Official repository of the CMSY++ data-limited stock assessment method.
All files should be copied in the same directory and the required libraries should be installed (automatic installation is set as the default in the main script).
CMSYUserGuideMarch2021.pdf is the official user guide.
CMSY++16.R: R-code executing the CMSY++ and BSM models
ffnn.bin: File containing the trained neural network used by CMSY++
Train_Catch_9e.csv: Catch and abundance data of the 400 stocks used for testing and training, in the format required by CMSY++
Train_ID_9e.csv: Stock identification and prior settings (defaults or user input), in the format required by CMSY++
NN_Bk_19a.R: R-code used to train and evaluate the neural network
Out_Train_ID_9e.csv: File containing the CMSY++ and BSM results for the 400 test stocks. This file was also used for training the neural network.
Out_March032021_Train_ID_9c.csv: Data file used by NN_Bk_19a.R
Train_Catch_9b.csv: Data file used by NN_Bk_19a.R
SimSpecCPUE_4_NA.csv: Prior settings for running CMSY++ and BSM with simulated data
SimCatchCPUE_4.csv: Simulated catch data
CMSY++16HW.R: Version of CMSY++16.R cleaned up by Henning Winker, suggested for use with new data (will become version 17 after more testing)