Merge pull request #106 from NOAA-EDAB/dev

Pull dev into master

README.md

@@ -1,6 +1,6 @@
 # tech-doc
 
-[![Travis-CI Build Status](https://travis-ci.org/NOAA-EDAB/tech-doc.svg?branch=master)](https://travis-ci.org/NOAA-EDAB/tech-doc)
+[![build-book](https://github.com/NOAA-EDAB/tech-doc/actions/workflows/bookdown.yaml/badge.svg)](https://github.com/NOAA-EDAB/tech-doc/actions/workflows/bookdown.yaml)
 ![gitleaks](https://github.com/NOAA-EDAB/tech-doc/workflows/gitleaks/badge.svg)
 
 Technical documentation for State of the Ecosystem indicators and general methods. 

_bookdown.yml

@@ -1,84 +1,132 @@
 book_filename: "tech_doc"
-rmd_files: ["index.Rmd",
-"chapters/erddap_query_and_build.Rmd",
-"chapters/aggregate_groups.rmd",
-"chapters/Annual_SST_cycle_indicator.Rmd",
-"chapters/Aquaculture_indicators.Rmd",
-"chapters/Bennet_indicator.Rmd",
-"chapters/bottom_temperature_GLORYS.Rmd",
-"chapters/bottom_temperature_highres.Rmd",
-"chapters/bottom_temperature_insitu.Rmd",
-"chapters/calanus_stage.Rmd",
-"chapters/Catch_and_Fleet_Diversity_indicators.Rmd",
-"chapters/ches_bay_sal.Rmd",
-#"chapters/ches_bay_temp.Rmd",
-"chapters/ches_bay_sst.Rmd",
-"chapters/ches_bay_water_quality.Rmd",
-"chapters/cold_pool_index.Rmd", 
-"chapters/landings_data.Rmd",
-"chapters/conceptualmodels.Rmd",
-"chapters/EPU.Rmd",
-"chapters/ecosystem_overfishing.Rmd",
-"chapters/Expected_Number.Rmd", 
-#"chapters/forage_anomaly.Rmd",
-"chapters/Condition_indicator.Rmd",
-"chapters/productivity_for_tech_memo.Rmd",
-"chapters/Wind_area_fisheries_revenue.Rmd",
-"chapters/Comm_rel_vuln_indicator.Rmd",
-"chapters/Forage_Fish_Biomass_Index.Rmd",
-"chapters/forage_energy_density.Rmd",
-"chapters/seal_pups.Rmd",
-"chapters/gulf_stream_index.Rmd",
-"chapters/occupancy_indicator.Rmd",
-"chapters/habitat_diversity.Rmd",
-"chapters/habitat_vulnerability.Rmd",
-"chapters/HP_indicator.Rmd", 
-"chapters/habs_alexandrium.Rmd", 
-"chapters/MAB_HABs_indicator.Rmd",
-"chapters/NE_HABs_indicator.Rmd",
-"chapters/habs_psp.Rmd", 
-"chapters/hms_landings.Rmd",
-"chapters/hms_cpue.Rmd", 
-"chapters/hms_stock_status.Rmd",
-"chapters/hudson_river_flow.Rmd",
-#"chapters/Ich_div_indicator.Rmd",
-"chapters/inshore_bottom_trawl_surveys.Rmd",
-"chapters/long_term_sst_indicator.Rmd",
-"chapters/Quota_Catch_MA.Rmd", 
-"chapters/marine_heatwave.Rmd", 
-"chapters/ocean_acidification.Rmd", 
-"chapters/phytoplankton.Rmd",
-"chapters/plankton_diversity.Rmd",
-"chapters/protected_species_hotspots.Rmd", 
-"chapters/Quota_Catch_NE.Rmd", 
-"chapters/Recreational_Data.Rmd",
-"chapters/rec_hms.Rmd",
-"chapters/regime_shift_analysis.Rmd",
-"chapters/RW_indicator.rmd",
-"chapters/SAFMC_spp.Rmd",
-"chapters/sandlance.Rmd",
-"chapters/SAV.Rmd",
-"chapters/seabird_ne.Rmd",
-"chapters/Seasonal_SST_anomaly_maps_indicator.Rmd",
-"chapters/singlespp_status_indicator.Rmd",
-"chapters/slopewater_proportions.Rmd",
-"chapters/Species_density_estimates.Rmd",
-"chapters/Species_dist_indicators.Rmd",
-"chapters/stom_fullness.Rmd",
-"chapters/storminess.Rmd",
-"chapters/survey_data.rmd",
-"chapters/Thermal_hab_proj_indicator.Rmd",
-"chapters/trans_dates.Rmd",
-"chapters/Trend_analysis.Rmd",
-"chapters/observer_data_indicator.Rmd",
-"chapters/warm_core_rings.Rmd",
-"chapters/Seabird_MAB.Rmd",
-"chapters/wind_port_landings_EJ.Rmd",
-"chapters/Wind_dev_speed.Rmd",
-"chapters/wind_habitat_occupancy.Rmd",
-"chapters/Zooplankton_indicators.Rmd",
-"chapters/pl_lan_glossary.Rmd",
-"chapters/references.Rmd"]
+rmd_files:
+    - "index.Rmd"
+
+
+# ######################## METHODS ##################
+    -   "chapters/sectionHeaders/methods.rmd"
+    -   "chapters/erddap_query_and_build.Rmd"
+    -   "chapters/Trend_analysis.Rmd"
+    -   "chapters/regime_shift_analysis.Rmd"
+    -   "chapters/survdat.rmd"
+    -   "chapters/EPU.Rmd"
+    -   "chapters/conceptualmodels.Rmd"
+    -   "chapters/pl_lan_glossary.Rmd"
+#
+#  
+#################### LOWER TROPHIC ##################
+    -   "chapters/sectionHeaders/ltl.rmd" 
+    -   "chapters/ches_bay_wq.Rmd"
+    -   "chapters/chl_pp.Rmd"
+    #-   "chapters/phyto_size.Rmd" *Currently shares tech doc page with chl_pp
+    #-   "chapters/annual_chl_pp.Rmd" *Turned off in catalog
+    -   "chapters/habs.Rmd"
+    -   "chapters/SAV.Rmd"
+    #-   "chapters/calanus_variation.Rmd" *Missing tech doc page
+    -   "chapters/wbts_mesozooplankton.Rmd"
+    -   "chapters/zoo_abundance_anom.Rmd"
+    #-   "chapters/zoo_diversity.Rmd" *Missing tech doc page
+#
+#
+# #################### MEGAFAUNA ##################
+    -   "chapters/sectionHeaders/megafauna.rmd"
+    #-   "chapters/aggregate_biomass.Rmd" *Missing tech doc page
+    -   "chapters/mab_inshore_survey.Rmd"
+    #-   "chapters/mass_inshore_survey.Rmd" *Shares tech doc page with mab_inshore_survey
+    #-   "chapters/ne_inshore_survey.Rmd" *Shares tech doc page with mab_inshore_survey
+    #-   "chapters/osw_survey_impact.Rmd" *Missing tech doc page
+    -   "chapters/condition.Rmd"
+    -   "chapters/habitat_diversity.Rmd"
+    -   "chapters/species_dist.Rmd"
+    -   "chapters/energy_density.Rmd"
+    -   "chapters/spawn_timing.Rmd"
+    -   "chapters/exp_n.Rmd"
+    -   "chapters/forage_index.Rmd"
+    -   "chapters/harborporpoise.Rmd"
+    -   "chapters/hms_cpue.Rmd"
+    -   "chapters/hms_landings.Rmd"
+    -   "chapters/hms_stock_status.Rmd"
+    -   "chapters/HMS_species_distribution.Rmd"
+    -   "chapters/narw.rmd"
+    -   "chapters/productivity_anomaly.Rmd"
+    -   "chapters/seal_pups.Rmd"
+    -   "chapters/gom_salmon.Rmd"
+    -   "chapters/grayseal.Rmd"
+    -   "chapters/seabird_ne.Rmd"
+    -   "chapters/species_groupings.rmd"  
+#
+#
+# #################### OCEANOGRAPHIC ##################
+    -   "chapters/sectionHeaders/oceanographic.rmd" 
+    -   "chapters/bottom_temp.Rmd"
+    #-   "chapters/bottom_temp_comp.Rmd" *Missing tech doc page
+    -   "chapters/bottom_temp_seasonal_gridded.Rmd"
+    -   "chapters/seasonal_sst_anomaly_gridded.Rmd"
+    #-   "chapters/seasonal_oisst_anom.Rmd" *Missing tech doc page
+    -   "chapters/trans_dates.Rmd"
+    -   "chapters/long_term_sst.Rmd"
+    -   "chapters/cold_pool.Rmd"
+    -   "chapters/gsi.Rmd"
+    -   "chapters/slopewater.Rmd"
+    -   "chapters/persistent_hotspots.Rmd"
+    -   "chapters/wcr.Rmd"
+    #-   "chapters/thermal_habitat_area.Rmd" *Missing tech doc page
+    #-   "chapters/thermal_habitat_persistence.Rmd" *Missing tech doc page
+    -   "chapters/ch_bay_sal.Rmd"
+    -   "chapters/ch_bay_temp.Rmd"
+    -   "chapters/ches_bay_sst.Rmd"
+    #-   "chapters/ches_bay_synthesis.Rmd" *Missing tech doc page
+    -   "chapters/heatwave.Rmd"
+    #-   "chapters/heatwave_year.Rmd" *Shares tech doc page with heatwave
+    #-   "chapters/timing_shifts.Rmd" *Missing tech doc page
+    #-   "chapters/observation_synthesis.Rmd" *Missing tech doc page
+    -   "chapters/ocean_acidification.Rmd"  
+#
+#
+# ######################## ECONOMIC ##################
+    -   "chapters/sectionHeaders/economic.rmd"
+    -   "chapters/comdat.Rmd"
+    -   "chapters/commercial_div.Rmd"
+    -   "chapters/ppr.Rmd"
+    -   "chapters/recdat.Rmd"
+    -   "chapters/rec_hms.Rmd"
+    -   "chapters/abc_acl.Rmd"
+    -   "chapters/bennet.Rmd"
+    -   "chapters/stock_status.Rmd"
+    -   "chapters/engagement.Rmd"
+    -   "chapters/aquaculture.Rmd"
+    -   "chapters/Wind_dev_speed.Rmd"
+    -   "chapters/wind_port.Rmd"
+    -   "chapters/wind_revenue.Rmd"  
+#
+#
+# ######################## LEGACY PAGES ##################
+    -   "chapters/sectionHeaders/legacy.rmd" 
+    -   "chapters/Annual_SST_cycle_indicator.Rmd"
+    -   "chapters/bottom_temperature_GLORYS.Rmd"
+    -   "chapters/calanus_stage.Rmd"
+    #-   "chapters/forage_anomaly.Rmd"
+    -   "chapters/occupancy_indicator.Rmd"
+    -   "chapters/habitat_vulnerability.Rmd"
+    -   "chapters/MAB_HABs_indicator.Rmd"
+    -   "chapters/NE_HABs_indicator.Rmd"
+    -   "chapters/habs_psp.Rmd"
+    -   "chapters/hudson_river_flow.Rmd"
+    #-   "chapters/Ich_div_indicator.Rmd"
+    -   "chapters/plankton_diversity.Rmd"
+    -   "chapters/Quota_Catch_NE.Rmd"
+    -   "chapters/rec_hms.Rmd"
+    -   "chapters/SAFMC_spp.Rmd"
+    -   "chapters/sandlance.Rmd"
+    -   "chapters/Species_density_estimates.Rmd"
+    -   "chapters/stom_fullness.Rmd"
+    -   "chapters/storminess.Rmd"
+    -   "chapters/Thermal_hab_proj_indicator.Rmd"
+    -   "chapters/observer_data_indicator.Rmd"
+    -   "chapters/Seabird_MAB.Rmd"
+    -   "chapters/wind_habitat_occupancy.Rmd"
+    -   "chapters/references.Rmd"
+before_chapter_script: _common.R
 delete_merged_file: false
 output_dir: "_book"
 new_session: false

_common.R

@@ -0,0 +1,8 @@
+# example R options set globally
+options(width = 60)
+
+# example chunk options set globally
+knitr::opts_chunk$set(
+  comment = "#>",
+  collapse = TRUE
+  )

_output.yml

@@ -1,3 +1,34 @@
+bookdown::bs4_book:
+  split_bib: true
+  css: style.css
+  theme:
+    primary: "#4D6F8D"
+  repo: https://github.com/NOAA-EDAB/tech-doc
+
+bookdown::gitbook:
+  css: style.css
+  # includes:
+  #   in_header: [ga_script.html]
+  config:
+    # toc:
+    #   collapse: section
+    #   before: |
+    #     <li><a href="./">Mastering Shiny</a></li>
+    edit: https://github.com/NOAA-EDAB/tech-doc/edit/master/%s
+    download: []
+    sharing:
+      facebook: no
+      twitter: no
+      github: yes
+      all: []
+bookdown::pdf_book:
+  includes:
+    in_header: preamble.tex
+  latex_engine: xelatex
+  citation_package: natbib
+  keep_tex: yes
+bookdown::epub_book: default
+
 # bookdown::gitbook:
 #   lib_dir: asset
 #   css: css/style.css
@@ -20,17 +51,17 @@
 
 
 
-bookdown::gitbook:
-  css: css/style.css
-  config:
-    toc:
-      collapse: section
-      before: |
-        <li><a href="./">Technical Documentation, State of the Ecosystem Report</a></li>
-      after: |
-        <li><a href="https://github.com/NOAA-EDAB/tech-doc"></a></li>
-        <li><a href="./"Published with bookdown</a></li>
-    edit:
-      link: https://github.com/NOAA-EDAB/tech-doc/edit/master/%s
-bookdown::pdf_book:
-  keep_tex: yes
+#bookdown::gitbook:
+#  css: css/style.css
+#  config:
+#    toc:
+#      collapse: section
+#      before: |
+#        <li><a href="./">Technical Documentation, State of the Ecosystem Report</a></li>
+#      after: |
+#        <li><a href="https://github.com/NOAA-EDAB/tech-doc"></a></li>
+#        <li><a href="./"Published with bookdown</a></li>
+#    edit:
+#      link: https://github.com/NOAA-EDAB/tech-doc/edit/master/%s
+#bookdown::pdf_book:
+#  keep_tex: yes

bibliography/Forage_Fish_Biomass_Index.bib

@@ -107,3 +107,32 @@ @article{thorson2016
 pages = {66--74}
 }
 
+@article{gaichas_assessing_2023,
+	title = {Assessing small pelagic fish trends in space and time using piscivore stomach contents},
+	issn = {0706-652X, 1205-7533},
+	url = {https://cdnsciencepub.com/doi/10.1139/cjfas-2023-0093},
+	doi = {10.1139/cjfas-2023-0093},
+	abstract = {Changing distribution and abundance of small pelagic fishes may drive changes in predator distributions, affecting predator availability to fisheries and surveys. However, small pelagics are difficult to survey directly, so we developed a novel method of assessing the aggregate abundance of 21 small pelagic forage taxa via predator stomach contents. We used stomach contents collected from 22 piscivore species captured by multiple bottom trawl surveys within a vector autoregressive spatio-temporal model to assess trends of small pelagics on the Northeast US shelf. The goal was to develop a spatial “forage index” to inform survey and (or) fishery availability in the western North Atlantic bluefish ( Pomatomus saltatrix) stock assessment. This spatially resolved index compared favorably with more traditional design-based survey biomass indices for forage species well sampled by surveys. However, our stomach content-based index better represented smaller unmanaged forage species that surveys are not designed to capture. The stomach-based forage index helped explain bluefish availability to the recreational fishery for stock assessment and provided insight into pelagic forage trends throughout the regional ecosystem.},
+	language = {en},
+	urldate = {2024-02-15},
+	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
+	author = {Gaichas, Sarah K. and Gartland, James and Smith, Brian E. and Wood, Anthony D. and Ng, Elizabeth L. and Celestino, Michael and Drew, Katie and Tyrell, Abigail S. and Thorson, James T.},
+	month = oct,
+	year = {2023},
+	pages = {cjfas--2023--0093},
+	file = {Full Text PDF:/Users/sarah.gaichas/Zotero/storage/W4CMYQYY/Gaichas et al. - 2023 - Assessing small pelagic fish trends in space and t.pdf:application/pdf},
+}
+
+@book{collette_bigelow_2002,
+	address = {Washington, DC},
+	edition = {3rd ed. edition},
+	title = {Bigelow and {Schroeder}'s {Fishes} of the {Gulf} of {Maine}, {Third} {Edition}},
+	isbn = {978-1-56098-951-6},
+	abstract = {Fifteen years in the making, this updated edition raises the high standard of Bigelow and Schroeder's 1953 reference by drawing from a much larger base of information. Thirty-eight experts in fisheries biology and ichthyology clearly distill the enormous amount of knowledge gained during the past fifty years, including distribution figures from thirty years of annual trawl surveys; food habit accounts from surveys of the stomach contents of more than 30,000 fishes; and egg distribution data from a survey exceeding 10,000 samples. The contributors update Bigelow and Schroeder's 1953 material while presenting a wealth of new information, including thirty-three additional species accounts. By adding fifty percent more material and focusing the volume on data, the editors address the needs of today's biologists, the commercial fishing industry, and marine enthusiasts, and ensure that Bigelow and Schroeder's Fishes of the Gulf of Maine, Third Edition, will become the standard work in the field for the next fifty years.},
+	language = {English},
+	publisher = {Smithsonian Books},
+	author = {Collette, Bruce B. and Klein-Macphee, Grace},
+	month = jun,
+	year = {2002},
+	keywords = {Nature / Animals / Fish, Science / Life Sciences / Zoology / Ichthyology \& Herpetology},
+}