Supplement 1. The sample codes in R and ADMB for the estimation and simulations with a dummy data set.

File List
1. functions.R (MD5: 22fd7e17fd9b415ad00b83929c86a139)

2. gamma_ss4.tpl (MD5: 306a18eea79fd8158f58d72dfbaba741)

3. ndata1.csv (MD5: a2aa1f32de690becb6273395252c430e)

4. vpa.txt (MD5: c1ed50a7da11254696b2894fc3f4a3db)

5. R_code.R (MD5: c388cfe173fd72e1bcd4d81bfd8b9de3)

Description
The supplement includes 5 files. The R script functions.R merges variety of utility functions for conducting parameter estimation using GLM and GSSM and population dynamics simulations. The script gamma_ss4.tpl is written by ADMB and should be complied before using from R. The files ndata1.csv (daily catch and effort data) and vpa.txt (results of VPA) is the data for the simulation. Note that ndata1.csv is a “dummy data” created by a stochastic simulation using the estimated parameters because the raw data cannot be publically available. Therefore, the estimated values with this data are different from results described in the paper.

The main R script for the implementation of the entire analysis in the paper is R_code.R. The script describes how to read functions.R, ndata1.csv, and vpa.txt, compile gamma_ss4.tpl, and use variety of functions in functions.R for the simulation.