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Tighten longline landings selectivity priors
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@seananderson
seananderson committed Sep 19, 2024
1 parent 8b7c11c commit d9c094a
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Showing 22 changed files with 48 additions and 129 deletions.
93 changes: 6 additions & 87 deletions ss3/99-fix-stuff.R
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Original file line number Diff line number Diff line change
Expand Up @@ -6,93 +6,12 @@ if (FALSE) {
"A15_100discard",
"B1_1990inc", "B2_2010step", "B3_2005step", "B4_1990inc_lowM", "B5_2010step_lowM")

# for (i in seq_along(mods)) {
# f <- readLines(paste0("ss3/", mods[i], "/control.ss"))
# ii <- grep("NatM_p_1_Fem_GP_1", f)
# f[ii] <- gsub("0\\.074", "0.065", f[ii])
# writeLines(f, paste0("ss3/", mods[i], "/control.ss"))
# }
#
# mods <- c(
# "A10_highM"
# )
#
# for (i in seq_along(mods)) {
# f <- readLines(paste0("ss3/", mods[i], "/control.ss"))
# ii <- grep("NatM_p_1_Fem_GP_1", f)
# f[ii] <- gsub("0\\.074", "0.065", f[ii])
# writeLines(f, paste0("ss3/", mods[i], "/control.ss"))
# }
#
#

# for (i in seq_along(mods)) {
# f <- readLines(paste0("ss3/", mods[i], "/data.ss"))
# f[grep("1 -1 1 2 1 IPHC # 6", f)] <- "1 -1 1 1 1 IPHC # 6"
# f[grep("1 -1 1 2 1 HBLL # 7", f)] <- "1 -1 1 1 1 HBLL # 7"
# f[grep("1 -1 1 2 1 iRec # 9", f)] <- "1 -1 1 1 1 iRec # 9"
# f[grep("1 -1 1 2 1 Salmon_Bycatch # 10", f)] <- "1 -1 1 1 1 Salmon_Bycatch # 10"
# writeLines(f, paste0("ss3/", mods[i], "/data.ss"))
# }

for (i in seq_along(mods)) {
f <- readLines(paste0("ss3/", mods[i], "/data.ss"))

# previous:
# 2003 1 8 2.938 0.244
# 2004 1 8 4.053 0.113
# 2005 1 8 4.526 0.188
# 2006 1 8 4.684 0.101
# 2007 1 8 3.595 0.223
# 2008 1 8 2.974 0.114
# 2009 1 8 3.49 0.224
# 2010 1 8 4.982 0.133
# 2011 1 8 3.412 0.214
# 2012 1 8 2.702 0.144
# 2013 1 8 2.822 0.247
# 2014 1 8 2.643 0.197
# 2015 1 8 1.875 0.265
# 2016 1 8 1.589 0.149
# 2017 1 8 1.649 0.195
# 2018 1 8 1.567 0.126
# 2019 1 8 1.289 0.184
# 2020 1 8 0.801 0.236
# 2021 1 8 0.495 0.123
# 2022 1 8 0.813 0.142
# 2023 1 8 0.872 0.341


start <- grep("2003 1 8 2.938", f)
end <- grep("2023 1 8 0.872", f)

replacement <-
c(
"2003 1 8 2.669 0.228",
"2004 1 8 2.839 0.119",
"2005 1 8 2.938 0.169",
"2006 1 8 2.888 0.094",
"2007 1 8 2.218 0.157",
"2008 1 8 1.696 0.106",
"2009 1 8 2.198 0.161",
"2010 1 8 3.144 0.12",
"2011 1 8 2.299 0.157",
"2012 1 8 1.781 0.121",
"2013 1 8 1.754 0.149",
"2014 1 8 1.527 0.135",
"2015 1 8 1.257 0.176",
"2016 1 8 1.22 0.119",
"2017 1 8 1.209 0.143",
"2018 1 8 1.013 0.107",
"2019 1 8 0.766 0.178",
"2020 1 8 0.612 0.193",
"2021 1 8 0.48 0.096",
"2022 1 8 0.651 0.128",
"2023 1 8 0.664 0.256"
)
stopifnot(length(f[start:end])==length(replacement))

f[start:end] <- replacement

writeLines(f, paste0("ss3/", mods[i], "/data.ss"))
f <- readLines(paste0("ss3/", mods[i], "/control.ss"))
x1 <- grep("Size_DblN_peak_HookLine_Landings\\(4\\)", f)
x2 <- grep("SzSel_Male_Peak_HookLine_Landings\\(4\\)", f)
f[x1] <- gsub("28\\.5", "14.25", f[x1])
f[x2] <- gsub("28\\.5", "14.25", f[x2])
writeLines(f, paste0("ss3/", mods[i], "/control.ss"))
}
}
4 changes: 2 additions & 2 deletions ss3/A0/control.ss
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Original file line number Diff line number Diff line change
Expand Up @@ -376,13 +376,13 @@
-999 70 -999 0 0 0 -50 0 0 0 0 0 0 0 # SzSel_Male_Final_MidwaterTrawl(3)
0 1 0.884402 0.5 0.287717 2 3 0 0 0 0 0 0 0 # SzSel_Male_Scale_MidwaterTrawl(3)
# 4 HookLine_Landings LenSelex
35 110 101.432 95 28.5 6 3 0 0 0 0 0 0 0 # Size_DblN_peak_HookLine_Landings(4)
35 110 101.432 95 14.25 6 3 0 0 0 0 0 0 0 # Size_DblN_peak_HookLine_Landings(4)
-10 50 -10 0 0 0 -50 0 0 0 0 0 0 0 # Size_DblN_top_logit_HookLine_Landings(4)
-10 10 4.79594 4 0.3 6 3 0 0 0 0 0 0 0 # Size_DblN_ascend_se_HookLine_Landings(4)
-10 50 15 0 0 0 -50 0 0 0 0 0 0 0 # Size_DblN_descend_se_HookLine_Landings(4)
-999 70 -999 0 0 0 -50 0 0 0 0 0 0 0 # Size_DblN_start_logit_HookLine_Landings(4)
-999 999 -999 0 0 0 -50 0 0 0 0 0 0 0 # Size_DblN_end_logit_HookLine_Landings(4)
-100 0 -20.2021 -10 28.5 6 3 0 0 0 0 0 0 0 # SzSel_Male_Peak_HookLine_Landings(4)
-100 0 -20.2021 -10 14.25 6 3 0 0 0 0 0 0 0 # SzSel_Male_Peak_HookLine_Landings(4)
-10 10 -1.96691 0 0.3 6 3 0 0 0 0 0 0 0 # SzSel_Male_Ascend_HookLine_Landings(4)
-50 10 2.46477 -13.2 0.3 6 3 0 0 0 0 0 0 0 # SzSel_Male_Descend_HookLine_Landings(4)
-999 100 -999 0 0 0 -50 0 0 0 0 0 0 0 # SzSel_Male_Final_HookLine_Landings(4)
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4 changes: 2 additions & 2 deletions ss3/A1/control.ss
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Original file line number Diff line number Diff line change
Expand Up @@ -376,13 +376,13 @@
-999 70 -999 0 0 0 -50 0 0 0 0 0 0 0 # SzSel_Male_Final_MidwaterTrawl(3)
0 1 0.884402 0.5 0.287717 2 3 0 0 0 0 0 0 0 # SzSel_Male_Scale_MidwaterTrawl(3)
# 4 HookLine_Landings LenSelex
35 110 101.432 95 28.5 6 3 0 0 0 0 0 0 0 # Size_DblN_peak_HookLine_Landings(4)
35 110 101.432 95 14.25 6 3 0 0 0 0 0 0 0 # Size_DblN_peak_HookLine_Landings(4)
-10 50 -10 0 0 0 -50 0 0 0 0 0 0 0 # Size_DblN_top_logit_HookLine_Landings(4)
-10 10 4.79594 4 0.3 6 3 0 0 0 0 0 0 0 # Size_DblN_ascend_se_HookLine_Landings(4)
-10 50 15 0 0 0 -50 0 0 0 0 0 0 0 # Size_DblN_descend_se_HookLine_Landings(4)
-999 70 -999 0 0 0 -50 0 0 0 0 0 0 0 # Size_DblN_start_logit_HookLine_Landings(4)
-999 999 -999 0 0 0 -50 0 0 0 0 0 0 0 # Size_DblN_end_logit_HookLine_Landings(4)
-100 0 -20.2021 -10 28.5 6 3 0 0 0 0 0 0 0 # SzSel_Male_Peak_HookLine_Landings(4)
-100 0 -20.2021 -10 14.25 6 3 0 0 0 0 0 0 0 # SzSel_Male_Peak_HookLine_Landings(4)
-10 10 -1.96691 0 0.3 6 3 0 0 0 0 0 0 0 # SzSel_Male_Ascend_HookLine_Landings(4)
-50 10 2.46477 -13.2 0.3 6 3 0 0 0 0 0 0 0 # SzSel_Male_Descend_HookLine_Landings(4)
-999 100 -999 0 0 0 -50 0 0 0 0 0 0 0 # SzSel_Male_Final_HookLine_Landings(4)
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4 changes: 2 additions & 2 deletions ss3/A10_highM/control.ss
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Original file line number Diff line number Diff line change
Expand Up @@ -376,13 +376,13 @@
-999 70 -999 0 0 0 -50 0 0 0 0 0 0 0 # SzSel_Male_Final_MidwaterTrawl(3)
0 1 0.884402 0.5 0.287717 2 3 0 0 0 0 0 0 0 # SzSel_Male_Scale_MidwaterTrawl(3)
# 4 HookLine_Landings LenSelex
35 110 101.432 95 28.5 6 3 0 0 0 0 0 0 0 # Size_DblN_peak_HookLine_Landings(4)
35 110 101.432 95 14.25 6 3 0 0 0 0 0 0 0 # Size_DblN_peak_HookLine_Landings(4)
-10 50 -10 0 0 0 -50 0 0 0 0 0 0 0 # Size_DblN_top_logit_HookLine_Landings(4)
-10 10 4.79594 4 0.3 6 3 0 0 0 0 0 0 0 # Size_DblN_ascend_se_HookLine_Landings(4)
-10 50 15 0 0 0 -50 0 0 0 0 0 0 0 # Size_DblN_descend_se_HookLine_Landings(4)
-999 70 -999 0 0 0 -50 0 0 0 0 0 0 0 # Size_DblN_start_logit_HookLine_Landings(4)
-999 999 -999 0 0 0 -50 0 0 0 0 0 0 0 # Size_DblN_end_logit_HookLine_Landings(4)
-100 0 -20.2021 -10 28.5 6 3 0 0 0 0 0 0 0 # SzSel_Male_Peak_HookLine_Landings(4)
-100 0 -20.2021 -10 14.25 6 3 0 0 0 0 0 0 0 # SzSel_Male_Peak_HookLine_Landings(4)
-10 10 -1.96691 0 0.3 6 3 0 0 0 0 0 0 0 # SzSel_Male_Ascend_HookLine_Landings(4)
-50 10 2.46477 -13.2 0.3 6 3 0 0 0 0 0 0 0 # SzSel_Male_Descend_HookLine_Landings(4)
-999 100 -999 0 0 0 -50 0 0 0 0 0 0 0 # SzSel_Male_Final_HookLine_Landings(4)
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4 changes: 2 additions & 2 deletions ss3/A11_low_zfrac/control.ss
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Original file line number Diff line number Diff line change
Expand Up @@ -376,13 +376,13 @@
-999 70 -999 0 0 0 -50 0 0 0 0 0 0 0 # SzSel_Male_Final_MidwaterTrawl(3)
0 1 0.884402 0.5 0.287717 2 3 0 0 0 0 0 0 0 # SzSel_Male_Scale_MidwaterTrawl(3)
# 4 HookLine_Landings LenSelex
35 110 101.432 95 28.5 6 3 0 0 0 0 0 0 0 # Size_DblN_peak_HookLine_Landings(4)
35 110 101.432 95 14.25 6 3 0 0 0 0 0 0 0 # Size_DblN_peak_HookLine_Landings(4)
-10 50 -10 0 0 0 -50 0 0 0 0 0 0 0 # Size_DblN_top_logit_HookLine_Landings(4)
-10 10 4.79594 4 0.3 6 3 0 0 0 0 0 0 0 # Size_DblN_ascend_se_HookLine_Landings(4)
-10 50 15 0 0 0 -50 0 0 0 0 0 0 0 # Size_DblN_descend_se_HookLine_Landings(4)
-999 70 -999 0 0 0 -50 0 0 0 0 0 0 0 # Size_DblN_start_logit_HookLine_Landings(4)
-999 999 -999 0 0 0 -50 0 0 0 0 0 0 0 # Size_DblN_end_logit_HookLine_Landings(4)
-100 0 -20.2021 -10 28.5 6 3 0 0 0 0 0 0 0 # SzSel_Male_Peak_HookLine_Landings(4)
-100 0 -20.2021 -10 14.25 6 3 0 0 0 0 0 0 0 # SzSel_Male_Peak_HookLine_Landings(4)
-10 10 -1.96691 0 0.3 6 3 0 0 0 0 0 0 0 # SzSel_Male_Ascend_HookLine_Landings(4)
-50 10 2.46477 -13.2 0.3 6 3 0 0 0 0 0 0 0 # SzSel_Male_Descend_HookLine_Landings(4)
-999 100 -999 0 0 0 -50 0 0 0 0 0 0 0 # SzSel_Male_Final_HookLine_Landings(4)
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4 changes: 2 additions & 2 deletions ss3/A12_high_zfrac/control.ss
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Original file line number Diff line number Diff line change
Expand Up @@ -376,13 +376,13 @@
-999 70 -999 0 0 0 -50 0 0 0 0 0 0 0 # SzSel_Male_Final_MidwaterTrawl(3)
0 1 0.884402 0.5 0.287717 2 3 0 0 0 0 0 0 0 # SzSel_Male_Scale_MidwaterTrawl(3)
# 4 HookLine_Landings LenSelex
35 110 101.432 95 28.5 6 3 0 0 0 0 0 0 0 # Size_DblN_peak_HookLine_Landings(4)
35 110 101.432 95 14.25 6 3 0 0 0 0 0 0 0 # Size_DblN_peak_HookLine_Landings(4)
-10 50 -10 0 0 0 -50 0 0 0 0 0 0 0 # Size_DblN_top_logit_HookLine_Landings(4)
-10 10 4.79594 4 0.3 6 3 0 0 0 0 0 0 0 # Size_DblN_ascend_se_HookLine_Landings(4)
-10 50 15 0 0 0 -50 0 0 0 0 0 0 0 # Size_DblN_descend_se_HookLine_Landings(4)
-999 70 -999 0 0 0 -50 0 0 0 0 0 0 0 # Size_DblN_start_logit_HookLine_Landings(4)
-999 999 -999 0 0 0 -50 0 0 0 0 0 0 0 # Size_DblN_end_logit_HookLine_Landings(4)
-100 0 -20.2021 -10 28.5 6 3 0 0 0 0 0 0 0 # SzSel_Male_Peak_HookLine_Landings(4)
-100 0 -20.2021 -10 14.25 6 3 0 0 0 0 0 0 0 # SzSel_Male_Peak_HookLine_Landings(4)
-10 10 -1.96691 0 0.3 6 3 0 0 0 0 0 0 0 # SzSel_Male_Ascend_HookLine_Landings(4)
-50 10 2.46477 -13.2 0.3 6 3 0 0 0 0 0 0 0 # SzSel_Male_Descend_HookLine_Landings(4)
-999 100 -999 0 0 0 -50 0 0 0 0 0 0 0 # SzSel_Male_Final_HookLine_Landings(4)
Expand Down
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