From f05bb826fc22f0b47ed4f2a88bfdf83ce711b728 Mon Sep 17 00:00:00 2001 From: Jim Ianelli Date: Fri, 9 Feb 2024 15:39:06 -0800 Subject: [PATCH] updating? --- .github/.gitignore | 1 + .github/workflows/pkgdown.yaml | 35 + .gitignore | 2 + examples/.ai_re_sppcat.dat.swp | Bin 12288 -> 0 bytes examples/.ai_spm.dat.swp | Bin 12288 -> 0 bytes examples/Input_Log.rep | 12 +- examples/ai_re_sppcat.dat | 82 ++- examples/ai_spm.dat | 18 +- examples/means.out | 1254 ++++++++++++++++++++++++++++++-- examples/spm.r01 | 2 +- examples/spm.r02 | 2 +- examples/spm.rep | 2 +- 12 files changed, 1318 insertions(+), 92 deletions(-) create mode 100644 .github/.gitignore create mode 100644 .github/workflows/pkgdown.yaml delete mode 100644 examples/.ai_re_sppcat.dat.swp delete mode 100644 examples/.ai_spm.dat.swp diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 0000000..2d19fc7 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml new file mode 100644 index 0000000..63cbb18 --- /dev/null +++ b/.github/workflows/pkgdown.yaml @@ -0,0 +1,35 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/master/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main, master] + release: + types: [published] + workflow_dispatch: + +name: pkgdown + +jobs: + pkgdown: + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: + - uses: actions/checkout@v2 + + - uses: r-lib/actions/setup-pandoc@v1 + + - uses: r-lib/actions/setup-r@v1 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v1 + with: + extra-packages: pkgdown + needs: website + + - name: Deploy package + run: | + git config --local user.name "$GITHUB_ACTOR" + git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" + Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)' diff --git a/.gitignore b/.gitignore index 90d3093..209e61d 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,5 @@ inst/doc docs .Rproj.user +*.swp +*.r0. diff --git a/examples/.ai_re_sppcat.dat.swp b/examples/.ai_re_sppcat.dat.swp deleted file mode 100644 index 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nalts -13 +43 alt_list - 1943 0 0 0 0 0 0 0 0 0 0 0 0 + 1943 0 1 1 0 0 7 5 1 1 2 0 2 0 2 3 2 5 0 9 2 4 0 0 1 1 2 0 2 1 3 3 0 9 0 2 3 6 6 3 8 3 3 TAC_ABC -0 +2 SrType 0 Rec_Gen -0 +9 Fmsy_F35 0 Rec_Cond diff --git a/examples/ai_re_sppcat.dat b/examples/ai_re_sppcat.dat index 25b398d..08ab02a 100644 --- a/examples/ai_re_sppcat.dat +++ b/examples/ai_re_sppcat.dat @@ -1,37 +1,55 @@ - #_Number_of_years with specified catch (if begin-yr = 2004, and this number is "3", then subsequent values represent catches in 2004, 05, and 06 (to evaluate alts for 2007) - 2 - # Number of species - 1 - # OY Minimum -.1343248 # Note that this is for age-structured species 1330.148 - # OY Maximum -1943248 # Note that this is for age-structured species 1930.148 - # data files for each species - # 1 - data\ai_re_age10_m_22_1_original.dat - # ABC Multipliers - 1 - # scalars - 1 - # New Alt 4 Fabc SPRs (Rockfish = 0.75, other 0.6), Steller sea lion prey species between F40 and F60 (to meet OY Min) -0.75 - # Number of TAC model categories - 1 - # TAC model indices (for aggregating) - 1 - # Catch in each future year - 2022 305 - 2023 395 - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + +#nyrs_fixed_catch +2 +#nspp +1 +#OY_min +.1343248 # Note that this is for age-structured species 1330.148 +#OY_max +1943248 # Note that this is for age-structured species 1930.148 +# data files for each species +data\ai_re_age10_m_22_1_original.dat +#ABC_mults +1 +# scalars +1 +# New Alt 4 Fabc SPRs (Rockfish = 0.75, other 0.6), Steller sea lion prey species between F40 and F60 (to meet OY Min) +0.75 +# Number of TAC model categories +1 +# TAC model indices (for aggregating) +1 +# Catch in each future year + 2022 305 + 2023 395 diff --git a/examples/ai_spm.dat b/examples/ai_spm.dat index 6262fc1..9876642 100644 --- a/examples/ai_spm.dat +++ b/examples/ai_spm.dat @@ -3,15 +3,15 @@ AI_re #Tier 3 #nalts -1 +7 #alts 1 -#2 -#3 -#4 -#5 -#6 -#7 +2 +3 +4 +5 +6 +7 #tac_flag 1 #srr_type @@ -36,9 +36,9 @@ AI_re 1 #OY_min 10 -#OY_max +#OY_max 1943248 # Note that this is for age-structured species 1930.148 -#data_files for each species +#data_files ai_re.prj #ABC_mults 1 diff --git a/examples/means.out b/examples/means.out index 1538dec..97e6230 100644 --- a/examples/means.out +++ b/examples/means.out @@ -76,37 +76,37 @@ Year EquilAvgAgeF0 EquilAvgAgeFabc AvgAgeYr-1 -Alternative 0 Catch +Alternative 1 Catch Equil_Fabc Year -Alternative 0 ABCs +Alternative 1 ABCs Year -Alternative 0 TACs +Alternative 1 TACs Year -Alternative 0 Sp_Biomass +Alternative 1 Sp_Biomass Equil_Fabc Year -Alternative 0 Fishing Mortality +Alternative 1 Fishing Mortality Equil_Fabc Year -Alternative 0 Biomass +Alternative 1 Biomass Year -Alternative 0 Implied SPR rate +Alternative 1 Implied SPR rate Equil_Fabc Year @@ -115,37 +115,37 @@ Year EquilAvgAgeF0 EquilAvgAgeFabc AvgAgeYr-1 -Alternative 0 Catch +Alternative 1 Catch Equil_Fabc Year -Alternative 0 ABCs +Alternative 1 ABCs Year -Alternative 0 TACs +Alternative 1 TACs Year -Alternative 0 Sp_Biomass +Alternative 1 Sp_Biomass Equil_Fabc Year -Alternative 0 Fishing Mortality +Alternative 1 Fishing Mortality Equil_Fabc Year -Alternative 0 Biomass +Alternative 1 Biomass Year -Alternative 0 Implied SPR rate +Alternative 1 Implied SPR rate Equil_Fabc Year @@ -232,37 +232,37 @@ Year EquilAvgAgeF0 EquilAvgAgeFabc AvgAgeYr-1 -Alternative 0 Catch +Alternative 7 Catch Equil_Fabc Year -Alternative 0 ABCs +Alternative 7 ABCs Year -Alternative 0 TACs +Alternative 7 TACs Year -Alternative 0 Sp_Biomass +Alternative 7 Sp_Biomass Equil_Fabc Year -Alternative 0 Fishing Mortality +Alternative 7 Fishing Mortality Equil_Fabc Year -Alternative 0 Biomass +Alternative 7 Biomass Year -Alternative 0 Implied SPR rate +Alternative 7 Implied SPR rate Equil_Fabc Year @@ -271,37 +271,37 @@ Year EquilAvgAgeF0 EquilAvgAgeFabc AvgAgeYr-1 -Alternative 0 Catch +Alternative 5 Catch Equil_Fabc Year -Alternative 0 ABCs +Alternative 5 ABCs Year -Alternative 0 TACs +Alternative 5 TACs Year -Alternative 0 Sp_Biomass +Alternative 5 Sp_Biomass Equil_Fabc Year -Alternative 0 Fishing Mortality +Alternative 5 Fishing Mortality Equil_Fabc Year -Alternative 0 Biomass +Alternative 5 Biomass Year -Alternative 0 Implied SPR rate +Alternative 5 Implied SPR rate Equil_Fabc Year @@ -310,37 +310,37 @@ Year EquilAvgAgeF0 EquilAvgAgeFabc AvgAgeYr-1 -Alternative 0 Catch +Alternative 1 Catch Equil_Fabc Year -Alternative 0 ABCs +Alternative 1 ABCs Year -Alternative 0 TACs +Alternative 1 TACs Year -Alternative 0 Sp_Biomass +Alternative 1 Sp_Biomass Equil_Fabc Year -Alternative 0 Fishing Mortality +Alternative 1 Fishing Mortality Equil_Fabc Year -Alternative 0 Biomass +Alternative 1 Biomass Year -Alternative 0 Implied SPR rate +Alternative 1 Implied SPR rate Equil_Fabc Year @@ -349,37 +349,76 @@ Year EquilAvgAgeF0 EquilAvgAgeFabc AvgAgeYr-1 -Alternative 0 Catch +Alternative 1 Catch Equil_Fabc Year -Alternative 0 ABCs +Alternative 1 ABCs Year -Alternative 0 TACs +Alternative 1 TACs Year -Alternative 0 Sp_Biomass +Alternative 1 Sp_Biomass Equil_Fabc Year -Alternative 0 Fishing Mortality +Alternative 1 Fishing Mortality Equil_Fabc Year -Alternative 0 Biomass +Alternative 1 Biomass Year -Alternative 0 Implied SPR rate +Alternative 1 Implied SPR rate + +Equil_Fabc +Year + + +EquilAvgAgeF0 +EquilAvgAgeFabc +AvgAgeYr-1 +Alternative 2 Catch + +Equil_Fabc +Year + +Alternative 2 ABCs + + +Year + +Alternative 2 TACs + + +Year + +Alternative 2 Sp_Biomass + +Equil_Fabc +Year + +Alternative 2 Fishing Mortality + +Equil_Fabc +Year + +Alternative 2 Biomass + + +Year + +Alternative 2 Implied SPR rate Equil_Fabc Year @@ -424,6 +463,45 @@ Equil_Fabc Year +EquilAvgAgeF0 +EquilAvgAgeFabc +AvgAgeYr-1 +Alternative 2 Catch + +Equil_Fabc +Year + +Alternative 2 ABCs + + +Year + +Alternative 2 TACs + + +Year + +Alternative 2 Sp_Biomass + +Equil_Fabc +Year + +Alternative 2 Fishing Mortality + +Equil_Fabc +Year + +Alternative 2 Biomass + + +Year + +Alternative 2 Implied SPR rate + +Equil_Fabc +Year + + EquilAvgAgeF0 EquilAvgAgeFabc AvgAgeYr-1 @@ -463,6 +541,162 @@ Equil_Fabc Year +EquilAvgAgeF0 +EquilAvgAgeFabc +AvgAgeYr-1 +Alternative 2 Catch + +Equil_Fabc +Year + +Alternative 2 ABCs + + +Year + +Alternative 2 TACs + + +Year + +Alternative 2 Sp_Biomass + +Equil_Fabc +Year + +Alternative 2 Fishing Mortality + +Equil_Fabc +Year + +Alternative 2 Biomass + + +Year + +Alternative 2 Implied SPR rate + +Equil_Fabc +Year + + +EquilAvgAgeF0 +EquilAvgAgeFabc +AvgAgeYr-1 +Alternative 3 Catch + +Equil_Fabc +Year + +Alternative 3 ABCs + + +Year + +Alternative 3 TACs + + +Year + +Alternative 3 Sp_Biomass + +Equil_Fabc +Year + +Alternative 3 Fishing Mortality + +Equil_Fabc +Year + +Alternative 3 Biomass + + +Year + +Alternative 3 Implied SPR rate + +Equil_Fabc +Year + + +EquilAvgAgeF0 +EquilAvgAgeFabc +AvgAgeYr-1 +Alternative 2 Catch + +Equil_Fabc +Year + +Alternative 2 ABCs + + +Year + +Alternative 2 TACs + + +Year + +Alternative 2 Sp_Biomass + +Equil_Fabc +Year + +Alternative 2 Fishing Mortality + +Equil_Fabc +Year + +Alternative 2 Biomass + + +Year + +Alternative 2 Implied SPR rate + +Equil_Fabc +Year + + +EquilAvgAgeF0 +EquilAvgAgeFabc +AvgAgeYr-1 +Alternative 5 Catch + +Equil_Fabc +Year + +Alternative 5 ABCs + + +Year + +Alternative 5 TACs + + +Year + +Alternative 5 Sp_Biomass + +Equil_Fabc +Year + +Alternative 5 Fishing Mortality + +Equil_Fabc +Year + +Alternative 5 Biomass + + +Year + +Alternative 5 Implied SPR rate + +Equil_Fabc +Year + + EquilAvgAgeF0 EquilAvgAgeFabc AvgAgeYr-1 @@ -502,6 +736,942 @@ Equil_Fabc Year +EquilAvgAgeF0 +EquilAvgAgeFabc +AvgAgeYr-1 +Alternative 9 Catch + +Equil_Fabc +Year + +Alternative 9 ABCs + + +Year + +Alternative 9 TACs + + +Year + +Alternative 9 Sp_Biomass + +Equil_Fabc +Year + +Alternative 9 Fishing Mortality + +Equil_Fabc +Year + +Alternative 9 Biomass + + +Year + +Alternative 9 Implied SPR rate + +Equil_Fabc +Year + + +EquilAvgAgeF0 +EquilAvgAgeFabc +AvgAgeYr-1 +Alternative 2 Catch + +Equil_Fabc +Year 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8 Sp_Biomass + +Equil_Fabc +Year + +Alternative 8 Fishing Mortality + +Equil_Fabc +Year + +Alternative 8 Biomass + + +Year + +Alternative 8 Implied SPR rate + +Equil_Fabc +Year + + +EquilAvgAgeF0 +EquilAvgAgeFabc +AvgAgeYr-1 +Alternative 3 Catch + +Equil_Fabc +Year + +Alternative 3 ABCs + + +Year + +Alternative 3 TACs + + +Year + +Alternative 3 Sp_Biomass + +Equil_Fabc +Year + +Alternative 3 Fishing Mortality + +Equil_Fabc +Year + +Alternative 3 Biomass + + +Year + +Alternative 3 Implied SPR rate + +Equil_Fabc +Year + + +EquilAvgAgeF0 +EquilAvgAgeFabc +AvgAgeYr-1 +Alternative 3 Catch + +Equil_Fabc +Year + +Alternative 3 ABCs + + +Year + +Alternative 3 TACs + + +Year + +Alternative 3 Sp_Biomass + +Equil_Fabc +Year + +Alternative 3 Fishing Mortality + +Equil_Fabc +Year + +Alternative 3 Biomass + + +Year + +Alternative 3 Implied SPR rate + +Equil_Fabc +Year + + EquilAvgAgeF0 EquilAvgAgeFabc AvgAgeYr-1 diff --git a/examples/spm.r01 b/examples/spm.r01 index 2e11df6..878dcd2 100644 --- a/examples/spm.r01 +++ b/examples/spm.r01 @@ -3,4 +3,4 @@ EquilAvgAgeF0 EquilAvgAgeFabc Generation_Time_(assumes_recruitment_age=1) Options SR_Type Project_Recr_Assmption SR_Condition - 0 0 0 0 + 0 9 0 0 diff --git a/examples/spm.r02 b/examples/spm.r02 index 2e11df6..878dcd2 100644 --- a/examples/spm.r02 +++ b/examples/spm.r02 @@ -3,4 +3,4 @@ EquilAvgAgeF0 EquilAvgAgeFabc Generation_Time_(assumes_recruitment_age=1) Options SR_Type Project_Recr_Assmption SR_Condition - 0 0 0 0 + 0 9 0 0 diff --git a/examples/spm.rep b/examples/spm.rep index 746877c..930c882 100644 --- a/examples/spm.rep +++ b/examples/spm.rep @@ -3,7 +3,7 @@ EquilAvgAgeF0 EquilAvgAgeFabc Generation_Time_(assumes_recruitment_age=1) Options SR_Type Project_Recr_Assmption SR_Condition - 0 0 0 0 + 0 9 0 0 Stock B100 B40 B35 F40 F35 F_0