_bookdown.yml

book_filename: "aed_science.Rmd"
repo: https://github.com/AquaticEcoDynamics/aed-science/
output_dir: "docs"
rmd_files: ["index.Rmd",
           # "02-foreward.Rmd",
            "03-preface.Rmd",
            "04-intro.Rmd",
            "05-nomenclature.Rmd",
            "06-organisation_and_structure.Rmd",
            #"07-host_model_coupling.Rmd",
            #"08-tracers_water_age.Rmd",
            #"09-suspended_sediment.Rmd",
            "10-dissolved_oxygen.Rmd",
            "11-carbon.Rmd",
            "12-nitrogen.Rmd",
            "13-phosphorous.Rmd",
            "14-silica.Rmd",
            "15-organic_matter.Rmd",
            "16-phytoplankton.Rmd",
            #"17-zooplankton.Rmd",
            #"18-totals.Rmd",
            "19-aqueous_geochemistry.Rmd",
            "20-pathogens_microbial_indicators.Rmd",
            "21-pesticides.Rmd",
            #"21-stable_isotopes.Rmd",
            #"22-bioactive_particles.Rmd",
            "23-sediment_biogeochemistry.Rmd",
            #"24-submerged_macrophytes.Rmd",
            #"25-macroalgae.Rmd",
            "26-bivalves.Rmd",
            "27-benthic_habitat_quality.Rmd",
            #"28-soil_hydrology.Rmd",
            #"29-soil_biogeochemistry.Rmd",
            #"30-acid_sulphate_soils.Rmd",
            #"31-riparian_vegetation.Rmd",
            #"32-riparian_habitat_quality.Rmd",
            "33-generic_utilities_functions.Rmd",
            "34-publications.Rmd",
            #"35-abbreviations.Rmd",
            "37-forthcoming.Rmd",
            "36-references.Rmd"]
clean: [packages.bib, bookdown.bbl]
new_session: no
delete_merged_file: true