DOI: 10.5061/dryad.v6wwpzgr3
title: Complete tag loss in capture-recapture studies affects abundance estimates: an elephant seal case study

description: 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.
description: This mark-recapture study data was simulated using R.  
description: 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