Data and code from: Accounting for unobserved population dynamics and aging error in close-kin mark-recapture assessments

Obtaining robust estimates of population abundance is a central challenge hindering the conservation and management of many threatened and exploited species. Close-kin mark-recapture (CKMR) is a genetics-based approach that has strong potential to improve monitoring of data-limited species by enabling estimates of abundance, survival, and other parameters for populations that are challenging to assess. However, CKMR models have received limited sensitivity testing under realistic population dynamics and sampling scenarios, impeding application of the method in population monitoring programs and stock assessments. Here, we use individual-based simulation to examine how unmodeled population dynamics and aging uncertainty affect the accuracy and precision of CKMR parameter estimates under different sampling strategies. We then present adapted models that correct the biases that arise from model misspecification. Our results demonstrate that a simple base-case CKMR model produces robust est..., The simulation code was written for this manuscript and the results were generated by running the code on the Massachusetts Green High Performance Computing Cluster. Kinship data for lemon sharks comes from: Feldheim, K. A., S. H. Gruber, J. D. DiBattista, E. A. Babcock, S. T. Kessel, A. P. Hendry, E. K. Pikitch, M. V. Ashley, and D. D. Chapman. 2014. Two decades of genetic profiling yields first evidence of natal philopatry and long-term fidelity to parturition sites in sharks. Molecular Ecology 23:110–117 and can be accessed at: https://doi.org/10.5061/dryad.1q9r8., , # Data and code from: Accounting for unobserved population dynamics and aging error in close-kin mark-recapture assessments

This compilation of data and code contains three primary folders that can be accessed from the main directory:

1. Data_used_in_MS
2. JAGS_models
3. Scripts_used_in_MS
4. Simulation_log_key

Each of these folders/files and the structure of subfolders is described in details below.

## Description of the data and file structure

* **Data_used_in_MS**: This folder contains the final data that are presented in the manuscript (MS), as well as the code used to analyze it. The structure and content of this directory are as follows:

* **04_DataViz**: This folder contains two primary scripts, as well as several functions that are sourced. The code assumes that the working directory is set to the same directory as the script, and that all folders and files from the repository are present.

* `mcmc analysis.R` contains code for examining convergence...