reran documents after DISTANCE_FISHED_KM description updated

afsc-gap-products · Jan 14, 2025 · e235f7c · e235f7c
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diff --git a/GAP-Production-Data-Documentation.tex b/GAP-Production-Data-Documentation.tex
diff --git a/content/akfin-oracle-sql-r_files/figure-pdf/test-1-plot-1.pdf b/content/akfin-oracle-sql-r_files/figure-pdf/test-1-plot-1.pdf
diff --git a/content/akfin-oracle-sql-r_files/figure-pdf/test-2-plot-1.pdf b/content/akfin-oracle-sql-r_files/figure-pdf/test-2-plot-1.pdf
diff --git a/content/akfin-oracle-sql-r_files/figure-pdf/test-3-plot-1.pdf b/content/akfin-oracle-sql-r_files/figure-pdf/test-3-plot-1.pdf
diff --git a/content/akfin-oracle-sql-r_files/figure-pdf/test-4-fig-1.pdf b/content/akfin-oracle-sql-r_files/figure-pdf/test-4-fig-1.pdf
diff --git a/content/akfin-oracle-sql-r_files/figure-pdf/test-5-fig-1.pdf b/content/akfin-oracle-sql-r_files/figure-pdf/test-5-fig-1.pdf
diff --git a/content/akfin-oracle-sql-r_files/figure-pdf/test-6-fig-1.pdf b/content/akfin-oracle-sql-r_files/figure-pdf/test-6-fig-1.pdf
diff --git a/content/foss-api-r_files/figure-pdf/pollock-multi-idw-1.pdf b/content/foss-api-r_files/figure-pdf/pollock-multi-idw-1.pdf
diff --git a/content/foss-api-r_files/figure-pdf/pollock-multi-loc-1.pdf b/content/foss-api-r_files/figure-pdf/pollock-multi-loc-1.pdf
diff --git a/content/foss-api-r_files/figure-pdf/pollock-multi1-loc-1.pdf b/content/foss-api-r_files/figure-pdf/pollock-multi1-loc-1.pdf
diff --git a/content/foss-api-r_files/figure-pdf/pollock-multi2-loc-1.pdf b/content/foss-api-r_files/figure-pdf/pollock-multi2-loc-1.pdf
diff --git a/content/intro-workflow_files/figure-docx/mermaid-figure-4.png b/content/intro-workflow_files/figure-docx/mermaid-figure-4.png
diff --git a/content/intro-workflow_files/figure-docx/mermaid-figure-5.png b/content/intro-workflow_files/figure-docx/mermaid-figure-5.png
diff --git a/content/intro-workflow_files/figure-docx/mermaid-figure-6.png b/content/intro-workflow_files/figure-docx/mermaid-figure-6.png
diff --git a/content/references.bib b/content/references.bib
@@ -337,7 +337,7 @@ @article{defilippo2023evaluating
   pages = {1219283},
   year = {2023},
   publisher = {Frontiers Media SA}, 
-  doi = {https://doi.org/10.3389/fmars.2023.1219283}
+  doi = {10.3389/fmars.2023.1219283}
 }
 
 @article{Drummetal2016,
@@ -2180,9 +2180,9 @@ @inproceedings{RN914
 
 @misc{GAPakfin,
   author = {{Alaska Fisheries Information Network (AKFIN)}}, 
-  institution = {{NOAA Fisheries Alaska Fisheries Science Center, Goundfish Assessment Program}},
+  institution = {{NOAA Fisheries Alaska Fisheries Science Center, Groundfish Assessment Program}},
   year = {2024}, 
-  title = {AFSC Goundfish Assessment Program Design-Based Production Data},
+  title = {AFSC Groundfish Assessment Program Design-Based Production Data},
   howpublished = {https://akfinbi.psmfc.org/analytics/},
   url = {https://www.psmfc.org/program/alaska-fisheries-information-network-akfin},
   publisher = {{U.S. Dep. Commer.}},

diff --git a/content/references.csl b/content/references.csl
@@ -92,6 +92,11 @@
       <term name="et-al">et al.</term>
     </terms>
   </locale>
+  <locale xml:lang="ro">
+    <terms>
+      <term name="et-al">et al.</term>
+    </terms>
+  </locale>
   <!-- For Indigeneous Knowledge, assume the item is stored as `document` or `speech`
        and that Nation/Community, treaty, where the Elder lives, 
        and topic are all stored in `title`

diff --git a/docs/GAP-Production-Data-Documentation.docx b/docs/GAP-Production-Data-Documentation.docx
diff --git a/docs/GAP-Production-Data-Documentation.pdf b/docs/GAP-Production-Data-Documentation.pdf
diff --git a/docs/content/akfin-intro.html b/docs/content/akfin-intro.html
@@ -398,23 +398,23 @@ <h2 class="anchored" data-anchor-id="cite-this-data">Cite this data</h2>
 <p>Use the below bibtext citation, as cited in our group’s <a href="https://github.com/afsc-gap-products/citations/blob/main/cite/bibliography.bib">citation repository</a> for citing the data created and maintained in this repo <span class="citation" data-cites="GAPakfin">(<a href="end-refs.html#ref-GAPakfin" role="doc-biblioref">Alaska Fisheries Information Network (AKFIN), 2024</a>)</span>. Add “note = {Accessed: mm/dd/yyyy}” to append the day this data was accessed.</p>
 <div class="cell">
 <div class="cell-output cell-output-stdout">
-<pre><code> [1] "@misc{GAPakfin,"                                                                                  
- [2] "  author = {{Alaska Fisheries Information Network (AKFIN)}}, "                                    
- [3] "  institution = {{NOAA Fisheries Alaska Fisheries Science Center, Goundfish Assessment Program}},"
- [4] "  year = {2024}, "                                                                                
- [5] "  title = {AFSC Goundfish Assessment Program Design-Based Production Data},"                      
- [6] "  howpublished = {https://akfinbi.psmfc.org/analytics/},"                                         
- [7] "  url = {https://www.psmfc.org/program/alaska-fisheries-information-network-akfin},"              
- [8] "  publisher = {{U.S. Dep. Commer.}},"                                                             
- [9] "  copyright = {Public Domain} "                                                                   
-[10] "}"                                                                                                </code></pre>
+<pre><code> [1] "@misc{GAPakfin,"                                                                                   
+ [2] "  author = {{Alaska Fisheries Information Network (AKFIN)}}, "                                     
+ [3] "  institution = {{NOAA Fisheries Alaska Fisheries Science Center, Groundfish Assessment Program}},"
+ [4] "  year = {2024}, "                                                                                 
+ [5] "  title = {AFSC Groundfish Assessment Program Design-Based Production Data},"                      
+ [6] "  howpublished = {https://akfinbi.psmfc.org/analytics/},"                                          
+ [7] "  url = {https://www.psmfc.org/program/alaska-fisheries-information-network-akfin},"               
+ [8] "  publisher = {{U.S. Dep. Commer.}},"                                                              
+ [9] "  copyright = {Public Domain} "                                                                    
+[10] "}"                                                                                                 </code></pre>
 </div>
 </div>
 
 
 <div id="refs" class="references csl-bib-body hanging-indent" data-entry-spacing="0" data-line-spacing="2" role="list" style="display: none">
 <div id="ref-GAPakfin" class="csl-entry" role="listitem">
-Alaska Fisheries Information Network (AKFIN). (2024). <em>AFSC goundfish assessment program design-based production data</em>. <span>NOAA Fisheries Alaska Fisheries Science Center, Goundfish Assessment Program</span>; https://akfinbi.psmfc.org/analytics/; <span>U.S. Dep. Commer.</span> <a href="https://www.psmfc.org/program/alaska-fisheries-information-network-akfin">https://www.psmfc.org/program/alaska-fisheries-information-network-akfin</a>
+Alaska Fisheries Information Network (AKFIN). (2024). <em>AFSC groundfish assessment program design-based production data</em>. <span>NOAA Fisheries Alaska Fisheries Science Center, Groundfish Assessment Program</span>; https://akfinbi.psmfc.org/analytics/; <span>U.S. Dep. Commer.</span> <a href="https://www.psmfc.org/program/alaska-fisheries-information-network-akfin">https://www.psmfc.org/program/alaska-fisheries-information-network-akfin</a>
 </div>
 </div>
 </section>

diff --git a/docs/content/akfin-metadata.html b/docs/content/akfin-metadata.html
@@ -362,7 +362,7 @@ <h1 class="title"><span class="chapter-title">Data description</span></h1>
 <h2 class="anchored" data-anchor-id="data-tables">Data tables</h2>
 <section id="akfin_agecomp" class="level3">
 <h3 class="anchored" data-anchor-id="akfin_agecomp">AKFIN_AGECOMP</h3>
-<p>snapshot table for snapshot GAP_PRODUCTS.AKFIN_AGECOMP</p>
+<p>Mirror of GAP_PRODUCTS.AGECOMP. This table was created by the Resource Assessment and Conservation Engineering Division (RACE) Groundfish Assessment Program (GAP) of the Alaska Fisheries Science Center (AFSC). The GitHub repository for the scripts that created this code can be found at (https://github.com/afsc-gap-products/gap_products). There are no legal restrictions on access to the data. Last updated on 11 December 2024.</p>
 <p>Number of rows: 683,178</p>
 <p>Number of columns: 10</p>
 <table class="table table-striped" style="margin-left: auto; margin-right: auto;">
@@ -561,7 +561,7 @@ <h3 class="anchored" data-anchor-id="akfin_agecomp">AKFIN_AGECOMP</h3>
 </section>
 <section id="akfin_area" class="level3">
 <h3 class="anchored" data-anchor-id="akfin_area">AKFIN_AREA</h3>
-<p>snapshot table for snapshot GAP_PRODUCTS.AKFIN_AREA</p>
+<p>Mirror of GAP_PRODUCTS.AREA. This table was created by the Resource Assessment and Conservation Engineering Division (RACE) Groundfish Assessment Program (GAP) of the Alaska Fisheries Science Center (AFSC). The GitHub repository for the scripts that created this code can be found at (https://github.com/afsc-gap-products/gap_products). There are no legal restrictions on access to the data. Last updated on 11 December 2024.</p>
 <p>Number of rows: 395</p>
 <p>Number of columns: 9</p>
 <table class="table table-striped" style="margin-left: auto; margin-right: auto;">
@@ -743,7 +743,7 @@ <h3 class="anchored" data-anchor-id="akfin_area">AKFIN_AREA</h3>
 </section>
 <section id="akfin_biomass" class="level3">
 <h3 class="anchored" data-anchor-id="akfin_biomass">AKFIN_BIOMASS</h3>
-<p>snapshot table for snapshot GAP_PRODUCTS.AKFIN_BIOMASS</p>
+<p>Mirror of GAP_PRODUCTS.BIOMASS. This table was created by the Resource Assessment and Conservation Engineering Division (RACE) Groundfish Assessment Program (GAP) of the Alaska Fisheries Science Center (AFSC). The GitHub repository for the scripts that created this code can be found at (https://github.com/afsc-gap-products/gap_products). There are no legal restrictions on access to the data. Last updated on 11 December 2024.</p>
 <p>Number of rows: 2,623,956</p>
 <p>Number of columns: 16</p>
 <table class="table table-striped" style="margin-left: auto; margin-right: auto;">
@@ -1044,7 +1044,7 @@ <h3 class="anchored" data-anchor-id="akfin_biomass">AKFIN_BIOMASS</h3>
 </section>
 <section id="akfin_catch" class="level3">
 <h3 class="anchored" data-anchor-id="akfin_catch">AKFIN_CATCH</h3>
-<p>snapshot table for snapshot GAP_PRODUCTS.AKFIN_CATCH</p>
+<p>Non-zero catch records from RACEBASE.CATCH subsetted for standard GAP bottom trawl stations (i.e., HAULJOIN values associated with ABUNDANCE_HAUL = Y in RACEBASE.HAUL). This table was created by the Resource Assessment and Conservation Engineering Division (RACE) Groundfish Assessment Program (GAP) of the Alaska Fisheries Science Center (AFSC). The GitHub repository for the scripts that created this code can be found at (https://github.com/afsc-gap-products/gap_products). There are no legal restrictions on access to the data. Last updated on 11 December 2024.</p>
 <p>Number of rows: 973,538</p>
 <p>Number of columns: 6</p>
 <table class="table table-striped" style="margin-left: auto; margin-right: auto;">
@@ -1175,7 +1175,7 @@ <h3 class="anchored" data-anchor-id="akfin_catch">AKFIN_CATCH</h3>
 </section>
 <section id="akfin_cpue" class="level3">
 <h3 class="anchored" data-anchor-id="akfin_cpue">AKFIN_CPUE</h3>
-<p>snapshot table for snapshot GAP_PRODUCTS.AKFIN_CPUE</p>
+<p>Mirror of GAP_PRODUCTS.CPUE. This table was created by the Resource Assessment and Conservation Engineering Division (RACE) Groundfish Assessment Program (GAP) of the Alaska Fisheries Science Center (AFSC). The GitHub repository for the scripts that created this code can be found at (https://github.com/afsc-gap-products/gap_products). There are no legal restrictions on access to the data. Last updated on 11 December 2024.</p>
 <p>Number of rows: 21,558,257</p>
 <p>Number of columns: 7</p>
 <table class="table table-striped" style="margin-left: auto; margin-right: auto;">
@@ -1323,7 +1323,7 @@ <h3 class="anchored" data-anchor-id="akfin_cpue">AKFIN_CPUE</h3>
 </section>
 <section id="akfin_cruise" class="level3">
 <h3 class="anchored" data-anchor-id="akfin_cruise">AKFIN_CRUISE</h3>
-<p>snapshot table for snapshot GAP_PRODUCTS.AKFIN_CRUISE</p>
+<p>Cruise data for the five standard GAP bottom trawl regions. This table was created by the Resource Assessment and Conservation Engineering Division (RACE) Groundfish Assessment Program (GAP) of the Alaska Fisheries Science Center (AFSC). The GitHub repository for the scripts that created this code can be found at (https://github.com/afsc-gap-products/gap_products). There are no legal restrictions on access to the data. Last updated on 11 December 2024.</p>
 <p>Number of rows: 174</p>
 <p>Number of columns: 10</p>
 <table class="table table-striped" style="margin-left: auto; margin-right: auto;">
@@ -1505,7 +1505,7 @@ <h3 class="anchored" data-anchor-id="akfin_cruise">AKFIN_CRUISE</h3>
 </section>
 <section id="akfin_haul" class="level3">
 <h3 class="anchored" data-anchor-id="akfin_haul">AKFIN_HAUL</h3>
-<p>snapshot table for snapshot GAP_PRODUCTS.AKFIN_HAUL</p>
+<p>Standard GAP bottom trawl haul (station) data. This table was created by the Resource Assessment and Conservation Engineering Division (RACE) Groundfish Assessment Program (GAP) of the Alaska Fisheries Science Center (AFSC). The GitHub repository for the scripts that created this code can be found at (https://github.com/afsc-gap-products/gap_products). There are no legal restrictions on access to the data. Last updated on 11 December 2024.</p>
 <p>Number of rows: 34,263</p>
 <p>Number of columns: 25</p>
 <table class="table table-striped" style="margin-left: auto; margin-right: auto;">
@@ -1662,7 +1662,7 @@ <h3 class="anchored" data-anchor-id="akfin_haul">AKFIN_HAUL</h3>
 NUMBER(38,3)
 </td>
 <td style="text-align:left;">
-Distance the net fished (thousands of kilometers).
+Distance the net fished (kilometers).
 </td>
 </tr>
 <tr>
@@ -1959,7 +1959,7 @@ <h3 class="anchored" data-anchor-id="akfin_haul">AKFIN_HAUL</h3>
 </section>
 <section id="akfin_length" class="level3">
 <h3 class="anchored" data-anchor-id="akfin_length">AKFIN_LENGTH</h3>
-<p>snapshot table for snapshot GAP_PRODUCTS.AKFIN_LENGTH</p>
+<p>Length data subsetted for standard GAP bottom trawl stations (i.e., HAULJOIN values associated with ABUNDANCE_HAUL = Y in RACEBASE.HAUL). This table was created by the Resource Assessment and Conservation Engineering Division (RACE) Groundfish Assessment Program (GAP) of the Alaska Fisheries Science Center (AFSC). The GitHub repository for the scripts that created this code can be found at (https://github.com/afsc-gap-products/gap_products). There are no legal restrictions on access to the data. Last updated on 11 December 2024.</p>
 <p>Number of rows: 4,456,380</p>
 <p>Number of columns: 7</p>
 <table class="table table-striped" style="margin-left: auto; margin-right: auto;">
@@ -2221,7 +2221,7 @@ <h3 class="anchored" data-anchor-id="akfin_metadata_column">AKFIN_METADATA_COLUM
 </section>
 <section id="akfin_sizecomp" class="level3">
 <h3 class="anchored" data-anchor-id="akfin_sizecomp">AKFIN_SIZECOMP</h3>
-<p>snapshot table for snapshot GAP_PRODUCTS.AKFIN_SIZECOMP</p>
+<p>Mirror of GAP_PRODUCTS.SIZECOMP. This table was created by the Resource Assessment and Conservation Engineering Division (RACE) Groundfish Assessment Program (GAP) of the Alaska Fisheries Science Center (AFSC). The GitHub repository for the scripts that created this code can be found at (https://github.com/afsc-gap-products/gap_products). There are no legal restrictions on access to the data. Last updated on 11 December 2024.</p>
 <p>Number of rows: 3,284,629</p>
 <p>Number of columns: 7</p>
 <table class="table table-striped" style="margin-left: auto; margin-right: auto;">
@@ -2369,7 +2369,7 @@ <h3 class="anchored" data-anchor-id="akfin_sizecomp">AKFIN_SIZECOMP</h3>
 </section>
 <section id="akfin_specimen" class="level3">
 <h3 class="anchored" data-anchor-id="akfin_specimen">AKFIN_SPECIMEN</h3>
-<p>snapshot table for snapshot GAP_PRODUCTS.AKFIN_SPECIMEN</p>
+<p>Specimen data subsetted for standard GAP bottom trawl stations (i.e., HAULJOIN values associated with ABUNDANCE_HAUL = Y in RACEBASE.HAUL). This table was created by the Resource Assessment and Conservation Engineering Division (RACE) Groundfish Assessment Program (GAP) of the Alaska Fisheries Science Center (AFSC). The GitHub repository for the scripts that created this code can be found at (https://github.com/afsc-gap-products/gap_products). There are no legal restrictions on access to the data. Last updated on 11 December 2024.</p>
 <p>Number of rows: 589,317</p>
 <p>Number of columns: 12</p>
 <table class="table table-striped" style="margin-left: auto; margin-right: auto;">
@@ -2602,7 +2602,7 @@ <h3 class="anchored" data-anchor-id="akfin_specimen">AKFIN_SPECIMEN</h3>
 </section>
 <section id="akfin_stratum_groups" class="level3">
 <h3 class="anchored" data-anchor-id="akfin_stratum_groups">AKFIN_STRATUM_GROUPS</h3>
-<p>snapshot table for snapshot GAP_PRODUCTS.AKFIN_STRATUM_GROUPS</p>
+<p>Mirror of GAP_PRODUCTS.STRATUM_GROUPS. This table was created by the Resource Assessment and Conservation Engineering Division (RACE) Groundfish Assessment Program (GAP) of the Alaska Fisheries Science Center (AFSC). The GitHub repository for the scripts that created this code can be found at (https://github.com/afsc-gap-products/gap_products). There are no legal restrictions on access to the data. Last updated on 11 December 2024.</p>
 <p>Number of rows: 768</p>
 <p>Number of columns: 4</p>
 <table class="table table-striped" style="margin-left: auto; margin-right: auto;">
@@ -2699,7 +2699,7 @@ <h3 class="anchored" data-anchor-id="akfin_stratum_groups">AKFIN_STRATUM_GROUPS<
 </section>
 <section id="akfin_survey_design" class="level3">
 <h3 class="anchored" data-anchor-id="akfin_survey_design">AKFIN_SURVEY_DESIGN</h3>
-<p>snapshot table for snapshot GAP_PRODUCTS.AKFIN_SURVEY_DESIGN</p>
+<p>Mirror of GAP_PRODUCTS.SURVEY_DESIGN. This table was created by the Resource Assessment and Conservation Engineering Division (RACE) Groundfish Assessment Program (GAP) of the Alaska Fisheries Science Center (AFSC). The GitHub repository for the scripts that created this code can be found at (https://github.com/afsc-gap-products/gap_products). There are no legal restrictions on access to the data. Last updated on 11 December 2024.</p>
 <p>Number of rows: 87</p>
 <p>Number of columns: 3</p>
 <table class="table table-striped" style="margin-left: auto; margin-right: auto;">
@@ -2779,7 +2779,7 @@ <h3 class="anchored" data-anchor-id="akfin_survey_design">AKFIN_SURVEY_DESIGN</h
 </section>
 <section id="akfin_taxonomic_classification" class="level3">
 <h3 class="anchored" data-anchor-id="akfin_taxonomic_classification">AKFIN_TAXONOMIC_CLASSIFICATION</h3>
-<p>snapshot table for snapshot GAP_PRODUCTS.AKFIN_TAXONOMIC_CLASSIFICATION</p>
+<p>Mirror of GAP_PRODUCTS.TAXONOMIC_CLASSIFICATION, subsetting for SURVEY_SPECIES = 1 includes taxonomic classification information accepted by the AFSC GAP bottom trawl survey. This table was created by the Resource Assessment and Conservation Engineering Division (RACE) Groundfish Assessment Program (GAP) of the Alaska Fisheries Science Center (AFSC). The GitHub repository for the scripts that created this code can be found at (https://github.com/afsc-gap-products/gap_products). There are no legal restrictions on access to the data. Last updated on 11 December 2024.</p>
 <p>Number of rows: 2,718</p>
 <p>Number of columns: 19</p>
 <table class="table table-striped" style="margin-left: auto; margin-right: auto;">
@@ -3131,7 +3131,7 @@ <h3 class="anchored" data-anchor-id="akfin_taxonomic_classification">AKFIN_TAXON
 </section>
 <section id="akfin_taxonomic_groups" class="level3">
 <h3 class="anchored" data-anchor-id="akfin_taxonomic_groups">AKFIN_TAXONOMIC_GROUPS</h3>
-<p>snapshot table for snapshot GAP_PRODUCTS.AKFIN_TAXONOMIC_GROUPS</p>
+<p>Mirror of GAP_PRODUCTS.TAXON_GROUPS. This table was created by the Resource Assessment and Conservation Engineering Division (RACE) Groundfish Assessment Program (GAP) of the Alaska Fisheries Science Center (AFSC). The GitHub repository for the scripts that created this code can be found at (https://github.com/afsc-gap-products/gap_products). There are no legal restrictions on access to the data. Last updated on 11 December 2024.</p>
 <p>Number of rows: 2,777</p>
 <p>Number of columns: 22</p>
 <table class="table table-striped" style="margin-left: auto; margin-right: auto;">