geostat-survey

This repository contains the R codes used for calculations and figure plotting related to our research:

Yalcin, S., Anderson, S., Regular, P., English, P. (2023). Exploring the limits of spatiotemporal and design-based index standardization under reduced survey coverage. ICES Journal of Marine Science. DOI: 10.1093/icesjms/fsad155

Note: The code and data generated from this research are being archived on Zenodo [DOI: 10.5281/zenodo.8326526].

Main Scripts:

1_cod_like_indices_calculations.R

• Description: Calculation of cod-like species design and model-based indices.

2_yellowtail_like_indices_calculations.R

• Description: Calculation of yellowtail-like species design and model-based indices.

3_main_figures.R

• Description: Script used for main figure plotting.

Appendices:

4_appendix_1_additional_figures.R

• Description: Script containing additional figures for Appendix 1.

5_appendix_2_testing_sampling_variation.R

• Description: Codes for testing sampling variation in Appendix 2.

6_appendix_3_recovery_spillover.R

• Description: Script for mapping the base scenario, recovery of the closed area, and recovery with spillover effect in Appendix 3.

Functions:

bootstrapping_fn.R

• Description: Bootstrap function for design-based indices.

data_prep_fn.R

• Description: Data preparation functions.

model_run_fn.R

• Description: Model functions.

pop_cod_fn.R

• Description: Functions related to cod-like population simulations.

pop_yellowtail_fn.R

• Description: Functions related to yellowtail-like population simulations.

Data folder:

• This folder includes the data generated through the analysis and can be used for plotting.