assign_allocation_shares
                        Assign allocation shares to emission variables
                        by commodity
calc_allocated_emissions
                        Calculate allocated greenhouse gas emissions
                        (GHG)
calc_allocation_shares
                        Calculate allocation shares for livestock
                        commodities
calc_avg_weights        Calculate average and final live weights by
                        cohort
calc_ch4_enteric        Calculate daily enteric methane emissions
calc_ch4_manure         Calculate methane (CH4) emissions from manure
                        management systems
calc_ch4_ration_rice    Calculate a ration component's contribution to
                        methane (CH4) emissions from rice cultivation
calc_co2_ration_crop_activities
                        Calculate a ration component's contribution to
                        carbon dioxide (CO2) emissions from on-field
                        agricultural activities
calc_co2_ration_fertilizer
                        Calculate a ration component's contribution to
                        carbon dioxide (CO2) emissions from fertilizer
                        manufacture
calc_co2_ration_luc_nopeat
                        Calculate a ration component's contribution to
                        carbon dioxide (CO2) emissions from land-use
                        change (excluding peatland drainage)
calc_co2_ration_luc_peat
                        Calculate a ration component's contribution to
                        carbon dioxide (CO2) emissions from peatland
                        drainage
calc_co2_ration_pesticides
                        Calculate a ration component's contribution to
                        carbon dioxide (CO2) emissions from pesticide
                        manufacture
calc_co2eq              Convert methane (CH4) and nitrous oxide (N2O)
                        emissions to CO2-equivalents (CO2eq) using
                        Global Warming Potentials (GWP) factors
calc_cohort_to_herd_aggregation
                        Aggregate cohort-level to herd-level data
calc_cohort_totals      Calculate totals by cohort
calc_cohort_weights     Calculate live weights by cohort and life stage
calc_conversion_factor_ym
                        Calculate methane conversion factor (ym)
calc_daily_weight_gain
                        Calculate daily weight gain by cohort
calc_fecundity_rates    Calculate daily fecundity rates
calc_feed_digestibility_fraction
                        Calculate feed digestibility fraction
calc_fibre_allocation_energy
                        Calculate fibre energy requirements (for
                        biophysical allocation)
calc_fibre_production   Calculate fibre production
calc_meat_allocation_energy
                        Calculate meat energy requirements (for
                        biophysical allocation)
calc_meat_production    Calculate meat production
calc_metabolic_energy_req_activity
                        Calculate metabolic energy requirements for
                        activity
calc_metabolic_energy_req_fibre
                        Calculate metabolic energy requirements for
                        fibre production
calc_metabolic_energy_req_growth
                        Calculate metabolic energy requirements for
                        growth
calc_metabolic_energy_req_lactation
                        Calculate metabolic energy requirements for
                        lactation
calc_metabolic_energy_req_maintenance
                        Calculate metabolic energy requirements for
                        maintenance
calc_metabolic_energy_req_pregnancy
                        Calculate metabolic energy requirements for
                        pregnancy
calc_metabolic_energy_req_work
                        Calculate metabolic energy requirements for
                        work
calc_milk_allocation_energy
                        Calculate milk energy requirements (for
                        biophysical allocation)
calc_milk_production    Calculate milk production
calc_n2o_manure_direct
                        Calculate direct Nitrous Oxide (N2O) emissions
                        from manure management systems
calc_n2o_manure_leaching
                        Calculate indirect Nitrous Oxide (N2O)
                        emissions from manure leaching and runoff
calc_n2o_manure_total   Calculate total Nitrous Oxide (N2O) emissions
                        from manure
calc_n2o_manure_volatilization
                        Calculate indirect Nitrous Oxide (N2O)
                        emissions from manure volatilization
calc_n2o_ration_crop_residues
                        Calculate a ration component's contribution to
                        nitrous oxide (N2O) emissions from crop
                        residues decomposition
calc_n2o_ration_fertilizer
                        Calculate a ration component's contribution to
                        nitrous oxide (N2O) emissions from fertilizer
                        use
calc_n2o_ration_manure
                        Calculate a ration component's contribution to
                        nitrous oxide (N2O) emissions from manure
                        application and deposition
calc_nitrogen_excretion
                        Calculate daily nitrogen excretion
calc_nitrogen_intake    Calculate daily nitrogen intake
calc_nitrogen_retention
                        Calculate daily nitrogen retention
calc_projected_population_size
                        Calculate one year of steady-state population
                        dynamics
calc_ration_ash         Calculate diet ash contribution for a ration
                        component
calc_ration_digestibility
                        Calculate diet digestibility contribution for a
                        ration component
calc_ration_gross_energy
                        Calculate diet gross energy contribution for a
                        ration component
calc_ration_intake      Calculate daily ration intake in dry matter
calc_ration_metabolizable_energy
                        Calculate diet metabolizable energy
                        contribution for a ration component
calc_ration_nitrogen_content
                        Calculate diet nitrogen contribution for a
                        ration component
calc_ration_urinary_energy_fraction
                        Calculate urinary energy fraction contribution
                        for a ration component
calc_reg_growth         Calculate the ratio of net energy available for
                        growth in the diet (REG – Net Energy for Growth
                        / Digestible Energy)
calc_rem_maintenance    Calculate ratio of net energy available for
                        maintenance in the diet (REM - Net Energy for
                        Maintenance / Digestible Energy)
calc_steady_state_structure
                        Calculate steady-state population structure
calc_summary_offtake    Summarise offtake and stock Variation for a
                        steady-state year
calc_total_metabolic_energy_req
                        Calculate total metabolic energy requirements
calc_transition_probabilities
                        Calculate transition probabilities for sex-age
                        classes
calc_volatile_solids    Calculate Volatile Solids (VS)
calc_work_allocation_energy
                        Calculate work energy requirements (for
                        biophysical allocation)
run_aggregation_module
                        Run Aggregation Module Pipeline
run_allocation_module   Run Allocation Module Pipeline
run_demographic_herd_module
                        Run Demographic Herd Module Pipeline
run_emissions_enteric_module
                        Run Enteric Methane (CH4) Emissions Module
                        Pipeline
run_emissions_manure_module
                        Run Emissions from Manure Module Pipeline
run_emissions_ration_module
                        Run Emissions from Feed Production Module
                        Pipeline
run_gleam               Run the full Global Livestock Environmental
                        Assessment Model (GLEAM) Pipeline
run_metabolic_energy_req_module
                        Run Metabolic Energy Requirements and Dry
                        Matter Intake Module Pipeline
run_nitrogen_balance_module
                        Run Nitrogen Balance Module Pipeline
run_production_module   Run Production Module Pipeline
run_ration_quality_module
                        Run Ration Quality Module Pipeline
run_weights_module      Run Weights Module Pipeline
