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Complete tag loss in capture-recapture studies affects abundance estimates: an elephant seal case study


Malcolm-White, Emily; Cowen, Laura; McMahon, Clive (2020), Complete tag loss in capture-recapture studies affects abundance estimates: an elephant seal case study, Dryad, Dataset,


1. In capture-recapture studies, recycled individuals occur when individuals lose all of their tags and are recaptured as though they were new individuals. Typically, the effect of these recycled individuals is assumed negligible.

2. Through a simulation-based study of double tagging experiments, we examined the effect of recycled individuals on parameter estimates in the Jolly-Seber model with tag loss (Cowen & Schwarz, 2006). We validated the simulation framework using long-term census data of elephant seals.

3. Including recycled individuals did not affect estimates of capture, survival, and tag-retention probabilities. However, with low tag-retention rates, high capture rates, and high survival rates, recycled individuals produced over estimates of population size. For the elephant seal case study, we found population size estimates to be between 8 and 53% larger when recycled individuals were ignored.

4. Ignoring the effects of recycled individuals can cause large biases in population size estimates. These results are particularly noticeable in longer studies.


This mark-recapture study data was simulated using R.  

Usage Notes

The simulated data is available for all 6 considered scenarios are available in the files with the prefixes DATA.  

  • Six different scenarios for each model were considered: 
    • GJSTL1 - scenario with N=1000, double-tagging=100%, 10 time periods
    • GJSTL2 - scenario with N=100000, double-tagging=100%, 10 time periods
    • GJSTL3 - scenario with N=100000, double-tagging=50%, 10 time periods
    • GJSTL4 - scenario with N=1000, double-tagging=50%, 10 time periods
    • GJSTL5 - scenario with N=1000, double-tagging=100%, 5 time periods
    • GJSTL6 - scenario with N=1000, double-tagging=100%, 7 time periods
  • The following following number (1-27) represents the combination of survival, capture, and tag retention probabilities. There were 3 levels for each of the 3 parameters, giving 3^3=27 different combinations. 
  • Parameter Estimates (ests) and Standard Errror (se) are given for the model including (RECYCLED) and excluding the recycled individuals. 

For example, GJSTL1_4.seRECYCLED.txt will contain the standard errors for the analysis including recycled individuals. It will be for the 1st scenario (scenario with N=1000, double-tagging=100%, 10 time periods) and the 4th combination of survival, capture, and tag, retention probabilities. 

Within each file, the rows represent the simulations of that parameter combination. For each parameter combination, 100 simulations were attempted. If the MLE did not converge for a particular simulation, a row will be missing. This occurs more often when data is scarce (low capture, low tag retention, low survival). The columns represent the estimates or standard errors of (in order): survival, capture, tag retention, entry probabilities (number varies depending on how many time periods there were), population size at each time period (number varies depending on how many time periods there were), and the super population size. Note that no estimates of standard error are given for super population size. 

The data for the Elephant Seals is in Seals_Data.xlsx