bsb-CMR

This is data and code that contributed to the following paper:

Recruitment limitation increases susceptibility to fishing-induced collapse in a spawning aggregation fishery

Erica T. Jarvis Mason¹, Thomas V. Riecke², Lyall F. Bellquist^1,3, Daniel J. Pondella II⁴, Brice X. Semmens¹

¹Scripps Institution of Oceanography, University of California San Diego, California, USA
²Department of Ecosystem and Conservation Sciences, University of Montana, USA
³California Oceans Program, The Nature Conservancy, California, USA
⁴Vantuna Research Group, Occidental College, California, USA

citation: Jarvis Mason ET, Riecke TV, Bellquist LF, Pondella DJ, Semmens BX (2024) Recruitment limitation increases susceptibility to fishing-induced collapse in a spawning aggregation fishery. Mar Ecol Prog Ser 738:203-224

R-script files:

1. Double-tag_TagRetentionModel_Masonetal.R (Tag retention model for double-tagging data with individual recovery times) Includes the following sections:

   • Explore relationship between the ratio of fish with 2 vs 1 tag
   • Simulate data and define model
   • Test model
   • Load and format Kelp Bass double tag data
   • Tag retention model (tag loss as a function of age of tag)
   • Run tag retention model on double-tag data
   • Plot cumulative and non-cumulative tag retention over time

2. Age_Growth_Masonetal.R (Age and Growth Model Fits using the Traditional Von Bertalanffy and Francis parameterizations)

3. CMR_wGrowth_Masonetal.R (Capture-mark-reencounter data simulation and model testing) Includes the following sections:

   • Simulate CMR data
   • Define CMR model in JAGS
   • Set up and run model in JAGS

4. 60s_Final_Masonetal.R (Capture-mark-reencounter model for modeling the 1960s CDFW CMR data)

5. 90s_Final_Masonetal.R (Capture-mark-reencounter model for modeling the 1990s CDFW CMR data)

6. 10s_Final_Masonetal.R (Capture-mark-reencounter model for modeling the 2010s L. Bellquist CMR data)