_bookdown.yml

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"]
delete_merged_file: false
output_dir: "_book"
new_session: false