_bookdown.yml

book_filename: "catalog"
rmd_files: 
    -   "index.Rmd"
    #-   "chapters/introduction.rmd"


#################### LOWER TROPHIC ##################
    -   "chapters/sectionHeaders/ltl.rmd" 
    -   "chapters/ches_bay_wq.rmd"
    -   "chapters/chl_pp.rmd"
    -   "chapters/phyto_size.rmd"
    #-   "chapters/annual_chl_pp.rmd"
    -   "chapters/habs.rmd"
    -   "chapters/SAV.rmd"
    -   "chapters/calanus_variation.rmd"
    -   "chapters/wbts_mesozooplankton.rmd"
    -   "chapters/zoo_abundance_anom.rmd"
    -   "chapters/zoo_diversity.rmd"
#
#
# #################### MEGAFAUNA ##################
    -   "chapters/sectionHeaders/megafauna.rmd"
    -   "chapters/aggregate_biomass.rmd"
    -   "chapters/mab_inshore_survey.rmd"
    -   "chapters/mass_inshore_survey.rmd"
    -   "chapters/ne_inshore_survey.rmd"
    -   "chapters/osw_survey_impact.rmd"
    -   "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"
    -   "chapters/bottom_temp_seasonal_gridded.rmd"
    -   "chapters/seasonal_sst_anomaly_gridded.rmd"
    -   "chapters/seasonal_oisst_anom.rmd"
    -   "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"
    -   "chapters/thermal_habitat_persistence.rmd"
    -   "chapters/ch_bay_sal.rmd"
    -   "chapters/ch_bay_temp.rmd"
    -   "chapters/ches_bay_sst.rmd"
    -   "chapters/ches_bay_synthesis.rmd"
    -   "chapters/heatwave.rmd"
    -   "chapters/heatwave_year.rmd"
    -   "chapters/timing_shifts.rmd"
    -   "chapters/observation_synthesis.rmd"
    -   "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/ocean_acidification.rmd"
    -   "chapters/wind_dev_speed.rmd"
    -   "chapters/wind_port.rmd"
    -   "chapters/wind_revenue.rmd"

    -   "chapters/glossary.Rmd"
    -   "chapters/references.Rmd"
before_chapter_script: _common.R
delete_merged_file: true
output_dir: "_book"
new_session: false #(if true all rmds need to be in root folder)