/cayman-grouper-assess

Length-based assessment of Cayman Islands Nassau Grouper spawning aggregations

Primary LanguageR

Pulse recruitment and recovery of Cayman Islands Nassau Grouper (Epinephelus striatus) spawning aggregations revealed by in situ length-frequency data

This repository holds the analysis for: Stock, BC, SA Heppell, L Waterhouse, IC Dove, CV Pattengill-Semmens, CM McCoy, PG Bush, G Ebanks-Petrie, and BX Semmens. Pulse recruitment and recovery of Cayman Islands Nassau Grouper (Epinephelus striatus) spawning aggregations revealed by in situ length-frequency data. ICES Journal of Marine Science. In press.

To recreate the analysis, you can run the .R files in the code folder in order. Intermediate model results are saved in results. Figures will be produced in the plots folder.

In addition to the .R code files, there are three .cpp files with TMB models:

  1. growth_REisland.cpp: hierarchical growth model inspired by Helser and Lai (2004). We used this model to estimate island-specific growth parameters as random effects, and then use these estimates in the LBSPR and LIME-fixed-k assessment models.

  2. LIME.cpp: we made some minor modifications to LIME appropriate for Little Cayman Nassau Grouper (see text). LIME assumes that growth parameters are fixed/known, and in the text we refer to this as the "LIME-fixed-k" model.

  3. LIME_integrated_REisland.cpp: we merged the above two models to conduct an integrated assessment where growth parameters were estimated internally, the "LIME-integrated" model. This propagates the uncertainty in growth parameters into estimates of recruitment, depletion, etc.