In Bai-Li-NOAA/IFA4EBFM: Interdisciplinary Forecasting Approach for Ecosystem-Based Fisheries Management

knitr::opts_chunk$set(echo = FALSE, 
                      message = FALSE,
                      warning = FALSE,
                      fig.width = 12,
                      fig.height = 10,
                      results = 'asis')
options(scipen = 1, digits = 4)

Depletion-Based Stock Reduction Analysis(DB-SRA) from DLMtool

• GitHub repo: https://github.com/Blue-Matter/DLMtool
• Package website: https://dlmtool.openmse.com/

devtools::load_all()

required_pkg <- c("DLMtool", "here", "ggplot2", "reshape2",
                  "RColorBrewer", "scales", "fmsb", 
                  "Polychrome") ## DLMtool: version 6.0.3; 

pkg_to_install <- required_pkg[!(required_pkg %in%
                                   installed.packages()[, "Package"])]
if (length(pkg_to_install)) install.packages(pkg_to_install, repos = "http://cran.us.r-project.org")

invisible(lapply(required_pkg, library, character.only = TRUE))

EwE without environmental effects and without fleet dynamics

Year 2012 Assessment with low CV in data and without environmental link in the estimation model

scenario_filename <- "_lowCV"
terminal_year <- 2012
fishery_CV_input <- 0.05
survey_CV_input <- 0.1
add_environmental_effects <- FALSE
add_fleet_dynamics <- FALSE
cat(knitr::knit_child('_OM3_data_poor_stock_assessment_template.Rmd',
                      envir = environment(),
                      quiet = TRUE))

EwE with environmental effects and without fleet dynamics

Year 2012 Assessment with low CV in data and without environmental link in the estimation model

scenario_filename <- "_lowCV"
terminal_year <- 2012
fishery_CV_input <- 0.05
survey_CV_input <- 0.1
add_environmental_effects <- TRUE
add_fleet_dynamics <- FALSE
cat(knitr::knit_child('_OM3_data_poor_stock_assessment_template.Rmd',
                      envir = environment(),
                      quiet = TRUE))

EwE with environmental effects and fleet dynamics

Year 2012 Assessment with low CV in data and without environmental link in the estimation model

scenario_filename <- "_lowCV"
terminal_year <- 2012
fishery_CV_input <- 0.05
survey_CV_input <- 0.1
add_environmental_effects <- TRUE
add_fleet_dynamics <- TRUE
cat(knitr::knit_child('_OM3_data_poor_stock_assessment_template.Rmd',
                      envir = environment(),
                      quiet = TRUE))

Bai-Li-NOAA/IFA4EBFM documentation built on May 1, 2024, 9:24 p.m.