finishing changes from co-working session

.quarto/xref/14aca4aa

@@ -1 +1 @@
-{"entries":[],"options":{"chapters":true},"headings":["our-objective","user-resources","background-of-the-gap_products-repo","major-advantages"]}
+{"headings":["our-objective","user-resources","background-of-the-gap_products-repo","major-advantages"],"entries":[],"options":{"chapters":true}}

content/intro-survey-background.qmd

@@ -205,7 +205,7 @@ table_print <- table_raw %>%
     area = "Area (km2)", 
     STRATUM = "# Statistical Areas", 
     STATION = "# Possible Stations" ) %>% 
-    theme_flextable_nmfstm(x = ., 
+  theme_flextable_nmfstm(x = ., 
                            font0 = "Arial", 
                            pad = 0, 
                            row_lines = FALSE, 

content/other-intro.qmd

@@ -8,12 +8,19 @@ title: Product Outputs
 
 To accompany these data, we also produce data products to make using our data more accessible and straightforward. 
 
-```{r}
+```{r, echo=FALSE}
 library(googledrive)
 library(magrittr)
 library(flextable)
 googledrive::drive_auth()
 2
+```
+
+```{r prod-table}
+#| tbl-cap: Survey of products developed by GAP
+#| message: false
+#| warning: false
+#| echo: false
 
 googledrive::drive_download(file = googledrive::as_id("1FJe2kqkcKpgOh4YS1_QJqaPX2wvOdhGu0DkPBF-SsQs"), 
                               type = "csv",
@@ -25,9 +32,9 @@ table_raw <- read.csv(file = here::here("temp", "other_products.csv"),
   dplyr::arrange(product_type)  %>% 
   dplyr::mutate(product_type = stringr::str_to_title(product_type), 
                 poc_goa_ai = gsub(x = poc_goa_ai, 
-                                  replacement = " & ", pattern = " &\n"), 
+                                  pattern = " & ", replacement = " &\n"), 
                 poc_bs = gsub(x = poc_bs, 
-                                  replacement = " & ", pattern = " &\n"), 
+                                  pattern = " & ", replacement = " &\n"), 
                 include = ifelse(is.na(include), TRUE, include)) %>% 
   dplyr::filter(include) %>% 
   dplyr::select(-include)
@@ -62,7 +69,7 @@ table_print <-
   flextable::color(j = "product", i = ~ is.na(product_type), 
                    color = "darkblue", part = "body") %>% 
   flextable::bg(i = ~ !is.na(product_type), bg = "grey70") %>% 
-  # flextable::bold(i = ~ !is.na(product_type), bold = TRUE) %>% 
+  flextable::bold(i = ~ is.na(product_type), bold = TRUE, j = "product") %>%
   flextable::italic(i = ~ !is.na(product_type), italic = TRUE) %>% 
     flextable::padding(padding.left = 10, 
                      j = "product", 

docs/search.json

@@ -263,7 +263,7 @@
     "href": "content/other-intro.html",
     "title": "Product Outputs",
     "section": "",
-    "text": "To accompany these data, we also produce data products to make using our data more accessible and straightforward.\n\n\n[1] 2\n\n\n\nProductPoint of ContactGOA/AIPoint of ContactBSDescriptionAnalysisDesign-based indices for target speciesNed LamanRebecca HaehnDesign-based age or length compositionNed LamanRebecca HaehnModel-based indices, age comps (stock assessment), area occupied, and COG (ESP)Cecilia O'Leary Lewis BarnettAnnual bottom and surface temperature summary (ESR, stock assessment)Cecilia O'LearySean Rohan & Lewis BarnettSalinity indicator (ESR in 2024)Sean Rohan & Ned CokeletBering Sea cold pool index and temperature data products (ESR, ESP, stock assessment)Sean Rohan & Lewis BarnettAnnual fish condition (ESR)Cecilia O'LearyBianca Prohaska & Sean RohanGroundfish morphometric condition indicators for fish in the Bering Sea, Aleutian Islands, and Gulf of AlaskaRockfish indices vs environmental gradients (ESR)Alexandra DowlinStructure-Forming Invertebrates-Habitat Areas of Particular Concern (SFI-HAPC) (ESR)Ned LamanForage fishes (ESR)Ned LamanMiscellaneous species (ESR)Ned LamanThaddeus BuserJellies (ESR)Ned LamanThaddeus BuserEssential fish habitatMegsie Siple Sean RohanCommunicationAnnual survey data reportMegsie Siple & Bethany RiggleEmily Markowitz & Liz DawsonThe Alaska Fisheries Science Center uses the NOAA Technical Memorandum series to issue informal scientific and technical publications when complete formal review and editorial processing are not appropriate or feasible. Documents within this series reflect sound professional work and may be referenced in the formal scientific and technical literature. These are available online and the latest publications for each survey are listed below (https://repository.library.noaa.gov/). ADF&G report of research activitiesAlexandra DowlinNicole Charriere & Rebecca HaehnPlan team survey results presentationNed LamanDuane StevensonEach year, the survey teams present their findings to the North Pacific Groundfish Plan Team. Find those presentations, recordings, and attachments on the North Pacific Fishery Management Council website (https://www.npfmc.org/about-the-council/plan-teams/bsai-and-goa-groundfish/). Community highlights reportTBDEmily MarkowitzEach year, the Groundfish Assessment Program compiles it’s survey findings for communities around Alaska. DataFinalized bottom trawl dataNed LamanDuane StevensonData requestsNancy RobersonNancy RobersonSpecies codebookNancy RobersonNancy RobersonThe Species and Gear Code book is a listing of codes used for fish and invertebrates identified in RACE Division surveys. Survey protocolsNancy RobersonNancy RobersonGroundfish bottom trawl survey protocols are documented in NOAA protocols for groundfish bottom trawl surveys of the nation’s fishery resources. Visualization ToolsAlaska groundfish maps (CPUE, etc.)Sean Rohan"
+    "text": "To accompany these data, we also produce data products to make using our data more accessible and straightforward.\n\n\n[1] 2\n\n\n\n\n\nSurvey of products developed by GAPProductPoint of ContactGOA/AIPoint of ContactBSDescriptionAnalysisDesign-based indices for target speciesNed LamanRebecca HaehnDesign-based age or length compositionNed LamanRebecca HaehnModel-based indices, age comps (stock assessment), area occupied, and COG (ESP)Cecilia O'Leary Lewis BarnettAnnual bottom and surface temperature summary (ESR, stock assessment)Cecilia O'LearySean Rohan &Lewis BarnettSalinity indicator (ESR in 2024)Sean Rohan &Ned CokeletR package for developing salinity indicators (Will be available for the ESR in 2024)Bering Sea cold pool index and temperature data products (ESR, ESP, stock assessment)Sean Rohan &Lewis BarnettR package for Bering Sea cold pool index and temperature data products (ESR, ESP, stock assessment)Annual fish condition (ESR)Cecilia O'LearyBianca Prohaska &Sean RohanR package for developing the groundfish morphometric condition indicators for fish in the Bering Sea, Aleutian Islands, and Gulf of AlaskaRockfish indices vs environmental gradients (ESR)Alexandra DowlinStructure-Forming Invertebrates-Habitat Areas of Particular Concern (SFI-HAPC) (ESR)Ned LamanForage fishes (ESR)Ned LamanMiscellaneous species (ESR)Ned LamanThaddeus BuserJellies (ESR)Ned LamanThaddeus BuserEssential fish habitatMegsie Siple Sean RohanCommunicationAnnual survey data reportMegsie Siple &Bethany RiggleEmily Markowitz &Liz DawsonThe Alaska Fisheries Science Center uses the NOAA Technical Memorandum series to issue informal scientific and technical publications when complete formal review and editorial processing are not appropriate or feasible. Documents within this series reflect sound professional work and may be referenced in the formal scientific and technical literature. These are available online and the latest publications for each survey are listed below (https://repository.library.noaa.gov/). ADF&G report of research activitiesAlexandra DowlinNicole Charriere &Rebecca HaehnPlan team survey results presentationNed LamanDuane StevensonEach year, the survey teams present their findings to the North Pacific Groundfish Plan Team. Find those presentations, recordings, and attachments on the North Pacific Fishery Management Council website (https://www.npfmc.org/about-the-council/plan-teams/bsai-and-goa-groundfish/). Community highlights reportTBDEmily MarkowitzEach year, the Groundfish Assessment Program compiles it’s survey findings for communities around Alaska. DataFinalized bottom trawl dataNed LamanDuane StevensonData requestsNancy RobersonNancy RobersonSpecies codebookNancy RobersonNancy RobersonThe Species and Gear Code book is a listing of codes used for fish and invertebrates identified in RACE Division surveys. Survey protocolsNancy RobersonNancy RobersonGroundfish bottom trawl survey protocols are documented in NOAA protocols for groundfish bottom trawl surveys of the nation’s fishery resources. Visualization ToolsAlaska groundfish maps (CPUE, etc.)Sean RohanR package of Alaska groundfish maping tools"
   },
   {
     "objectID": "content/other-pkgs.html#r-packages",

docs/sitemap.xml

@@ -2,102 +2,102 @@
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/index.html</loc>
-    <lastmod>2023-10-11T21:59:34.071Z</lastmod>
+    <lastmod>2023-10-11T22:17:41.573Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/intro-survey-background.html</loc>
-    <lastmod>2023-10-11T21:59:34.110Z</lastmod>
+    <lastmod>2023-10-11T22:17:41.588Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/intro-workflow.html</loc>
-    <lastmod>2023-10-11T21:59:34.119Z</lastmod>
+    <lastmod>2023-10-11T22:17:41.598Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/intro-news.html</loc>
-    <lastmod>2023-10-11T21:59:34.128Z</lastmod>
+    <lastmod>2023-10-11T22:17:41.605Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/product-intro.html</loc>
-    <lastmod>2023-10-11T21:59:34.157Z</lastmod>
+    <lastmod>2023-10-11T22:17:41.613Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/product-metadata.html</loc>
-    <lastmod>2023-10-11T21:59:34.180Z</lastmod>
+    <lastmod>2023-10-11T22:17:41.633Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/akfin-intro.html</loc>
-    <lastmod>2023-10-11T21:59:34.212Z</lastmod>
+    <lastmod>2023-10-11T22:17:41.640Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/akfin-metadata.html</loc>
-    <lastmod>2023-10-11T21:59:34.260Z</lastmod>
+    <lastmod>2023-10-11T22:17:41.684Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/akfin-oracle-sql-r.html</loc>
-    <lastmod>2023-10-11T21:59:34.330Z</lastmod>
+    <lastmod>2023-10-11T22:17:41.751Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/akfin-api-r.html</loc>
-    <lastmod>2023-10-11T21:59:34.341Z</lastmod>
+    <lastmod>2023-10-11T22:17:41.767Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/foss-intro.html</loc>
-    <lastmod>2023-10-11T21:59:34.370Z</lastmod>
+    <lastmod>2023-10-11T22:17:41.777Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/foss-metadata.html</loc>
-    <lastmod>2023-10-11T21:59:34.399Z</lastmod>
+    <lastmod>2023-10-11T22:17:41.802Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/foss-platform.html</loc>
-    <lastmod>2023-10-11T21:59:34.413Z</lastmod>
+    <lastmod>2023-10-11T22:17:41.812Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/foss-api-r.html</loc>
-    <lastmod>2023-10-11T21:59:34.470Z</lastmod>
+    <lastmod>2023-10-11T22:17:41.860Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/foss-api-py.html</loc>
-    <lastmod>2023-10-11T21:59:34.493Z</lastmod>
+    <lastmod>2023-10-11T22:17:41.935Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/foss-oracle-r.html</loc>
-    <lastmod>2023-10-11T21:59:34.508Z</lastmod>
+    <lastmod>2023-10-11T22:17:41.955Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/other-intro.html</loc>
-    <lastmod>2023-10-11T21:59:34.569Z</lastmod>
+    <lastmod>2023-10-11T22:17:41.981Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/other-pkgs.html</loc>
-    <lastmod>2023-10-11T21:59:34.582Z</lastmod>
+    <lastmod>2023-10-11T22:17:41.994Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/end-contact-us.html</loc>
-    <lastmod>2023-10-11T21:59:34.598Z</lastmod>
+    <lastmod>2023-10-11T22:17:42.002Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/end-run-notes.html</loc>
-    <lastmod>2023-10-11T21:59:34.611Z</lastmod>
+    <lastmod>2023-10-11T22:17:42.013Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/end-data-constraints.html</loc>
-    <lastmod>2023-10-11T21:59:34.625Z</lastmod>
+    <lastmod>2023-10-11T22:17:42.021Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/end-acknowledgements.html</loc>
-    <lastmod>2023-10-11T21:59:34.642Z</lastmod>
+    <lastmod>2023-10-11T22:17:42.033Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/content/end-refs.html</loc>
-    <lastmod>2023-10-11T21:59:34.654Z</lastmod>
+    <lastmod>2023-10-11T22:17:42.043Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/GAP-Production-Data-Documentation.pdf</loc>
-    <lastmod>2023-10-11T21:59:12.641Z</lastmod>
+    <lastmod>2023-10-11T22:17:21.786Z</lastmod>
   </url>
   <url>
     <loc>https://afsc-gap-products.github.io/gap_products/GAP-Production-Data-Documentation.docx</loc>
-    <lastmod>2023-10-11T21:59:27.591Z</lastmod>
+    <lastmod>2023-10-11T22:17:35.333Z</lastmod>
   </url>
 </urlset>