor
Department of Mathematics and Computer Sciences (IMADA)
and Interdisciplinary Center on Population Dynamics (CPop)

Tlf.              +45 65 50 46 35
Email           colchero at imada.sdu.dk<mailto:colchero at imada.sdu.dk>
Web            www.sdu.dk/staff/colchero
Pers. web     www.colchero.com
Adr.             Campusvej 55, 5230, Odense, Dk

University of Southern Denmark
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From: Basta-users <basta-users-bounces at lists.r-forge.r-project.org> on behalf of Luisa Fitzpatrick <luisa.fitzpatrick at utas.edu.au>
Date: Tuesday, 23 April 2024 at 09.13
To: basta-users at lists.r-forge.r-project.org <basta-users at lists.r-forge.r-project.org>
Subject: [Basta-users] juvenile survival
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Hi everyone,

I have used Basta to model mortality curves in two populations of a lizard species. I have mark-recapture data for around 22 years with all individuals born in the lab, and then recaptured at maturity (age 2 or 3 if they survived) and every subsequent year that they reproduce (max lifespan 13 years).

My question is on how to incorporate survival from birth to maturity (or until first observation). Basta doesn't allow me to include observations before birth and I ran into issues for having birth dates with no observations present. I was thinking I could possibly use time intervals other than year. e.g. all the individuals that are born I can include as observations at age 1 month. Then instead of age 2,3,4 I can have observations at age 24, 36, 48.

As it is, I have conditioned the analyses to survival beyond age 2 to examine patterns in adult/reproductive life. This gives me mortality trajectories that start at mortality rate 0 at age 0 and shoot up, which gives the impression early mortality is low. The life table for ages 2-3 has a death rate of 0, and for ages 3-4 has a death rate of 0.002. When in fact I know from the dataset that survival rates from birth to maturity are approximately 20% and from age 2-3 are around 50%.

Does anyone have any feedback on the idea of using months instead of years or any suggestions for another way to address this issue?

Thanks in advance,

Luisa

Dr Luisa Fitzpatrick (she/her)
Postdoctoral Fellow Life History Evolution and Ageing
Behavioural and Evolutionary Ecology Research Group
University of Tasmania, Sandy Bay TAS 7005
https://beergrouputas.wordpress.com/



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