Momoko Ichinokawa
National Research Institute of Fisheries Science, Fisheries Research Agency
2-12-4 Fukuura, Kanazawa-ku,
Yokohama, Kanagawa 236-8648 Japan
E-mail: [email protected]

Hiroshi Okamura
National Research Institute of Fisheries Science, Fisheries Research Agency
2-12-4 Fukuura, Kanazawa-ku
Yokohama, Kanagawa 236-8648 Japan

Atsushi Kawabata
National Research Institute of Fisheries Science, Fisheries Research Agency
2-12-4 Fukuura, Kanazawa-ku
Yokohama, Kanagawa 236-8648 Japan

Chikako Watanabe
National Research Institute of Fisheries Science, Fisheries Research Agency
2-12-4 Fukuura, Kanazawa-ku
Yokohama, Kanagawa 236-8648 Japan

Yoshioki Oozeki
Tohoku National Fisheries Research Institute, Fisheries Research Agency
3-27-5, Shinhama-cho, Shiogama
Miyagi, 985-0001, Japan

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)

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.