models/model_STAR_requests.R
In iantaylor-NOAA/Lingcod_2021: Estimate the Status of Lingcod off the US West Coast in 2021
### random collection of STAR-request-related code
# request 2, plotting implied fit to no_CPFV_DebWV_index sensitivity
get_mod('s', 14) # south base
get_mod('s', 14, 320) # sensitivity to removing CPFV DebWV
# comparison plots
dir.create('figures/STAR_Day1_request2')
r4ss::SSplotComparisons(r4ss::SSsummarize(list(mod.2021.s.014.001,
mod.2021.s.014.320)),
indexUncertainty=TRUE,
plotdir = 'figures/STAR_Day1_request2',
print = TRUE,
plot = FALSE,
legendlabels = c("South base", "no_CPFV_DebWV_index")
)
# request 8, changes to north comp data with and without sex-selectivity offset
devtools::load_all()
run_sensitivities(get_dir_ling("n", 23),
type = c("sens_create"),
numbers = c(221:224,404)
)
setwd("c:/ss/lingcod/lingcod_2021")
devtools::load_all()
run_sensitivities(get_dir_ling("n", 23),
type = c("sens_run"),
numbers = c(221:224,404)
)
# reverse retro on fishery ages
setwd("c:/ss/lingcod/lingcod_2021")
devtools::load_all()
run_sensitivities(get_dir_ling("n", 23),
type = c("sens_create", "sens_run"),
numbers = c(225:226)
)
dir.create('figures/STAR_request8')
mod.sum <- r4ss::SSsummarize(list(mod.2021.n.023.001,
mod.2021.n.023.221,
mod.2021.n.023.222,
mod.2021.n.023.223,
mod.2021.n.023.224,
mod.2021.n.023.404
))
r4ss::SSplotComparisons(mod.sum,
indexUncertainty=TRUE,
plotdir = 'figures/STAR_request8',
print = TRUE,
plot = FALSE,
legendloc = "topleft",
legendlabels = c("North new base",
"no FG ages",
"no FG ages 1999-2011",
"no FG ages + sex-selex-offset",
"no FG ages 1999-2011 + sex-selex-offset",
"sex-selex-offset")
)
# make sens table for STAR request 8
dir.create('models/2021.n.023.001_fixWAreccatchhistory/custom_plots/')
sens_make_table(
area = "n",
num = 23,
sens_base = 1,
sens_nums = c(221:224, 404),
sens_type = "star08",
write = TRUE
)
dir.create('figures/STAR_request8_extras')
mod.sum <- r4ss::SSsummarize(list(mod.2021.n.023.001,
mod.2021.n.023.221,
mod.2021.n.023.225,
mod.2021.n.023.226
))
r4ss::SSplotComparisons(mod.sum,
indexUncertainty=TRUE,
plotdir = 'figures/STAR_request8_extras',
print = TRUE,
plot = FALSE,
legendloc = "topleft",
legendlabels = c("North new base",
"no FG ages",
"no fishery ages prior to 1990",
"no fishery ages prior to 2000")
)
# make sens table for STAR request 8
sens_make_table(
area = "n",
num = 23,
sens_nums = c(221, 225, 226),
sens_type = "star08_extras_with_h",
write = TRUE,
#plot = FALSE
)
# comparison plots for STAR request 8 extras
dir.create('figures/STAR_request8_extras')
mod.sum <- r4ss::SSsummarize(list(mod.2021.n.023.001,
mod.2021.n.023.221,
mod.2021.n.023.225,
mod.2021.n.023.226
))
r4ss::SSplotComparisons(mod.sum,
indexUncertainty=TRUE,
plotdir = 'figures/STAR_request8_extras',
print = TRUE,
plot = FALSE,
legendloc = "topleft",
legendlabels = c("North new base",
"no FG ages",
"no fishery ages prior to 1990",
"no fishery ages prior to 2000")
)
# make sens table for STAR request 8 extras
sens_make_table(
area = "n",
num = 23,
sens_nums = c(221, 225, 226),
sens_type = "star08_extras_with_h",
write = TRUE,
#plot = FALSE
)
### request 11
setwd("c:/ss/lingcod/lingcod_2021")
devtools::load_all()
run_sensitivities(get_dir_ling("n", 23),
type = c("sens_create", "sens_run"),
numbers = c(411)
)
setwd("c:/ss/lingcod/lingcod_2021")
devtools::load_all()
run_sensitivities(get_dir_ling("s", 17),
type = c("sens_create", "sens_run"),
numbers = c(411)
)
dir.create('figures/STAR_request11')
mod.list <- list(mod.2021.n.023.001,
mod.2021.n.023.411,
mod.2021.s.017.001,
mod.2021.s.017.411
)
mod.sum <- r4ss::SSsummarize(mod.list)
mod.names <- c("North new base",
"North sex selex for fisheries",
"South new base",
"South sex selex for fisheries")
r4ss::SSplotComparisons(mod.sum,
indexUncertainty=TRUE,
plotdir = 'figures/STAR_request11',
print = TRUE,
plot = FALSE,
subplot = 1:12,
legendloc = "topleft",
legendlabels = mod.names)
)
mod.names <- c("North_new_base",
"North_sex_selex",
"South_new_base",
"South_sex_selex")
# make sens table for STAR request 11
sens_make_table(
area = "n",
num = 23,
plot_dir = 'figures/STAR_request11',
sens_mods = mod.list[1:2],
sens_base = 1,
sens_type = "star11",
write = TRUE
)
tab <- read.csv('tables/sens_table_n_star11.csv')
tab$Label <- gsub("Retained", "Ret.", tab$Label)
names(tab) <- c("Label", mod.names[1:2])
write.csv(tab, file = 'tables/sens_table_n_star11.csv', row.names = FALSE)
# make sens table for STAR request 11
sens_make_table(
area = "s",
num = 17,
plot_dir = 'figures/STAR_request11',
sens_mods = mod.list[3:4],
sens_base = 1,
sens_type = "star11",
write = TRUE
)
tab <- read.csv('tables/sens_table_s_star11.csv')
tab$Label <- gsub("Retained", "Ret.", tab$Label)
names(tab) <- c("Label", mod.names[3:4])
write.csv(tab, file = 'tables/sens_table_s_star11.csv', row.names = FALSE)
#### example call to get profile
# get directory with profiles in it
profiledir <- paste0(get_dir_ling("s", 17), '_profile_NatM_uniform_Fem_GP_1')
# load .Rdat file saved by nwfscDiag
load(file.path('models', profiledir, 'NatM_uniform_Fem_GP_1_profile_output.Rdat'))
# make profile plot with cutoff at ~0.66 to see where it intersects the profile
r4ss::SSplotProfile(profile_output$profilesummary,
minfraction = 0.001,
print=TRUE,
legendloc='top',
add_cutoff = TRUE,
ymax = 2, #example inputs to revise as needed
xlim = c(0.11, 0.29), #example inputs to revise as needed
cutoff_prob = 0.75,
plotdir = profiledir,
profile.string = "NatM_uniform_Fem",
profile.label="Female natural mortality (M)")
################################################################################
# STAR request 20 (states of nature for north model)
setwd("c:/ss/lingcod/lingcod_2021")
devtools::load_all()
run_sensitivities(get_dir_ling("n", 23),
type = c("sens_create", "sens_run"),
numbers = c(204)
)
plot_twopanel_comparison(list(mod.2021.n.023.001,
mod.2021.n.023.204,
mod.2021.n.023.420),
legendlabels = c("North base model",
"High state (no fishery ages)",
"Low state (sex-specific selectivity)"))
newdir <- 'figures/north_states'
dir.create(newdir)
compare_table <- sens_make_table(
area = "n",
num = 23,
sens_mods = list(mod.2021.n.023.001,
mod.2021.n.023.204,
mod.2021.n.023.420),
sens_names = c("North base model",
"High state (no fishery ages)",
"Low state A (sex-sel)"),
sens_type = "random",
plot = TRUE,
plot_dir = newdir,
table_dir = newdir,
write = TRUE,
)
# profile on south
##################################################################################
# mortality profile
dir.mod <- get_dir_ling('s', 18)
dir.profile.M <- "models/2021.s.018.001_fixTri3_newMprofile_down"
copy_SS_inputs(dir.old = dir.mod,
dir.new = dir.profile.M,
use_ss_new = TRUE,
copy_exe = TRUE,
copy_par = TRUE,
overwrite = TRUE)
start <- SS_readstarter(file = file.path(dir.profile.M, "starter.ss"),
verbose = FALSE)
start$ctlfile <- "control_modified.ss"
start$prior_like <- 1 # include prior likelihood for non-estimated parameters
SS_writestarter(start, dir = dir.profile.M, overwrite = TRUE)
setwd('c:/ss/lingcod/lingcod_2021/')
devtools::load_all()
dir.profile.M <- "models/2021.s.018.001_fixTri3_newMprofile_up"
M.vec = seq(0.18, 0.22, 0.01)
#dir.profile.M <- "models/2021.s.018.001_fixTri3_newMprofile_down"
#M.vec = seq(0.16, 0.10, -0.01)
r4ss::SS_profile(dir = dir.profile.M,
masterctlfile = "ling_control.ss",
newctlfile = "control_modified.ss",
string = "NatM_uniform_Fem",
profilevec = M.vec,
extras = "-nohess -nox")
mods.up <- SSgetoutput(keyvec=1:6, dirvec = "models/2021.s.018.001_fixTri3_newMprofile_up")
mods.down <- SSgetoutput(keyvec=1:6, dirvec = "models/2021.s.018.001_fixTri3_newMprofile_down")
test <- c(rev(mods.down), list(mod.2021.s.018.001), mods.up[1:5])
profilesummary <- test %>% SSsummarize()
SSplotProfile(profilesummary, # summary object
minfraction = 0.001,
print=FALSE,
ymax = 5.0,
profile.string = "NatM_uniform_Fem", # substring of profile parameter
profile.label="Female natural mortality (M)") # axis label
### random collection of STAR-request-related code
# request 2, plotting implied fit to no_CPFV_DebWV_index sensitivity
get_mod('s', 14) # south base
get_mod('s', 14, 320) # sensitivity to removing CPFV DebWV
# comparison plots
dir.create('figures/STAR_Day1_request2')
r4ss::SSplotComparisons(r4ss::SSsummarize(list(mod.2021.s.014.001,
mod.2021.s.014.320)),
indexUncertainty=TRUE,
plotdir = 'figures/STAR_Day1_request2',
print = TRUE,
plot = FALSE,
legendlabels = c("South base", "no_CPFV_DebWV_index")
)
# request 8, changes to north comp data with and without sex-selectivity offset
devtools::load_all()
run_sensitivities(get_dir_ling("n", 23),
type = c("sens_create"),
numbers = c(221:224,404)
)
setwd("c:/ss/lingcod/lingcod_2021")
devtools::load_all()
run_sensitivities(get_dir_ling("n", 23),
type = c("sens_run"),
numbers = c(221:224,404)
)
# reverse retro on fishery ages
setwd("c:/ss/lingcod/lingcod_2021")
devtools::load_all()
run_sensitivities(get_dir_ling("n", 23),
type = c("sens_create", "sens_run"),
numbers = c(225:226)
)
dir.create('figures/STAR_request8')
mod.sum <- r4ss::SSsummarize(list(mod.2021.n.023.001,
mod.2021.n.023.221,
mod.2021.n.023.222,
mod.2021.n.023.223,
mod.2021.n.023.224,
mod.2021.n.023.404
))
r4ss::SSplotComparisons(mod.sum,
indexUncertainty=TRUE,
plotdir = 'figures/STAR_request8',
print = TRUE,
plot = FALSE,
legendloc = "topleft",
legendlabels = c("North new base",
"no FG ages",
"no FG ages 1999-2011",
"no FG ages + sex-selex-offset",
"no FG ages 1999-2011 + sex-selex-offset",
"sex-selex-offset")
)
# make sens table for STAR request 8
dir.create('models/2021.n.023.001_fixWAreccatchhistory/custom_plots/')
sens_make_table(
area = "n",
num = 23,
sens_base = 1,
sens_nums = c(221:224, 404),
sens_type = "star08",
write = TRUE
)
dir.create('figures/STAR_request8_extras')
mod.sum <- r4ss::SSsummarize(list(mod.2021.n.023.001,
mod.2021.n.023.221,
mod.2021.n.023.225,
mod.2021.n.023.226
))
r4ss::SSplotComparisons(mod.sum,
indexUncertainty=TRUE,
plotdir = 'figures/STAR_request8_extras',
print = TRUE,
plot = FALSE,
legendloc = "topleft",
legendlabels = c("North new base",
"no FG ages",
"no fishery ages prior to 1990",
"no fishery ages prior to 2000")
)
# make sens table for STAR request 8
sens_make_table(
area = "n",
num = 23,
sens_nums = c(221, 225, 226),
sens_type = "star08_extras_with_h",
write = TRUE,
#plot = FALSE
)
# comparison plots for STAR request 8 extras
dir.create('figures/STAR_request8_extras')
mod.sum <- r4ss::SSsummarize(list(mod.2021.n.023.001,
mod.2021.n.023.221,
mod.2021.n.023.225,
mod.2021.n.023.226
))
r4ss::SSplotComparisons(mod.sum,
indexUncertainty=TRUE,
plotdir = 'figures/STAR_request8_extras',
print = TRUE,
plot = FALSE,
legendloc = "topleft",
legendlabels = c("North new base",
"no FG ages",
"no fishery ages prior to 1990",
"no fishery ages prior to 2000")
)
# make sens table for STAR request 8 extras
sens_make_table(
area = "n",
num = 23,
sens_nums = c(221, 225, 226),
sens_type = "star08_extras_with_h",
write = TRUE,
#plot = FALSE
)
### request 11
setwd("c:/ss/lingcod/lingcod_2021")
devtools::load_all()
run_sensitivities(get_dir_ling("n", 23),
type = c("sens_create", "sens_run"),
numbers = c(411)
)
setwd("c:/ss/lingcod/lingcod_2021")
devtools::load_all()
run_sensitivities(get_dir_ling("s", 17),
type = c("sens_create", "sens_run"),
numbers = c(411)
)
dir.create('figures/STAR_request11')
mod.list <- list(mod.2021.n.023.001,
mod.2021.n.023.411,
mod.2021.s.017.001,
mod.2021.s.017.411
)
mod.sum <- r4ss::SSsummarize(mod.list)
mod.names <- c("North new base",
"North sex selex for fisheries",
"South new base",
"South sex selex for fisheries")
r4ss::SSplotComparisons(mod.sum,
indexUncertainty=TRUE,
plotdir = 'figures/STAR_request11',
print = TRUE,
plot = FALSE,
subplot = 1:12,
legendloc = "topleft",
legendlabels = mod.names)
)
mod.names <- c("North_new_base",
"North_sex_selex",
"South_new_base",
"South_sex_selex")
# make sens table for STAR request 11
sens_make_table(
area = "n",
num = 23,
plot_dir = 'figures/STAR_request11',
sens_mods = mod.list[1:2],
sens_base = 1,
sens_type = "star11",
write = TRUE
)
tab <- read.csv('tables/sens_table_n_star11.csv')
tab$Label <- gsub("Retained", "Ret.", tab$Label)
names(tab) <- c("Label", mod.names[1:2])
write.csv(tab, file = 'tables/sens_table_n_star11.csv', row.names = FALSE)
# make sens table for STAR request 11
sens_make_table(
area = "s",
num = 17,
plot_dir = 'figures/STAR_request11',
sens_mods = mod.list[3:4],
sens_base = 1,
sens_type = "star11",
write = TRUE
)
tab <- read.csv('tables/sens_table_s_star11.csv')
tab$Label <- gsub("Retained", "Ret.", tab$Label)
names(tab) <- c("Label", mod.names[3:4])
write.csv(tab, file = 'tables/sens_table_s_star11.csv', row.names = FALSE)
#### example call to get profile
# get directory with profiles in it
profiledir <- paste0(get_dir_ling("s", 17), '_profile_NatM_uniform_Fem_GP_1')
# load .Rdat file saved by nwfscDiag
load(file.path('models', profiledir, 'NatM_uniform_Fem_GP_1_profile_output.Rdat'))
# make profile plot with cutoff at ~0.66 to see where it intersects the profile
r4ss::SSplotProfile(profile_output$profilesummary,
minfraction = 0.001,
print=TRUE,
legendloc='top',
add_cutoff = TRUE,
ymax = 2, #example inputs to revise as needed
xlim = c(0.11, 0.29), #example inputs to revise as needed
cutoff_prob = 0.75,
plotdir = profiledir,
profile.string = "NatM_uniform_Fem",
profile.label="Female natural mortality (M)")
################################################################################
# STAR request 20 (states of nature for north model)
setwd("c:/ss/lingcod/lingcod_2021")
devtools::load_all()
run_sensitivities(get_dir_ling("n", 23),
type = c("sens_create", "sens_run"),
numbers = c(204)
)
plot_twopanel_comparison(list(mod.2021.n.023.001,
mod.2021.n.023.204,
mod.2021.n.023.420,
mod.2021.n.023.003),
legendlabels = c("North base model",
"High state (no fishery ages)",
"Low state option 1 (sex-specific selectivity)",
"Low state option 2 (M = 0.3)"))
newdir <- 'figures/STAR_request20'
dir.create(newdir)
compare_table <- sens_make_table(
area = "n",
num = 23,
sens_mods = list(mod.2021.n.023.001,
mod.2021.n.023.204,
mod.2021.n.023.420,
mod.2021.n.023.003),
sens_names = c("North base model",
"High state (no fishery ages)",
"Low state A (sex-sel)",
"Low state B (M = 0.3)"),
sens_type = "random",
plot = TRUE,
plot_dir = newdir,
table_dir = newdir,
write = TRUE,
)
# profile on south
##################################################################################
# mortality profile
dir.mod <- get_dir_ling('s', 18)
dir.profile.M <- "models/2021.s.018.001_fixTri3_newMprofile_down"
copy_SS_inputs(dir.old = dir.mod,
dir.new = dir.profile.M,
use_ss_new = TRUE,
copy_exe = TRUE,
copy_par = TRUE,
overwrite = TRUE)
start <- SS_readstarter(file = file.path(dir.profile.M, "starter.ss"),
verbose = FALSE)
start$ctlfile <- "control_modified.ss"
start$prior_like <- 1 # include prior likelihood for non-estimated parameters
SS_writestarter(start, dir = dir.profile.M, overwrite = TRUE)
setwd('c:/ss/lingcod/lingcod_2021/')
devtools::load_all()
#dir.profile.M <- "models/2021.s.018.001_fixTri3_newMprofile_up"
#M.vec = seq(0.18, 0.22, 0.01)
dir.profile.M <- "models/2021.s.018.001_fixTri3_newMprofile_down"
M.vec = seq(0.16, 0.10, -0.01)
SS_profile(dir = dir.profile.M,
masterctlfile = "ling_control.ss",
newctlfile = "control_modified.ss",
string = "NatM_uniform_Fem",
profilevec = M.vec,
extras = "-nohess -nox")
#extras = "-nox")
iantaylor-NOAA/Lingcod_2021 documentation built on Oct. 30, 2024, 6:42 p.m.
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### random collection of STAR-request-related code
# request 2, plotting implied fit to no_CPFV_DebWV_index sensitivity
get_mod('s', 14) # south base
get_mod('s', 14, 320) # sensitivity to removing CPFV DebWV
# comparison plots
dir.create('figures/STAR_Day1_request2')
r4ss::SSplotComparisons(r4ss::SSsummarize(list(mod.2021.s.014.001,
mod.2021.s.014.320)),
indexUncertainty=TRUE,
plotdir = 'figures/STAR_Day1_request2',
print = TRUE,
plot = FALSE,
legendlabels = c("South base", "no_CPFV_DebWV_index")
)
# request 8, changes to north comp data with and without sex-selectivity offset
devtools::load_all()
run_sensitivities(get_dir_ling("n", 23),
type = c("sens_create"),
numbers = c(221:224,404)
)
setwd("c:/ss/lingcod/lingcod_2021")
devtools::load_all()
run_sensitivities(get_dir_ling("n", 23),
type = c("sens_run"),
numbers = c(221:224,404)
)
# reverse retro on fishery ages
setwd("c:/ss/lingcod/lingcod_2021")
devtools::load_all()
run_sensitivities(get_dir_ling("n", 23),
type = c("sens_create", "sens_run"),
numbers = c(225:226)
)
dir.create('figures/STAR_request8')
mod.sum <- r4ss::SSsummarize(list(mod.2021.n.023.001,
mod.2021.n.023.221,
mod.2021.n.023.222,
mod.2021.n.023.223,
mod.2021.n.023.224,
mod.2021.n.023.404
))
r4ss::SSplotComparisons(mod.sum,
indexUncertainty=TRUE,
plotdir = 'figures/STAR_request8',
print = TRUE,
plot = FALSE,
legendloc = "topleft",
legendlabels = c("North new base",
"no FG ages",
"no FG ages 1999-2011",
"no FG ages + sex-selex-offset",
"no FG ages 1999-2011 + sex-selex-offset",
"sex-selex-offset")
)
# make sens table for STAR request 8
dir.create('models/2021.n.023.001_fixWAreccatchhistory/custom_plots/')
sens_make_table(
area = "n",
num = 23,
sens_base = 1,
sens_nums = c(221:224, 404),
sens_type = "star08",
write = TRUE
)
dir.create('figures/STAR_request8_extras')
mod.sum <- r4ss::SSsummarize(list(mod.2021.n.023.001,
mod.2021.n.023.221,
mod.2021.n.023.225,
mod.2021.n.023.226
))
r4ss::SSplotComparisons(mod.sum,
indexUncertainty=TRUE,
plotdir = 'figures/STAR_request8_extras',
print = TRUE,
plot = FALSE,
legendloc = "topleft",
legendlabels = c("North new base",
"no FG ages",
"no fishery ages prior to 1990",
"no fishery ages prior to 2000")
)
# make sens table for STAR request 8
sens_make_table(
area = "n",
num = 23,
sens_nums = c(221, 225, 226),
sens_type = "star08_extras_with_h",
write = TRUE,
#plot = FALSE
)
# comparison plots for STAR request 8 extras
dir.create('figures/STAR_request8_extras')
mod.sum <- r4ss::SSsummarize(list(mod.2021.n.023.001,
mod.2021.n.023.221,
mod.2021.n.023.225,
mod.2021.n.023.226
))
r4ss::SSplotComparisons(mod.sum,
indexUncertainty=TRUE,
plotdir = 'figures/STAR_request8_extras',
print = TRUE,
plot = FALSE,
legendloc = "topleft",
legendlabels = c("North new base",
"no FG ages",
"no fishery ages prior to 1990",
"no fishery ages prior to 2000")
)
# make sens table for STAR request 8 extras
sens_make_table(
area = "n",
num = 23,
sens_nums = c(221, 225, 226),
sens_type = "star08_extras_with_h",
write = TRUE,
#plot = FALSE
)
### request 11
setwd("c:/ss/lingcod/lingcod_2021")
devtools::load_all()
run_sensitivities(get_dir_ling("n", 23),
type = c("sens_create", "sens_run"),
numbers = c(411)
)
setwd("c:/ss/lingcod/lingcod_2021")
devtools::load_all()
run_sensitivities(get_dir_ling("s", 17),
type = c("sens_create", "sens_run"),
numbers = c(411)
)
dir.create('figures/STAR_request11')
mod.list <- list(mod.2021.n.023.001,
mod.2021.n.023.411,
mod.2021.s.017.001,
mod.2021.s.017.411
)
mod.sum <- r4ss::SSsummarize(mod.list)
mod.names <- c("North new base",
"North sex selex for fisheries",
"South new base",
"South sex selex for fisheries")
r4ss::SSplotComparisons(mod.sum,
indexUncertainty=TRUE,
plotdir = 'figures/STAR_request11',
print = TRUE,
plot = FALSE,
subplot = 1:12,
legendloc = "topleft",
legendlabels = mod.names)
)
mod.names <- c("North_new_base",
"North_sex_selex",
"South_new_base",
"South_sex_selex")
# make sens table for STAR request 11
sens_make_table(
area = "n",
num = 23,
plot_dir = 'figures/STAR_request11',
sens_mods = mod.list[1:2],
sens_base = 1,
sens_type = "star11",
write = TRUE
)
tab <- read.csv('tables/sens_table_n_star11.csv')
tab$Label <- gsub("Retained", "Ret.", tab$Label)
names(tab) <- c("Label", mod.names[1:2])
write.csv(tab, file = 'tables/sens_table_n_star11.csv', row.names = FALSE)
# make sens table for STAR request 11
sens_make_table(
area = "s",
num = 17,
plot_dir = 'figures/STAR_request11',
sens_mods = mod.list[3:4],
sens_base = 1,
sens_type = "star11",
write = TRUE
)
tab <- read.csv('tables/sens_table_s_star11.csv')
tab$Label <- gsub("Retained", "Ret.", tab$Label)
names(tab) <- c("Label", mod.names[3:4])
write.csv(tab, file = 'tables/sens_table_s_star11.csv', row.names = FALSE)
#### example call to get profile
# get directory with profiles in it
profiledir <- paste0(get_dir_ling("s", 17), '_profile_NatM_uniform_Fem_GP_1')
# load .Rdat file saved by nwfscDiag
load(file.path('models', profiledir, 'NatM_uniform_Fem_GP_1_profile_output.Rdat'))
# make profile plot with cutoff at ~0.66 to see where it intersects the profile
r4ss::SSplotProfile(profile_output$profilesummary,
minfraction = 0.001,
print=TRUE,
legendloc='top',
add_cutoff = TRUE,
ymax = 2, #example inputs to revise as needed
xlim = c(0.11, 0.29), #example inputs to revise as needed
cutoff_prob = 0.75,
plotdir = profiledir,
profile.string = "NatM_uniform_Fem",
profile.label="Female natural mortality (M)")
################################################################################
# STAR request 20 (states of nature for north model)
setwd("c:/ss/lingcod/lingcod_2021")
devtools::load_all()
run_sensitivities(get_dir_ling("n", 23),
type = c("sens_create", "sens_run"),
numbers = c(204)
)
plot_twopanel_comparison(list(mod.2021.n.023.001,
mod.2021.n.023.204,
mod.2021.n.023.420),
legendlabels = c("North base model",
"High state (no fishery ages)",
"Low state (sex-specific selectivity)"))
newdir <- 'figures/north_states'
dir.create(newdir)
compare_table <- sens_make_table(
area = "n",
num = 23,
sens_mods = list(mod.2021.n.023.001,
mod.2021.n.023.204,
mod.2021.n.023.420),
sens_names = c("North base model",
"High state (no fishery ages)",
"Low state A (sex-sel)"),
sens_type = "random",
plot = TRUE,
plot_dir = newdir,
table_dir = newdir,
write = TRUE,
)
# profile on south
##################################################################################
# mortality profile
dir.mod <- get_dir_ling('s', 18)
dir.profile.M <- "models/2021.s.018.001_fixTri3_newMprofile_down"
copy_SS_inputs(dir.old = dir.mod,
dir.new = dir.profile.M,
use_ss_new = TRUE,
copy_exe = TRUE,
copy_par = TRUE,
overwrite = TRUE)
start <- SS_readstarter(file = file.path(dir.profile.M, "starter.ss"),
verbose = FALSE)
start$ctlfile <- "control_modified.ss"
start$prior_like <- 1 # include prior likelihood for non-estimated parameters
SS_writestarter(start, dir = dir.profile.M, overwrite = TRUE)
setwd('c:/ss/lingcod/lingcod_2021/')
devtools::load_all()
dir.profile.M <- "models/2021.s.018.001_fixTri3_newMprofile_up"
M.vec = seq(0.18, 0.22, 0.01)
#dir.profile.M <- "models/2021.s.018.001_fixTri3_newMprofile_down"
#M.vec = seq(0.16, 0.10, -0.01)
r4ss::SS_profile(dir = dir.profile.M,
masterctlfile = "ling_control.ss",
newctlfile = "control_modified.ss",
string = "NatM_uniform_Fem",
profilevec = M.vec,
extras = "-nohess -nox")
mods.up <- SSgetoutput(keyvec=1:6, dirvec = "models/2021.s.018.001_fixTri3_newMprofile_up")
mods.down <- SSgetoutput(keyvec=1:6, dirvec = "models/2021.s.018.001_fixTri3_newMprofile_down")
test <- c(rev(mods.down), list(mod.2021.s.018.001), mods.up[1:5])
profilesummary <- test %>% SSsummarize()
SSplotProfile(profilesummary, # summary object
minfraction = 0.001,
print=FALSE,
ymax = 5.0,
profile.string = "NatM_uniform_Fem", # substring of profile parameter
profile.label="Female natural mortality (M)") # axis label
### random collection of STAR-request-related code
# request 2, plotting implied fit to no_CPFV_DebWV_index sensitivity
get_mod('s', 14) # south base
get_mod('s', 14, 320) # sensitivity to removing CPFV DebWV
# comparison plots
dir.create('figures/STAR_Day1_request2')
r4ss::SSplotComparisons(r4ss::SSsummarize(list(mod.2021.s.014.001,
mod.2021.s.014.320)),
indexUncertainty=TRUE,
plotdir = 'figures/STAR_Day1_request2',
print = TRUE,
plot = FALSE,
legendlabels = c("South base", "no_CPFV_DebWV_index")
)
# request 8, changes to north comp data with and without sex-selectivity offset
devtools::load_all()
run_sensitivities(get_dir_ling("n", 23),
type = c("sens_create"),
numbers = c(221:224,404)
)
setwd("c:/ss/lingcod/lingcod_2021")
devtools::load_all()
run_sensitivities(get_dir_ling("n", 23),
type = c("sens_run"),
numbers = c(221:224,404)
)
# reverse retro on fishery ages
setwd("c:/ss/lingcod/lingcod_2021")
devtools::load_all()
run_sensitivities(get_dir_ling("n", 23),
type = c("sens_create", "sens_run"),
numbers = c(225:226)
)
dir.create('figures/STAR_request8')
mod.sum <- r4ss::SSsummarize(list(mod.2021.n.023.001,
mod.2021.n.023.221,
mod.2021.n.023.222,
mod.2021.n.023.223,
mod.2021.n.023.224,
mod.2021.n.023.404
))
r4ss::SSplotComparisons(mod.sum,
indexUncertainty=TRUE,
plotdir = 'figures/STAR_request8',
print = TRUE,
plot = FALSE,
legendloc = "topleft",
legendlabels = c("North new base",
"no FG ages",
"no FG ages 1999-2011",
"no FG ages + sex-selex-offset",
"no FG ages 1999-2011 + sex-selex-offset",
"sex-selex-offset")
)
# make sens table for STAR request 8
dir.create('models/2021.n.023.001_fixWAreccatchhistory/custom_plots/')
sens_make_table(
area = "n",
num = 23,
sens_base = 1,
sens_nums = c(221:224, 404),
sens_type = "star08",
write = TRUE
)
dir.create('figures/STAR_request8_extras')
mod.sum <- r4ss::SSsummarize(list(mod.2021.n.023.001,
mod.2021.n.023.221,
mod.2021.n.023.225,
mod.2021.n.023.226
))
r4ss::SSplotComparisons(mod.sum,
indexUncertainty=TRUE,
plotdir = 'figures/STAR_request8_extras',
print = TRUE,
plot = FALSE,
legendloc = "topleft",
legendlabels = c("North new base",
"no FG ages",
"no fishery ages prior to 1990",
"no fishery ages prior to 2000")
)
# make sens table for STAR request 8
sens_make_table(
area = "n",
num = 23,
sens_nums = c(221, 225, 226),
sens_type = "star08_extras_with_h",
write = TRUE,
#plot = FALSE
)
# comparison plots for STAR request 8 extras
dir.create('figures/STAR_request8_extras')
mod.sum <- r4ss::SSsummarize(list(mod.2021.n.023.001,
mod.2021.n.023.221,
mod.2021.n.023.225,
mod.2021.n.023.226
))
r4ss::SSplotComparisons(mod.sum,
indexUncertainty=TRUE,
plotdir = 'figures/STAR_request8_extras',
print = TRUE,
plot = FALSE,
legendloc = "topleft",
legendlabels = c("North new base",
"no FG ages",
"no fishery ages prior to 1990",
"no fishery ages prior to 2000")
)
# make sens table for STAR request 8 extras
sens_make_table(
area = "n",
num = 23,
sens_nums = c(221, 225, 226),
sens_type = "star08_extras_with_h",
write = TRUE,
#plot = FALSE
)
### request 11
setwd("c:/ss/lingcod/lingcod_2021")
devtools::load_all()
run_sensitivities(get_dir_ling("n", 23),
type = c("sens_create", "sens_run"),
numbers = c(411)
)
setwd("c:/ss/lingcod/lingcod_2021")
devtools::load_all()
run_sensitivities(get_dir_ling("s", 17),
type = c("sens_create", "sens_run"),
numbers = c(411)
)
dir.create('figures/STAR_request11')
mod.list <- list(mod.2021.n.023.001,
mod.2021.n.023.411,
mod.2021.s.017.001,
mod.2021.s.017.411
)
mod.sum <- r4ss::SSsummarize(mod.list)
mod.names <- c("North new base",
"North sex selex for fisheries",
"South new base",
"South sex selex for fisheries")
r4ss::SSplotComparisons(mod.sum,
indexUncertainty=TRUE,
plotdir = 'figures/STAR_request11',
print = TRUE,
plot = FALSE,
subplot = 1:12,
legendloc = "topleft",
legendlabels = mod.names)
)
mod.names <- c("North_new_base",
"North_sex_selex",
"South_new_base",
"South_sex_selex")
# make sens table for STAR request 11
sens_make_table(
area = "n",
num = 23,
plot_dir = 'figures/STAR_request11',
sens_mods = mod.list[1:2],
sens_base = 1,
sens_type = "star11",
write = TRUE
)
tab <- read.csv('tables/sens_table_n_star11.csv')
tab$Label <- gsub("Retained", "Ret.", tab$Label)
names(tab) <- c("Label", mod.names[1:2])
write.csv(tab, file = 'tables/sens_table_n_star11.csv', row.names = FALSE)
# make sens table for STAR request 11
sens_make_table(
area = "s",
num = 17,
plot_dir = 'figures/STAR_request11',
sens_mods = mod.list[3:4],
sens_base = 1,
sens_type = "star11",
write = TRUE
)
tab <- read.csv('tables/sens_table_s_star11.csv')
tab$Label <- gsub("Retained", "Ret.", tab$Label)
names(tab) <- c("Label", mod.names[3:4])
write.csv(tab, file = 'tables/sens_table_s_star11.csv', row.names = FALSE)
#### example call to get profile
# get directory with profiles in it
profiledir <- paste0(get_dir_ling("s", 17), '_profile_NatM_uniform_Fem_GP_1')
# load .Rdat file saved by nwfscDiag
load(file.path('models', profiledir, 'NatM_uniform_Fem_GP_1_profile_output.Rdat'))
# make profile plot with cutoff at ~0.66 to see where it intersects the profile
r4ss::SSplotProfile(profile_output$profilesummary,
minfraction = 0.001,
print=TRUE,
legendloc='top',
add_cutoff = TRUE,
ymax = 2, #example inputs to revise as needed
xlim = c(0.11, 0.29), #example inputs to revise as needed
cutoff_prob = 0.75,
plotdir = profiledir,
profile.string = "NatM_uniform_Fem",
profile.label="Female natural mortality (M)")
################################################################################
# STAR request 20 (states of nature for north model)
setwd("c:/ss/lingcod/lingcod_2021")
devtools::load_all()
run_sensitivities(get_dir_ling("n", 23),
type = c("sens_create", "sens_run"),
numbers = c(204)
)
plot_twopanel_comparison(list(mod.2021.n.023.001,
mod.2021.n.023.204,
mod.2021.n.023.420,
mod.2021.n.023.003),
legendlabels = c("North base model",
"High state (no fishery ages)",
"Low state option 1 (sex-specific selectivity)",
"Low state option 2 (M = 0.3)"))
newdir <- 'figures/STAR_request20'
dir.create(newdir)
compare_table <- sens_make_table(
area = "n",
num = 23,
sens_mods = list(mod.2021.n.023.001,
mod.2021.n.023.204,
mod.2021.n.023.420,
mod.2021.n.023.003),
sens_names = c("North base model",
"High state (no fishery ages)",
"Low state A (sex-sel)",
"Low state B (M = 0.3)"),
sens_type = "random",
plot = TRUE,
plot_dir = newdir,
table_dir = newdir,
write = TRUE,
)
# profile on south
##################################################################################
# mortality profile
dir.mod <- get_dir_ling('s', 18)
dir.profile.M <- "models/2021.s.018.001_fixTri3_newMprofile_down"
copy_SS_inputs(dir.old = dir.mod,
dir.new = dir.profile.M,
use_ss_new = TRUE,
copy_exe = TRUE,
copy_par = TRUE,
overwrite = TRUE)
start <- SS_readstarter(file = file.path(dir.profile.M, "starter.ss"),
verbose = FALSE)
start$ctlfile <- "control_modified.ss"
start$prior_like <- 1 # include prior likelihood for non-estimated parameters
SS_writestarter(start, dir = dir.profile.M, overwrite = TRUE)
setwd('c:/ss/lingcod/lingcod_2021/')
devtools::load_all()
#dir.profile.M <- "models/2021.s.018.001_fixTri3_newMprofile_up"
#M.vec = seq(0.18, 0.22, 0.01)
dir.profile.M <- "models/2021.s.018.001_fixTri3_newMprofile_down"
M.vec = seq(0.16, 0.10, -0.01)
SS_profile(dir = dir.profile.M,
masterctlfile = "ling_control.ss",
newctlfile = "control_modified.ss",
string = "NatM_uniform_Fem",
profilevec = M.vec,
extras = "-nohess -nox")
#extras = "-nox")
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