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Author: Ovec8hkin

doc/00_sablefish_example.R

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+## ----load_base_om, eval=FALSE-------------------------------------------------
+# nyears <- 100
+# 
+# sable_om <- readRDS("data/sablefish_om_big.RDS")
+# 
+# # Also load the historical recruitment timeseries
+# assessment <- dget("data/sablefish_assessment_2023.rdat")
+# hist_recruits <- assessment$natage.female[,1]*2
+
+## ----om1, eval=FALSE----------------------------------------------------------
+# om1 <- sable_om
+# om1$recruitment$func <- resample_recruits
+# om1$recruitment$pars <- list(
+#     hist_recruits = hist_recruits,
+#     nyears = nyears
+# )
+
+## ----om2, eval=FALSE----------------------------------------------------------
+# om2 <- sable_om
+# om2$recruitment$func <- resample_regime_recruits
+# om2$recruitment$pars <- list(
+#     regime1_recruits = hist_recruits[hist_recruits <= 35],
+#     regime2_recruits = hist_recruits[hist_recruits > 35],
+#     nyears = 10*nyears,
+#     regime_length = c(20, 5),
+#     starting_regime = 0
+# )
+
+## ----om4, eval=FALSE----------------------------------------------------------
+# om4 <- sable_om
+# om4$recruitment$func <- regime_recruits
+# om4$recruitment$pars <- list(
+#     mus = c(mean(hist_recruits[hist_recruits <= 35])),
+#     cvs = c(sd(hist_recruits[hist_recruits <= 35])/mean(hist_recruits[hist_recruits <= 35])),
+#     nyears = 10*nyears,
+#     regime_length = c(nyears*10),
+#     starting_regime = 0
+# )
+
+## ----om5, eval=FALSE----------------------------------------------------------
+# om6 <- sable_om
+# om6$recruitment$func <- recruits_crash
+# om6$recruitment$pars <- list(
+#     crash_start_year = 1,
+#     crash_length = 10,
+#     crash_value = 0,
+#     hist_recruits = hist_recruits,
+#     nyears = 10*nyears
+# )
+
+## ----om_list, eval=FALSE------------------------------------------------------
+# om_list <- listN(om1, om2, om3, om4, om6)
+
+## ----setup_mp_options, eval=FALSE---------------------------------------------
+# mp_base <- setup_mp_options()
+
+## ----atainment_function, eval=FALSE-------------------------------------------
+# mp_base$management$tac_land_reduction <- list(
+#     func = stairstep_attainment,
+#     pars = list(
+#         breakpoints = c(20, 30),
+#         levels = c(0.874, 0.786, 0.647),
+#         phase_ins = 0
+#     )
+# )
+
+## ----mp1, eval=FALSE----------------------------------------------------------
+# mp1 <- mp_base
+# mp1$hcr <- list(
+#     func = tier3,
+#     extra_pars = NA,
+#     extra_options = list(
+#         max_stability = NA,
+#         harvest_cap = NA
+#     ),
+#     units = "F"
+# )
+
+## ----mp234, eval=FALSE--------------------------------------------------------
+# mp2 <- mp_base
+# mp2$hcr <- list(
+#     func = tier3,
+#     extra_pars = NA,
+#     extra_options = list(
+#         max_stability = 0.10,
+#         harvest_cap = NA
+#     ),
+#     units = "F"
+# )
+# 
+# mp3 <- mp_base
+# mp3$hcr <- list(
+#     func = tier3,
+#     extra_pars = NA,
+#     extra_options = list(
+#         max_stability = 0.15,
+#         harvest_cap = NA
+#     ),
+#     units = "F"
+# )
+# 
+# mp4 <- mp_base
+# mp4$hcr <- list(
+#     func = tier3,
+#     extra_pars = NA,
+#     extra_options = list(
+#         max_stability = 0.25,
+#         harvest_cap = NA
+#     ),
+#     units = "F"
+# )
+
+## ----mp5, eval=FALSE----------------------------------------------------------
+# mp5 <- mp_base
+# mp5$ref_points$spr_target <- 0.50
+# mp5$hcr <- list(
+#     func = tier3,
+#     extra_pars = NA,
+#     extra_options = list(
+#         max_stability = NA,
+#         harvest_cap = NA
+#     ),
+#     units = "F"
+# )
+
+## ----mp67, eval=FALSE---------------------------------------------------------
+# mp6 <- mp_base
+# mp6$hcr <- list(
+#     func = tier3,
+#     extra_pars = list(cutoff_age = 7),
+#     extra_options = list(
+#         max_stability = NA,
+#         harvest_cap = NA
+#     ),
+#     units = "F"
+# )
+# 
+# mp7 <- mp_base
+# mp7$hcr <- list(
+#     func = tier3,
+#     extra_pars = list(cutoff_age = 14),
+#     extra_options = list(
+#         max_stability = NA,
+#         harvest_cap = NA
+#     ),
+#     units = "F"
+# )
+
+## ----mp8, eval=FALSE----------------------------------------------------------
+# mp8 <- mp_base
+# mp8$ref_points$spr_target <- 0.45
+# mp8$hcr <- list(
+#     func = pfmc4010,
+#     extra_pars = NA,
+#     extra_options = list(
+#         max_stability = NA,
+#         harvest_cap = NA
+#     ),
+#     units = "TAC"
+# )
+
+## ----mp91011, eval=FALSE------------------------------------------------------
+# mp9 <- mp_base
+# mp9$hcr <- list(
+#     func = tier3,
+#     extra_pars = NA,
+#     extra_options = list(
+#         max_stability = NA,
+#         harvest_cap = 15
+#     ),
+#     units = "F"
+# )
+# 
+# mp10 <- mp_base
+# mp10$hcr <- list(
+#     func = tier3,
+#     extra_pars = NA,
+#     extra_options = list(
+#         max_stability = NA,
+#         harvest_cap = 20
+#     ),
+#     units = "F"
+# )
+# 
+# mp11 <- mp_base
+# mp11$hcr <- list(
+#     func = tier3,
+#     extra_pars = NA,
+#     extra_options = list(
+#         max_stability = NA,
+#         harvest_cap = 25
+#     ),
+#     units = "F"
+# )
+
+## ----mp_list, eval=FALSE------------------------------------------------------
+# mp_list <- listN(mp1, mp2, mp, mp4, mp5, mp6, mp7, mp8, mp9, mp10, mp11)
+
+## ----mse_options, eval=FALSE--------------------------------------------------
+# mse_options <- setup_mse_options()
+
+## ----run_mse, eval=FALSE------------------------------------------------------
+# nsims <- 9
+# seed_list <- sample(1:(1000*nsims), nsims)
+# model_runs <- run_mse_multiple(
+#     om_list,
+#     hcr_list,
+#     seed_list,
+#     nyears=nyears,
+#     mse_options_list=mse_options_list
+# )
+
+## ----extra_columns, eval=FALSE------------------------------------------------
+# om_names <- c("Random Recruitment", "Cyclic Recruitment", "Beverton-Holt Recruitment", "Low Recruitment", "Recruitment Crash")
+# hcr_names <- c("F40", "F40 +/-10%", "F40 +/-15%", "F40 +/-25%", "F50", "F40 >7yo", "F40 >14yo", "PFMC 40-10", "F40 15k Cap", "F40 20k Cap", "F40 25k Cap")
+# 
+# extra_columns <- expand.grid(
+#     om = om_names,
+#     hcr = hcr_names
+# )
+
+## ----data_processing, eval=FALSE----------------------------------------------
+# ssb_data <- get_ssb_biomass(model_runs, extra_columns2, sable_om$dem_params)
+# f_data <- get_fishing_mortalities(model_runs, extra_columns2)
+# r_data <- get_recruits(model_runs, extra_columns2)
+# abctac <- get_management_quantities(model_runs, extra_columns2)
+# catch_data <- get_landed_catch(model_runs, extra_columns2)
+
+## ----plotting, eval=FALSE-----------------------------------------------------
+# plot_ssb(ssb_data, v1="hcr", v2="om")
+# plot_fishing_mortalities(f_data, v1="hcr", v2="om")
+# plot_recruitment(r_data, v1="hcr", v2="om")
+# plot_abc_tac(abctac, v1="hcr", v2="om")
+# plot_landed_catch(catch_data, v1="hcr", v2="om")
+
+## ----performance_metrics, eval=FALSE------------------------------------------
+# performance_metrics <- performance_metric_summary(
+#     model_runs,
+#     extra_columns2,
+#     sable_om$dem_params,
+# )
+# 
+# perf_data <- performance_metrics$perf_data
+# plot_performance_metric_summary(perf_data)
+# 
+