Merge pull request #17 from afsc-assessments/jim

Jim

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.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 "[email protected]"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

.gitignore

@@ -1,3 +1,5 @@
 inst/doc
 docs
 .Rproj.user
+*.swp
+*.r0.

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 
 
 
 
 
 
-
-
-
-
-
-
-
-
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+
+#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 

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