diff --git a/_bookdown.yml b/_bookdown.yml index f7e23a13..18689461 100644 --- a/_bookdown.yml +++ b/_bookdown.yml @@ -1,84 +1,127 @@ 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" + + +#################### 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/erddap_query_and_build.Rmd" + - "chapters/Annual_SST_cycle_indicator.Rmd" + - "chapters/bottom_temperature_GLORYS.Rmd" + - "chapters/calanus_stage.Rmd" + - "chapters/conceptualmodels.Rmd" + - "chapters/EPU.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/regime_shift_analysis.Rmd" + - "chapters/SAFMC_spp.Rmd" + - "chapters/sandlance.Rmd" + - "chapters/Species_density_estimates.Rmd" + - "chapters/stom_fullness.Rmd" + - "chapters/storminess.Rmd" + - "chapters/survey_data.rmd" + - "chapters/Thermal_hab_proj_indicator.Rmd" + - "chapters/Trend_analysis.Rmd" + - "chapters/observer_data_indicator.Rmd" + - "chapters/Seabird_MAB.Rmd" + - "chapters/wind_habitat_occupancy.Rmd" + - "chapters/pl_lan_glossary.Rmd" + - "chapters/references.Rmd" +before_chapter_script: _common.R delete_merged_file: false output_dir: "_book" new_session: false diff --git a/_common.R b/_common.R new file mode 100644 index 00000000..ff04b979 --- /dev/null +++ b/_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 + ) diff --git a/chapters/Quota_Catch_MA.Rmd b/chapters/abc_acl.Rmd similarity index 100% rename from chapters/Quota_Catch_MA.Rmd rename to chapters/abc_acl.Rmd diff --git a/chapters/Aquaculture_indicators.Rmd b/chapters/aquaculture.Rmd similarity index 100% rename from chapters/Aquaculture_indicators.Rmd rename to chapters/aquaculture.Rmd diff --git a/chapters/Bennet_indicator.Rmd b/chapters/bennet.Rmd similarity index 100% rename from chapters/Bennet_indicator.Rmd rename to chapters/bennet.Rmd diff --git a/chapters/bottom_temperature_insitu.Rmd b/chapters/bottom_temp.Rmd similarity index 100% rename from chapters/bottom_temperature_insitu.Rmd rename to chapters/bottom_temp.Rmd diff --git a/chapters/bottom_temperature_highres.Rmd b/chapters/bottom_temp_seasonal_gridded.Rmd similarity index 100% rename from chapters/bottom_temperature_highres.Rmd rename to chapters/bottom_temp_seasonal_gridded.Rmd diff --git a/chapters/ches_bay_sal.Rmd b/chapters/ch_bay_sal.Rmd similarity index 100% rename from chapters/ches_bay_sal.Rmd rename to chapters/ch_bay_sal.Rmd diff --git a/chapters/ches_bay_temp.Rmd b/chapters/ch_bay_temp.Rmd similarity index 100% rename from chapters/ches_bay_temp.Rmd rename to chapters/ch_bay_temp.Rmd diff --git a/chapters/ches_bay_water_quality.Rmd b/chapters/ches_bay_wq.Rmd similarity index 100% rename from chapters/ches_bay_water_quality.Rmd rename to chapters/ches_bay_wq.Rmd diff --git a/chapters/phytoplankton.Rmd b/chapters/chl_pp.Rmd similarity index 100% rename from chapters/phytoplankton.Rmd rename to chapters/chl_pp.Rmd diff --git a/chapters/cold_pool_index.Rmd b/chapters/cold_pool.Rmd similarity index 100% rename from chapters/cold_pool_index.Rmd rename to chapters/cold_pool.Rmd diff --git a/chapters/landings_data.Rmd b/chapters/comdat.Rmd similarity index 100% rename from chapters/landings_data.Rmd rename to chapters/comdat.Rmd diff --git a/chapters/Catch_and_Fleet_Diversity_indicators.Rmd b/chapters/commercial_div.Rmd similarity index 100% rename from chapters/Catch_and_Fleet_Diversity_indicators.Rmd rename to chapters/commercial_div.Rmd diff --git a/chapters/Condition_indicator.Rmd b/chapters/condition.Rmd similarity index 100% rename from chapters/Condition_indicator.Rmd rename to chapters/condition.Rmd diff --git a/chapters/forage_energy_density.Rmd b/chapters/energy_density.Rmd similarity index 100% rename from chapters/forage_energy_density.Rmd rename to chapters/energy_density.Rmd diff --git a/chapters/Comm_rel_vuln_indicator.Rmd b/chapters/engagement.Rmd similarity index 100% rename from chapters/Comm_rel_vuln_indicator.Rmd rename to chapters/engagement.Rmd diff --git a/chapters/Expected_Number.Rmd b/chapters/exp_n.Rmd similarity index 100% rename from chapters/Expected_Number.Rmd rename to chapters/exp_n.Rmd diff --git a/chapters/Forage_Fish_Biomass_Index.Rmd b/chapters/forage_index.Rmd similarity index 100% rename from chapters/Forage_Fish_Biomass_Index.Rmd rename to chapters/forage_index.Rmd diff --git a/chapters/gulf_stream_index.Rmd b/chapters/gsi.Rmd similarity index 100% rename from chapters/gulf_stream_index.Rmd rename to chapters/gsi.Rmd diff --git a/chapters/habs_alexandrium.Rmd b/chapters/habs.Rmd similarity index 100% rename from chapters/habs_alexandrium.Rmd rename to chapters/habs.Rmd diff --git a/chapters/HP_indicator.Rmd b/chapters/harborporpoise.Rmd similarity index 100% rename from chapters/HP_indicator.Rmd rename to chapters/harborporpoise.Rmd diff --git a/chapters/marine_heatwave.Rmd b/chapters/heatwave.Rmd similarity index 100% rename from chapters/marine_heatwave.Rmd rename to chapters/heatwave.Rmd diff --git a/chapters/long_term_sst_indicator.Rmd b/chapters/long_term_sst.Rmd similarity index 100% rename from chapters/long_term_sst_indicator.Rmd rename to chapters/long_term_sst.Rmd diff --git a/chapters/inshore_bottom_trawl_surveys.Rmd b/chapters/mab_inshore_survey.Rmd similarity index 100% rename from chapters/inshore_bottom_trawl_surveys.Rmd rename to chapters/mab_inshore_survey.Rmd diff --git a/chapters/RW_indicator.rmd b/chapters/narw.rmd similarity index 100% rename from chapters/RW_indicator.rmd rename to chapters/narw.rmd diff --git a/chapters/protected_species_hotspots.Rmd b/chapters/persistent_hotspots.Rmd similarity index 100% rename from chapters/protected_species_hotspots.Rmd rename to chapters/persistent_hotspots.Rmd diff --git a/chapters/ecosystem_overfishing.Rmd b/chapters/ppr.Rmd similarity index 100% rename from chapters/ecosystem_overfishing.Rmd rename to chapters/ppr.Rmd diff --git a/chapters/productivity_for_tech_memo.Rmd b/chapters/productivity_anomaly.Rmd similarity index 100% rename from chapters/productivity_for_tech_memo.Rmd rename to chapters/productivity_anomaly.Rmd diff --git a/chapters/Recreational_Data.Rmd b/chapters/recdat.Rmd similarity index 100% rename from chapters/Recreational_Data.Rmd rename to chapters/recdat.Rmd diff --git a/chapters/Seasonal_SST_anomaly_maps_indicator.Rmd b/chapters/seasonal_sst_anomaly_gridded.Rmd similarity index 100% rename from chapters/Seasonal_SST_anomaly_maps_indicator.Rmd rename to chapters/seasonal_sst_anomaly_gridded.Rmd diff --git a/chapters/sectionHeaders/economic.rmd b/chapters/sectionHeaders/economic.rmd new file mode 100644 index 00000000..e2e80c57 --- /dev/null +++ b/chapters/sectionHeaders/economic.rmd @@ -0,0 +1 @@ +# (PART\*) Economic & Social {.unnumbered} \ No newline at end of file diff --git a/chapters/sectionHeaders/ltl.rmd b/chapters/sectionHeaders/ltl.rmd new file mode 100644 index 00000000..0cb6bf55 --- /dev/null +++ b/chapters/sectionHeaders/ltl.rmd @@ -0,0 +1 @@ +# (PART\*) Lower Trophic Levels {.unnumbered} \ No newline at end of file diff --git a/chapters/sectionHeaders/megafauna.rmd b/chapters/sectionHeaders/megafauna.rmd new file mode 100644 index 00000000..ac834aea --- /dev/null +++ b/chapters/sectionHeaders/megafauna.rmd @@ -0,0 +1 @@ +# (PART\*) Megafauna {.unnumbered} \ No newline at end of file diff --git a/chapters/sectionHeaders/oceanographic.rmd b/chapters/sectionHeaders/oceanographic.rmd new file mode 100644 index 00000000..400c0cb8 --- /dev/null +++ b/chapters/sectionHeaders/oceanographic.rmd @@ -0,0 +1 @@ +# (PART\*) Oceanographic & Habitat {.unnumbered} \ No newline at end of file diff --git a/chapters/slopewater_proportions.Rmd b/chapters/slopewater.Rmd similarity index 100% rename from chapters/slopewater_proportions.Rmd rename to chapters/slopewater.Rmd diff --git a/chapters/Species_dist_indicators.Rmd b/chapters/species_dist.Rmd similarity index 100% rename from chapters/Species_dist_indicators.Rmd rename to chapters/species_dist.Rmd diff --git a/chapters/aggregate_groups.rmd b/chapters/species_groupings.rmd similarity index 100% rename from chapters/aggregate_groups.rmd rename to chapters/species_groupings.rmd diff --git a/chapters/singlespp_status_indicator.Rmd b/chapters/stock_status.Rmd similarity index 100% rename from chapters/singlespp_status_indicator.Rmd rename to chapters/stock_status.Rmd diff --git a/chapters/survey_data.rmd b/chapters/survdat.rmd similarity index 100% rename from chapters/survey_data.rmd rename to chapters/survdat.rmd diff --git a/chapters/mesoplankton_biomass.Rmd b/chapters/wbts_mesozooplankton.Rmd similarity index 100% rename from chapters/mesoplankton_biomass.Rmd rename to chapters/wbts_mesozooplankton.Rmd diff --git a/chapters/warm_core_rings.Rmd b/chapters/wcr.Rmd similarity index 100% rename from chapters/warm_core_rings.Rmd rename to chapters/wcr.Rmd diff --git a/chapters/wind_port_landings_EJ.Rmd b/chapters/wind_port.Rmd similarity index 100% rename from chapters/wind_port_landings_EJ.Rmd rename to chapters/wind_port.Rmd diff --git a/chapters/Wind_area_fisheries_revenue.Rmd b/chapters/wind_revenue.Rmd similarity index 100% rename from chapters/Wind_area_fisheries_revenue.Rmd rename to chapters/wind_revenue.Rmd diff --git a/chapters/Zooplankton_indicators.Rmd b/chapters/zoo_abundance_anom.Rmd similarity index 100% rename from chapters/Zooplankton_indicators.Rmd rename to chapters/zoo_abundance_anom.Rmd