Type:	Package
Title:	Global Livestock Environmental Assessment Model (GLEAM-X)
Version:	0.8.0
Description:	The official implementation of the Global Livestock Environmental Assessment Model (GLEAM) of the Food and Agriculture Organization of the United Nations (FAO) in R. GLEAM-X provides a modular, transparent framework for simulating livestock production systems and quantifying their environmental impacts. Methodological background: MacLeod et al. (2017) "Invited review: A position on the Global Livestock Environmental Assessment Model (GLEAM)" <doi:10.1017/S1751731117001847>. Further information: https://www.fao.org/gleam/en/.
License:	AGPL-3
URL:	https://github.com/un-fao/GLEAM/, https://www.fao.org/gleam/en/
BugReports:	https://github.com/un-fao/GLEAM/issues
Encoding:	UTF-8
RoxygenNote:	7.3.3
Imports:	cli (≥ 3.0.0), data.table (≥ 1.16.0)
Suggests:	knitr, rmarkdown, testthat (≥ 3.2.0)
VignetteBuilder:	knitr
Config/testthat/edition:	3
Depends:	R (≥ 4.4.0)
NeedsCompilation:	no
Packaged:	2026-04-11 15:10:06 UTC; ahmed
Author:	Ahmed Jou [aut, cre] (https://applitics.fr), Yassine Elaouni [aut] (https://applitics.fr), Dominik Wisser [aut] (GLEAM team lead, FAO), Lydia Lanzoni [aut] (Livestock and climate change specialist, FAO), Giuseppe Tempio [aut] (Livestock environmental impact analyst, FAO), Phyllis Ndungu' [ctb] (Livestock and climate change specialist, FAO), Yushan Li [ctb] (Livestock and sustainability specialist, FAO), Manling Xu [ctb] (Livestock data intern, FAO), Zixin Wang [ctb] (Livestock data intern, FAO), Narindra Rakotovao [ctb] (Livestock policy officer, FAO), Stewart Chikoloma [ctb] (Livestock data specialist, FAO), David OBrien [ctb] (https://applitics.fr), Food and Agriculture Organization of the United Nations FAO [cph] (Original GLEAM model framework), Federal Ministry of Agriculture, Food and Regional Identity of Germany BMELH [fnd] (Funding support)
Maintainer:	Ahmed Jou <ahmed@applitics.fr>
Repository:	CRAN
Date/Publication:	2026-04-16 18:30:08 UTC

gleam: Global Livestock Environmental Assessment Model (GLEAM-X)

Description

GLEAM-X is the official R implementation of FAO’s Global Livestock Environmental Assessment Model (GLEAM). The package provides a modular, transparent framework for simulating livestock production systems and quantifying their environmental impacts. Methodological background: MacLeod et al. (2017) "Invited review: A position on the Global Livestock Environmental Assessment Model (GLEAM)" doi:10.1017/S1751731117001847. Further information: https://www.fao.org/gleam/en/.

Author(s)

Maintainer: Ahmed Jou ahmed@applitics.fr (ORCID) (https://applitics.fr)

Authors:

• Yassine Elaouni yassine@applitics.fr (https://applitics.fr)

• Dominik Wisser dominik.wisser@fao.org (ORCID) (GLEAM team lead, FAO)

• Lydia Lanzoni lydia.lanzoni@fao.org (ORCID) (Livestock and climate change specialist, FAO)

• Giuseppe Tempio giuseppe.tempio@fao.org (ORCID) (Livestock environmental impact analyst, FAO)

Other contributors:

• Phyllis Ndungu' Phyllis.Ndungu@fao.org (Livestock and climate change specialist, FAO) [contributor]

• Yushan Li Yushan.Li@fao.org (Livestock and sustainability specialist, FAO) [contributor]

• Manling Xu Manling.Xu@fao.org (Livestock data intern, FAO) [contributor]

• Zixin Wang Zixin.Wang@fao.org (Livestock data intern, FAO) [contributor]

• Narindra Rakotovao Narindra.Rakotovao@fao.org (Livestock policy officer, FAO) [contributor]

• Stewart Chikoloma Stewart.Chikomola@fao.org (Livestock data specialist, FAO) [contributor]

• David OBrien david@applitics.fr (ORCID) (https://applitics.fr) [contributor]

• Food and Agriculture Organization of the United Nations FAO (Original GLEAM model framework) [copyright holder]

• Federal Ministry of Agriculture, Food and Regional Identity of Germany BMELH (Funding support) [funder]

See Also

Useful links:

• https://github.com/un-fao/GLEAM/

• https://www.fao.org/gleam/en/

• Report bugs at https://github.com/un-fao/GLEAM/issues

Assign allocation shares to emission variables by commodity

Description

Expands commodity-level allocation shares across emission sources and applies predefined allocation rules for excluded emission sources.

Usage

assign_allocation_shares(
  allocation_herd_long,
  emissions_vars,
  commodities,
  non_allocated_emission_sources,
  commodity_col,
  allocation_col
)

Arguments

Details

The function assigns commodity allocation shares to emission sources while also allowing for the implementation of specific allocation rules. Emission sources listed in non_allocated_emission_sources (e.g., emissions from manure burned as fuel or manure deposited on pasture) are treated as not attributable to livestock commodities under the chosen goal and scope. Consequently, these emissions are allocated entirely to the residual commodity category "None" and are not distributed across milk, meat, fibre, work, or egg outputs.

The following methodological rules apply to emission sources listed in non_allocated_emission_sources:

• Manure burned for fuel — Emissions are considered outside the life cycle assessment system boundaries under the defined goal and scope and are therefore not attributed to livestock commodities. A cut-off approach is applied, consistent with the IDF (2022) standard and LEAP guidelines (LEAP 2016a, 2016b, 2016c).

• Manure deposited on pastures — Emissions are not allocated to livestock commodities in order to avoid double counting. When upstream feed production is included in the inventory, emission factors of feed items already account for this source.

This function is part of the run_allocation_module().

Value

A data.table equal to allocation_herd_long expanded over all emissions_vars, with enforced allocation rules:

Non-allocated emission sources

allocation_col = 1 when commodity_col == "None", else 0.

Allocated emission sources

allocation_col = 0 when commodity_col == "None" (others unchanged).

References

IDF. (2022). The IDF Global Carbon Footprint Standard for the Dairy Sector. Bulletin of the IDF No. 520/2022. International Dairy Federation, Brussels.

FAO. (2016a). Environmental performance of large ruminant supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

FAO. (2016b). Greenhouse gas emissions and fossil energy use from small ruminant supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

FAO. (2016c). Greenhouse gas emissions and fossil energy use from poultry supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

See Also

run_allocation_module()

Calculate allocated greenhouse gas emissions (GHG)

Description

Calculates the greenhouse gas emissions (GHG) attributable to specific commodities by applying allocation shares to total herd-level emissions.

Usage

calc_allocated_emissions(value, allocation_share)

Arguments

Details

Allocation shares represent the fraction of total emissions assigned to each commodity (e.g., meat, milk, fibre). See run_allocation_module() for additional details.

Allocated emissions are calculated as:

value\_allocated = value \times allocation\_share

This function is part of the run_aggregation_module().

Value

Numeric. Allocated emissions for each commodity–emission combination (kg gas).

See Also

run_aggregation_module(), run_allocation_module()

Calculate allocation shares for livestock commodities

Description

Calculates biophysical allocation shares for commodities (meat, milk, fibre, work, eggs) based on their total energy requirements.

Usage

calc_allocation_shares(
  species_short,
  meat_allocation_energy,
  milk_allocation_energy,
  fibre_allocation_energy,
  work_allocation_energy,
  egg_allocation_energy
)

Arguments

Details

These fractions represent the proportions of total environmental burdens (e.g., GHG emissions) that will be allocated to each commodity in subsequent steps of the assessment.

This function is part of the run_allocation_module() of the Global Livestock Environmental Assessment Model (GLEAM), which incorporates a biophysical allocation approach, aligned with the IDF Global Carbon Footprint Standard for the Dairy Sector (IDF, 2022), and adapted from Thoma and Nemecek (2020), and is consistent with FAO LEAP livestock LCA guidelines (FAO, 2016a, 2016b, 2016c). This approach also aligns with ISO 14044:2006 (Section 4.3.4.2, Step 2) by using underlying physical (energy-based) relationships to assign shared inputs and outputs in multifunctional livestock production systems.

In accordance with ISO 14044:2006 (Section 4.3.4.2, Step 2), known processing or biophysical relationships may be used to assign shared inputs and outputs of a single production unit to individual products or sub-units. In livestock systems, this includes apportioning shared feed and energy use according to physiological energy requirements (e.g., net energy for lactation, growth..etc.). If the resulting process remains multifunctional, these energy terms may subsequently be used to derive allocation factors among co-products.

This function calculates biophysical allocation fractions for commodities (meat, milk, fibre, work, eggs) for all species. The allocation is based on commodity-specific energy requirements calculated using calc_meat_allocation_energy, calc_milk_allocation_energy, calc_fibre_allocation_energy, calc_work_allocation_energy, and calc_eggs_allocation_energy.

Pig species (PGS): allocation is not based on energy partitioning because pig production is treated as functionally single-output (edible meat). Consequently, 100% of the allocation is assigned to the meat commodity (meat share = 1; all other commodity shares = 0), independent of the energy inputs.

This function is part of the run_allocation_module().

Value

A named list of numeric vectors with same length as input, containing:

meat_share_allocation

Numeric. Allocation share assigned to meat (fraction).

milk_share_allocation

Numeric. Allocation share assigned to milk (fraction).

fibre_share_allocation

Numeric. Allocation share assigned to fibre (fraction).

work_share_allocation

Numeric. Allocation share assigned to work (fraction).

eggs_share_allocation

Numeric. Allocation share assigned to eggs (fraction).

References

ISO. (2006). Environmental management — Life cycle assessment — Requirements and guidelines (ISO 14044:2006). International Organization for Standardization, Geneva.

IDF. (2022). The IDF Global Carbon Footprint Standard for the Dairy Sector. Bulletin of the IDF No. 520/2022. International Dairy Federation, Brussels.

Thoma, G., and Nemecek, T. (2020). Allocation between milk and meat in dairy LCA: Critical discussion of the IDF’s standard methodology. In Proceedings of the 12th International Conference on Life Cycle Assessment of Food (LCAFood 2020) (pp. 83–89), 13–16 October, Berlin, Germany.

FAO. (2016a). Environmental performance of large ruminant supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

FAO. (2016b). Greenhouse gas emissions and fossil energy use from small ruminant supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

FAO. (2016c). Greenhouse gas emissions and fossil energy use from poultry supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

See Also

run_allocation_module, calc_meat_allocation_energy, calc_milk_allocation_energy, calc_fibre_allocation_energy, calc_work_allocation_energy, calc_eggs_allocation_energy

Calculate average and final live weights by cohort

Description

Calculates the average and final live weight for a given sex–age cohort based on initial weight, potential final weight, slaughter weight, and the offtake rate.

Usage

calc_avg_weights(
  live_weight_cohort_initial,
  live_weight_cohort_potential_final,
  live_weight_cohort_at_slaughter,
  offtake_rate
)

Arguments

Details

The calculation of live_weight_cohort_average and live_weight_cohort_final is performed considering that a fraction of animals is removed (offtake) during the cohort stage, while the remaining animals reach the potential final live weight.

The final live weight is computed as:

live\_weight\_cohort_final = (1 - offtake\_rate) \times live\_weight\_cohort\_potential\_final + offtake\_rate \times live\_weight\_cohort\_at\_slaughter

The average live weight over the stage is approximated as:

live\_weight\_cohort\_average = (live\_weight\_cohort\_initial + live\_weight\_cohort\_final)/2

This function is part of the run_weights_module().

Value

A named list with:

live_weight_cohort_average

Numeric. Average live weight over the cohort stage. Computed by accounting for the share of offtaken animals within the cohort, using their slaughter weight, and the potential final weight of animals that remain in the cohort (kg).

live_weight_cohort_final

Numeric. Live weight at the end of the cohort stage, accounting for both surviving and offtaken animals. Computed as a weighted average of the potential final weight of surviving animals and the slaughter weight of offtaken animals, based on the offtake rate (kg).

See Also

run_weights_module

Calculate daily enteric methane emissions

Description

Calculates daily enteric methane emissions (kg CH4/head/day) based on gross energy intake, methane conversion factor (ym), and dry matter intake.

Usage

calc_ch4_enteric(
  species_short,
  ch4_conversion_factor_ym,
  ch4_mitigation_factor,
  ration_gross_energy,
  ration_intake
)

Arguments

Details

The formula used to estimate daily enteric methane emissions is:

CH_4 = \frac{ration\_gross\_energy \times ration\_intake \times ch4\_conversion\_factor\_ym}{55.65 \times 100}

where 55.65 MJ/kg is the energy content of methane.

ration_gross_energy and ration_intake can be calculated with calc_ration_gross_energy and calc_ration_intake ( see also run_ration_quality_module and run_metabolic_energy_req_module).

This function is part of the run_emissions_enteric_module().

Value

Numeric. Average daily enteric methane (CH4) emissions (kg CH4/head/day).

References

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories. Chapter 10: Emissions from Livestock and Manure Management, Equation 10.21.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories. Chapter 10: Emissions from Livestock and Manure Management, Equation 10.21.

See Also

run_emissions_enteric_module, calc_ration_gross_energy, calc_ration_intake, run_ration_quality_module run_metabolic_energy_req_module

Calculate methane (CH4) emissions from manure management systems

Description

Calculates daily methane emissions from manure management using IPCC-based parameters and separates emissions from manure deposited on pasture, manure burned for fuel, and all other manure management systems.

Usage

calc_ch4_manure(ratio_m3CH4_to_kgCH4 = 0.67, volatile_solids, ...)

Arguments

Details

This calculation follows the structure of IPCC Equation 10.23 for methane (CH4) emission factors from manure management.

In the IPCC formulation, emissions are determined by combining:

• daily volatile solids excretion (volatile_solids) - see calc_volatile_solids,

• the maximum methane-producing capacity (b0),

• the methane conversion factor (mcf) for each manure management system,

• and the fraction of manure handled in each system (manure_management_system_fraction).

Applying the IPCC conversion factor from m3 CH4 to kg CH4 (0.67), daily methane emissions are calculated as:

CH4 = volatile\_solids \times b0 \times 0.67 \times \sum \left( \frac{mcf}{100} \times manure\_management\_system\_fraction \right)

The summation is taken over all manure management systems included in the calculation. Results are expressed at daily resolution (kg CH4/head/day), consistent with Equation 10.23 after adapting the original annual formulation to a daily basis.

This function is part of the run_emissions_manure_module().

Value

A named list with the following elements:

ch4_manure_pasture

Numeric. Methane (CH4) emissions from manure deposited on pasture (kg CH4/head/day).

ch4_manure_burned

Numeric. Methane (CH4) emissions from manure burned for fuel (kg CH4/head/day).

ch4_manure_other

Numeric. Methane (CH4) emissions from manure management systems, excluding emissions from manure deposited on pasture and burned for fuel (kg CH4/head/day).

ch4_manure_all_noburn

Numeric. Methane (CH4) emissions from manure management systems, excluding manure burned for fuel (kg CH4/head/day).

References

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management. Equation 10.23.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management. Equation 10.23.

See Also

run_emissions_manure_module, calc_volatile_solids

run_emissions_manure_module, calc_volatile_solids

Examples

calc_ch4_manure(
  ratio_m3CH4_to_kgCH4 = 0.67,
  volatile_solids   = 2.024,
  mms_burned = c(
    manure_management_system_fraction = 0.020,
    methane_conversion_factor_mcf = 10,
    ch4_max_producing_capacity_bo = 0.13
  ),
  mms_drylot = c(
    manure_management_system_fraction = 0.264,
    methane_conversion_factor_mcf = 2,
    ch4_max_producing_capacity_bo = 0.13
  ),
  mms_pasture = c(
    manure_management_system_fraction = 0.310,
    methane_conversion_factor_mcf = 0.47,
    ch4_max_producing_capacity_bo = 0.19
  ),
  mms_solid = c(
    manure_management_system_fraction = 0.406,
    methane_conversion_factor_mcf = 5,
    ch4_max_producing_capacity_bo = 0.13
  )
)

Calculate a ration component's contribution to methane (CH4) emissions from rice cultivation

Description

Calculates the contribution of an individual feed component to methane (CH4) emissions from rice cultivation in feed production, using feed-specific emission factors weighted by the component's share in the ration.

Usage

calc_ch4_ration_rice(feed_ration_fraction, ch4_feed_rice)

Arguments

Details

The contribution is computed as:

diet\_ch4\_feed\_rice = feed\_ration\_fraction \times ch4\_feed\_rice

This function is part of the run_emissions_ration_module().

Value

Numeric. Contribution of an individual feed component to the diet-level average methane (CH4) emission factor from rice cultivation in feed production (g CH4/kg DM).

See Also

run_emissions_ration_module

Calculate a ration component's contribution to carbon dioxide (CO2) emissions from on-field agricultural activities

Description

Calculates the contribution of an individual feed component to carbon dioxide (CO2) emissions from on-field agricultural activities in feed production (e.g., energy use for tillage and machinery operations), using feed-specific emission factors weighted by the component's share in the ration.

Usage

calc_co2_ration_crop_activities(feed_ration_fraction, co2_feed_crop_activities)

Arguments

Details

The contribution is computed as:

diet\_co2\_feed\_crop\_operations = feed\_ration\_fraction \times co2\_feed\_crop\_operations

This function is part of the run_emissions_ration_module().

Value

Numeric. Contribution of an individual feed component to the diet-level average carbon dioxide (CO2) emission factor from on-field agricultural activities in feed production (g CO2/kg DM).

See Also

run_emissions_ration_module

Calculate a ration component's contribution to carbon dioxide (CO2) emissions from fertilizer manufacture

Description

Calculates the contribution of an individual feed component to carbon dioxide (CO2) emissions from fertilizer manufacture in feed production, using feed-specific emission factors weighted by the component's share in the ration.

Usage

calc_co2_ration_fertilizer(feed_ration_fraction, co2_feed_fertilizer)

Arguments

Details

The contribution is computed as:

diet\_co2\_feed\_fertilizer = feed\_ration\_fraction \times co2\_feed\_fertilizer

This function is part of the run_emissions_ration_module().

Value

Numeric. Contribution of an individual feed component to the diet-level average carbon dioxide (CO2) emission factor from fertilizer manufacture in feed production (g CO2/kg DM).

See Also

run_emissions_ration_module

Calculate a ration component's contribution to carbon dioxide (CO2) emissions from land-use change (excluding peatland drainage)

Description

Calculates the contribution of an individual feed component to carbon dioxide (CO2) emissions from land-use change in feed production (excluding peatland drainage), using feed-specific emission factors weighted by the component's share in the ration.

Usage

calc_co2_ration_luc_nopeat(feed_ration_fraction, co2_feed_luc_nopeat)

Arguments

Details

The contribution is computed as:

diet\_co2\_feed\_luc\_nopeat = feed\_ration\_fraction \times co2\_feed\_luc\_nopeat

This function is part of the run_emissions_ration_module().

Value

Numeric. Contribution of an individual feed component to the diet-level average carbon dioxide (CO2) emission factor from land-use change (excluding peatland drainage) in feed production (g CO2/kg DM).

See Also

run_emissions_ration_module

Calculate a ration component's contribution to carbon dioxide (CO2) emissions from peatland drainage

Description

Calculates the contribution of an individual feed component to carbon dioxide (CO2) emissions from peatland drainage in feed production, using feed-specific emission factors weighted by the component's share in the ration.

Usage

calc_co2_ration_luc_peat(feed_ration_fraction, co2_feed_luc_peat)

Arguments

Details

The contribution is computed as:

diet\_co2\_feed\_luc\_peat = feed\_ration\_fraction \times co2\_feed\_luc\_peat

This function is part of the run_emissions_ration_module().

Value

Numeric. Contribution of an individual feed component to the diet-level average carbon dioxide (CO2) emission factor from peatland drainage in feed production (g CO2/kg DM).

See Also

run_emissions_ration_module

Calculate a ration component's contribution to carbon dioxide (CO2) emissions from pesticide manufacture

Description

Calculates the contribution of an individual feed component to carbon dioxide (CO2) emissions from pesticide manufacture in feed production, using feed-specific emission factors weighted by the component's share in the ration.

Usage

calc_co2_ration_pesticides(feed_ration_fraction, co2_feed_pesticides)

Arguments

Details

The contribution is computed as:

diet\_co2\_feed\_pesticides = feed\_ration\_fraction \times co2\_feed\_pesticides

Value

Numeric. Contribution of an individual feed component to the diet-level average carbon dioxide (CO2) emission factor from pesticide manufacture in feed production (g CO2/kg DM).

Convert methane (CH4) and nitrous oxide (N2O) emissions to CO2-equivalents (CO2eq) using Global Warming Potentials (GWP) factors

Description

Calculates CO2-equivalent (CO2eq) emissions for CH4 and N2O based on 100-year Global Warming Potentials (GWP) reported in IPCC assessment reports.

Usage

calc_co2eq(gas, value_allocated, global_warming_potential_set)

Arguments

Details

CO2-equivalent emissions are calculated as:

value\_co2eq = value\_allocated \times gwp

where gwp is the gas-specific 100-year Global Warming Potential factor from the selected IPCC assessment report.

This function is part of the run_aggregation_module().

Value

List with elements:

value_co2eq

Numeric vector. Emissions expressed as CO2-equivalents (kg CO2eq).

gwp

Numeric vector. Global Warming Potential factor applied to each observation (kg CO2eq/kg gas).

References

IPCC (2007). Climate Change 2007: The Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change.

IPCC (2013). Climate Change 2013: The Physical Science Basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change.

IPCC (2021). Climate Change 2021: The Physical Science Basis. Contribution of Working Group I to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change.

See Also

run_aggregation_module(),

Aggregate cohort-level to herd-level data

Description

This function aggregates a dataset from cohort level to herd level by summing specified variables over the defined 'id' columns.

Usage

calc_cohort_to_herd_aggregation(
  data_cohort,
  id_cols,
  vars_to_sum,
  cohort_short
)

Arguments

Value

A data.table at herd scale, in which selected cohort-level variables have been summed across all cohorts belonging to the same herd, as defined by id_herd.

This function is part of the run_allocation_module() and run_aggregation_module().

See Also

run_allocation_module(), run_aggregation_module()

Calculate totals by cohort

Description

Calculates the total value for each variable at the cohort level over the full assessment period. Values are harmonized to a common unit (kg/cohort/assessment duration) by accounting for cohort stock size and simulation duration.

Usage

calc_cohort_totals(
  value,
  cohort_stock_size,
  ration_intake,
  feed_emissions_list,
  simulation_duration,
  variable_name,
  variable_type
)

Arguments

Details

Production variables are already expressed at the cohort level for the entire assessment duration and are therefore returned unchanged. All other variables (emissions, feed, and nitrogen balance) are expressed per head per day and are scaled by cohort stock size and simulation duration to obtain cohort-level totals.

For production variables:

value\_total = value

For emissions (except emissions from feed), feed, and nitrogen balance variables:

value\_total = value \times cohort\_stock\_size \times simulation\_duration

For feed emissions variables:

value\_total = value \times ration\_intake \times cohort\_stock\_size \times simulation\_duration / 1000

This function is part of the run_aggregation_module().

Value

Numeric. Variable value expressed as (unit)/cohort/assessment duration for all variables.

See Also

run_aggregation_module()

Calculate live weights by cohort and life stage

Description

Determines the initial, potential final, and slaughter live weights for a given sex–age cohort based on species‑specific biological parameters. The function assigns weights according to the animal's life stage (juvenile, subadult, adult) and the sex of the cohort.

Usage

calc_cohort_weights(
  cohort_short,
  live_weight_female_adult = NA_real_,
  live_weight_male_adult = NA_real_,
  live_weight_at_birth = NA_real_,
  live_weight_female_at_slaughter = NA_real_,
  live_weight_male_at_slaughter = NA_real_,
  live_weight_at_weaning = NA_real_
)

Arguments

Details

The function attributes weights according to cohort and animal type:

• Juveniles ("FJ", "MJ"):

  • live_weight_cohort_initial = live_weight_at_birth

  • live_weight_cohort_potential_final = live_weight_at_weaning

  • live_weight_cohort_at_slaughter = live_weight_at_weaning

• Subadults ("FS", "MS"):

  • live_weight_cohort_initial = live_weight_at_weaning

  • live_weight_cohort_potential_final = adult weight for the cohort sex (live_weight_female_adult for "FS", live_weight_male_adult for "MS")

  • live_weight_cohort_at_slaughter = subadult slaughter weight for the cohort sex (live_weight_female_at_slaughter for "FS", live_weight_male_at_slaughter for "MS")

• Adults ("FA", "MA"):

  • live_weight_cohort_initial = live_weight_female_adult for "FA", and live_weight_cohort_initial = live_weight_male_adult for "MA"

  • live_weight_cohort_potential_final = adult weight for the cohort sex

  • live_weight_cohort_at_slaughter = adult weight for the cohort sex

This function is part of the run_weights_module().

Value

A named list with:

live_weight_cohort_initial

Numeric. Live weight at the beginning of the cohort stage (kg).

live_weight_cohort_potential_final

Numeric. Potential final live weight attainable at the end of the cohort stage in the absence of offtake (kg). (For juveniles: equals weaning weight; For subadults: equals adult live weight; For adults: equals adult live weight)

live_weight_cohort_at_slaughter

Numeric. Live weight at slaughter for animals removed from the cohort (kg).

live_weight_mature_stage

Numeric. Mature (adult) live weight that the animal can attain under given biological and management conditions (kg).

See Also

run_weights_module

Calculate methane conversion factor (ym)

Description

Calculates the methane conversion factor (ym, % of dietary gross energy in feed converted to methane) for a given species and cohort based on diet digestibility. Implements species- and cohort-specific rules consistent with IPCC Tier 2 approach.

Usage

calc_conversion_factor_ym(
  species_short,
  cohort_short,
  ration_digestibility_fraction
)

Arguments

Details

ym is computed using species- and cohort-specific default relationships with diet digestibility (Opio et al., 2013).

ration_digestibility_fraction can be calculated with calc_ration_digestibility - see also run_ration_quality_module.

• For CTL and BFL:

  ym = 9.75 - 0.05 \times (ration\_digestibility\_fraction \times 100)

• For SHP, GTS and CML:

  • FA and MA cohorts:

    ym = 9.75 - 0.05 \times (ration\_digestibility\_fraction \times 100)

  • FS and MS cohorts:

    ym = 7.75 - 0.05 \times (ration\_digestibility\_fraction \times 100)

• For PGS: ym is assigned fixed values by cohort:

  • FA and MA cohorts:

    ym = 1.01

  • FS and MS cohorts:

    ym = 0.39

ym is returned as 0 for juvenile cohorts (FJ, MJ), assuming negligible enteric methane production before weaning/rumen development.

This function is part of the run_emissions_enteric_module().

Value

Numeric. Methane (CH4) conversion factor (ym), representing the percentage of gross energy of the feed ration that is converted to CH4 (percentage).

References

Opio, C., Gerber, P., Mottet, A., Falcucci, A., Tempio, G., MacLeod, M., Vellinga, T., Henderson, B. & Steinfeld, H. (2013). Greenhouse gas emissions from ruminant supply chains – A global life cycle assessment. Food and Agriculture Organization of the United Nations (FAO), Rome.

Jørgensen, H., Theil, P. K. & Knudsen, K. E. B. (2011). Enteric methane emission from pigs. In: Planet Earth 2011 – Global Warming Challenges and Opportunities for Policy and Practice (p. 610; Table 2). InTech.

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories. Chapter 10: Emissions from Livestock and Manure Management, Equation 10.21.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories. Chapter 10: Emissions from Livestock and Manure Management, Equation 10.21.

See Also

run_emissions_enteric_module, calc_ration_digestibility, run_ration_quality_module

Calculate daily weight gain by cohort

Description

Calculates average daily weight gain for a given sex–age cohort based on the difference between potential final and initial live weights.

Usage

calc_daily_weight_gain(
  live_weight_cohort_potential_final,
  live_weight_cohort_initial,
  cohort_duration_days
)

Arguments

Details

Daily live weight gain is calculated as the difference between the potential final live weight and the initial live weight, divided by the duration of the cohort stage:

daily\_weight\_gain = (live\_weight\_cohort\_potential\_final - live\_weight\_cohort\_initial) / cohort\_duration\_days

This function is part of the run_weights_module().

Value

Numeric. Average live weight gain of the cohort over the cohort stage (kg/head/day).

See Also

run_weights_module

Calculate daily fecundity rates

Description

Calculates the daily number of male and female offspring produced per adult female.

Usage

calc_fecundity_rates(parturition_rate, litter_size, birth_fraction_female)

Arguments

Value

A named list with two elements:

fecundity_female

Numeric. Daily number of female offspring per adult female (# offspring/day)

fecundity_male

Numeric. Daily number of male offspring per adult female (# offspring/day)

This function is part of the run_demographic_herd_module().

See Also

run_demographic_herd_module()

Examples

calc_fecundity_rates(parturition_rate = 0.8, litter_size = 2, birth_fraction_female = 0.5)

Calculate feed digestibility fraction

Description

Calculates species-specific feed digestibility fractions by feed component.

Usage

calc_feed_digestibility_fraction(
  feed_digestible_energy_ruminant,
  feed_digestible_energy_pigs,
  feed_gross_energy
)

Arguments

Details

Digestibility is computed as the ratio of usable energy to gross energy:

feed\_digestibility\_fraction = usable\_energy / feed\_gross\_energy

For ruminants and pigs, usable energy is represented by digestible_energy (DE), which accounts for fecal energy losses.

This function is part of the run_ration_quality_module().

Value

List with elements:

feed_digestibility_fraction_ruminant

Numeric. Digestibility of a feed component for ruminants, expressed as the ratio of digestible energy to gross energy content (fraction).

feed_digestibility_fraction_pigs

Numeric. Digestibility of a feed component for pigs, expressed as the ratio of digestible energy to gross energy content (fraction).

See Also

run_ration_quality_module

Calculate fibre energy requirements (for biophysical allocation)

Description

Calculates the energy required for fibre production over the assessment period (MJ/cohort/assessment period), based on the daily energy requirement for fibre production, cohort size, and assessment duration.

Usage

calc_fibre_allocation_energy(
  species_short,
  cohort_stock_size = NA_real_,
  metabolic_energy_req_fibre_production = NA_real_,
  ratio_me_to_ne = NA_real_,
  simulation_duration = NA_real_
)

Arguments

Details

This function provides the fibre-related energy term used in a biophysical allocation framework to apportion emissions between milk and other co-products in multifunctional livestock production systems.

The approach implements the IDF (2022) standard, adapted from Thoma and Nemecek (2020), and is consistent with FAO LEAP livestock LCA guidelines (FAO, 2016a, 2016b, 2016c) and with ISO 14044:2006 (Section 4.3.4.2, Step 2).

In accordance with ISO 14044:2006 (Section 4.3.4.2, Step 2), known processing or biophysical relationships may be used to assign shared inputs and outputs of a single production unit to individual products or sub-units. In livestock systems, this includes apportioning shared feed and energy use according to physiological energy requirements (e.g., net energy for lactation, growth, etc.). If the resulting process remains multifunctional, these energy terms may subsequently be used to derive allocation factors among co-products.

Total fibre-related energy over the assessment period is computed for fibre-producing species (CML, SHP, GTS) and applicable cohorts ("FA", "FS", "MA", "MS").

The fibre_allocation_energy is calculated as follows:

energy\_allocation\_fibre = \frac{energy\_requirement\_fibre\_production}{ratio\_me\_to\_ne} \times simulation\_duration \times cohort\_stock\_size

for camels (CML), and:

energy\_allocation\_fibre = energy\_requirement\_fibre\_production \times simulation\_duration \times cohort\_stock\_size

for sheep (SHP) and goats (GTS).

where metabolic_energy_req_fibre_production can be computed using calc_metabolic_energy_req_fibre (see also run_metabolic_energy_req_module).

This function is part of the run_allocation_module().

Value

Numeric. Energy required to produce all fibre output by cohort (MJ/cohort/assessment period). Non-zero values are expected only for fibre-producing species (CML, SHP, GTS) and applicable cohorts ("FA", "FS", "MA", "MS").

References

ISO. (2006). Environmental management — Life cycle assessment — Requirements and guidelines (ISO 14044:2006). International Organization for Standardization, Geneva.

IDF. (2022). The IDF Global Carbon Footprint Standard for the Dairy Sector. Bulletin of the IDF No. 520/2022. International Dairy Federation, Brussels.

Thoma, G., and Nemecek, T. (2020). Allocation between milk and meat in dairy LCA: Critical discussion of the IDF’s standard methodology. In Proceedings of the 12th International Conference on Life Cycle Assessment of Food (LCAFood 2020) (pp. 83–89), 13–16 October, Berlin, Germany.

FAO. (2016a). Environmental performance of large ruminant supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

FAO. (2016b). Greenhouse gas emissions and fossil energy use from small ruminant supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

FAO. (2016c). Greenhouse gas emissions and fossil energy use from poultry supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

See Also

run_allocation_module, calc_metabolic_energy_req_fibre, run_metabolic_energy_req_module

Calculate fibre production

Description

Calculates fibre production for producing cohorts (FA, FS, MA, MS) of fibre-producing species (CML, SHP, GTS) over the assessment period (kg/cohort/assessment period).

Usage

calc_fibre_production(
  species_short,
  cohort_short,
  fibre_yield_year,
  simulation_duration,
  cohort_stock_size
)

Arguments

Details

Fibre production outputs are computed as follows:

fibre\_production = \frac{fibre\_yield\_year}{365} \times simulation\_duration \times cohort\_stock\_size

Non-zero fibre outputs are only expected for producing cohorts (FA, FS, MA, MS) of fibre-producing species (CML, SHP, GTS).

This function is part of the run_production_module().

Value

Numeric. Total fibre produced over the assessment period by cohort (kg /cohort/assessment period).

See Also

run_production_module

Calculate meat energy requirements (for biophysical allocation)

Description

Calculates the energy required for meat production over the assessment period (MJ/cohort/assessment period), based on total live weight gained by the cohort from birth to slaughter.

Usage

calc_meat_allocation_energy(
  species_short,
  cohort_short,
  meat_production_live_weight_cohort,
  live_weight_cohort_at_slaughter = NA_real_,
  live_weight_at_birth = NA_real_,
  ratio_me_to_ne = NA_real_
)

Arguments

Details

This function provides the meat-related energy term used in a biophysical allocation framework to apportion emissions between milk and other co-products in multifunctional livestock production systems.

The approach implements the IDF (2022) standard, adapted from Thoma and Nemecek (2020), and is consistent with FAO LEAP livestock LCA guidelines (FAO, 2016a, 2016b, 2016c) and with ISO 14044:2006 (Section 4.3.4.2, Step 2).

In accordance with ISO 14044:2006, known biophysical relationships may be used to assign shared inputs and outputs of a production system to individual products or sub-units. In livestock systems, this includes apportioning shared feed and energy use according to physiological energy requirements such as growth, lactation, and maintenance. If the resulting process remains multifunctional, these energy terms may subsequently be used to derive allocation factors among co-products.

The meat_allocation_energy is calculated as follows:

energy\_allocation\_meat = specific\_energy\_meat \times meat\_production\_live\_weight\_cohort

where

• specific_energy_meat is the average energy required to produce one kilogram of live weight, accounting for species- and cohort-specific growth characteristics (MJ/kg live weight).

• meat_production_live_weight_cohort is the total live weight of animals sold for meat over the assessment period. It can be computed using calc_meat_production (see also run_production_module).

Specific approaches by species:

• For CTL, BFL, CML, SHP, GTS:

  Growth energy is calculated using species- and cohort-specific biophysical relationships adapted from established growth energy formulations (further details in calc_metabolic_energy_req_growth).

• For PGS:

  Growth energy is not calculated in this function and 0 is returned. In downstream processing, calc_allocation_shares assigns 100% of the allocation to the edible meat commodity for pig systems.

This function is part of the run_allocation_module().

Value

Numeric. Energy required by a given sex–age cohort for total meat output by cohort during the assessment period, equal to the energy needed to produce all live-weight gain to reach the target slaughter weight (MJ/cohort/assessment period). For pigs (PGS), the function returns 0 by design.

References

ISO. (2006). Environmental management — Life cycle assessment — Requirements and guidelines (ISO 14044:2006). International Organization for Standardization, Geneva.

IDF. (2022). The IDF Global Carbon Footprint Standard for the Dairy Sector. Bulletin of the IDF No. 520/2022. International Dairy Federation, Brussels.

Thoma, G., and Nemecek, T. (2020). Allocation between milk and meat in dairy LCA: Critical discussion of the IDF’s standard methodology. In Proceedings of the 12th International Conference on Life Cycle Assessment of Food (LCAFood 2020) (pp. 83–89), 13–16 October, Berlin, Germany.

FAO. (2016a). Environmental performance of large ruminant supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

FAO. (2016b). Greenhouse gas emissions and fossil energy use from small ruminant supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

FAO. (2016c). Greenhouse gas emissions and fossil energy use from poultry supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

See Also

run_allocation_module, calc_meat_production, run_production_module, calc_allocation_shares

Calculate meat production

Description

Calculates cohort-level meat production outputs over the assessment period based on the number of animals removed from the herd (offtake). The function returns multiple production metrics expressed in live weight, carcass weight, bone-free meat, and meat protein (kg/cohort/assessment period).

Usage

calc_meat_production(
  offtake_heads_assessment,
  live_weight_cohort_at_slaughter,
  carcass_dressing_fraction,
  bone_free_meat_fraction,
  meat_protein_fraction
)

Arguments

Details

Meat production outputs are computed as follows:

• meat_production_live_weight_cohort is computed as:

  meat\_production\_live\_weight\_cohort = offtake\_heads\_assessment \times live\_weight\_cohort\_at\_slaughter

• meat_production_carcass_weight_cohort is computed as:

  meat\_production\_carcass\_weight\_cohort = meat\_production\_live\_weight\_cohort \times carcass\_dressing\_fraction

• meat_production_bone_free_meat_cohort is computed as:

  meat\_production\_bone\_free\_meat\_cohort = meat\_production\_carcass\_weight\_cohort \times bone\_free\_meat\_fraction

• meat_production_protein_cohort is computed as:

  meat\_production\_protein\_cohort = meat\_production\_bone\_free\_meat\_cohort \times meat\_protein\_fraction

This function is part of the run_production_module().

Value

A named list with:

meat_production_live_weight_cohort

Numeric . Total meat produced as live weight over the assessment period by cohort (kg/cohort/assessment period).

meat_production_carcass_weight_cohort

Numeric. Total meat as carcass weight (excluding organs, and other by-products after dressing) produced over the assessment period by cohort (kg/cohort/assessment period).

meat_production_bone_free_meat_cohort

Numeric. Total bone-free-meat (excluding bones, organs, and other by-products after dressing and bone removal) produced over the assessment period by cohort (kg/cohort/assessment period).

meat_production_protein_cohort

Numeric. Total meat protein (excluding bones, organs, and other by-products after dressing and bone removal) produced over the assessment period by cohort (kg protein/cohort/assessment period).

See Also

run_production_module, run_demographic_herd_module, run_weights_module

Calculate metabolic energy requirements for activity

Description

Calculates the energy requirement for activity by cohort (MJ/head/day), defined as the amount of energy needed to support animal movement and physical activity.

Usage

calc_metabolic_energy_req_activity(
  species_short,
  cohort_short,
  metabolic_energy_req_maintenance,
  live_weight_cohort_average,
  low_activity_fraction,
  high_activity_fraction
)

Arguments

Details

This approach follows the IPCC Tier 2 energy partitioning method and applies:

metabolic\_energy\_req\_activity = cact \times metabolic\_energy\_req\_maintenance

For SHP and GTS, activity energy is calculated as:

metabolic\_energy\_req\_activity = cact \times live\_weight\_cohort\_average

where

cact is an activity coefficient (dimensionless for CTL, BFL, PGS; MJ/day/kg for SHP, GTS) that reflects the animal’s feeding and management conditions. metabolic_energy_req_maintenance can be calculated using calc_metabolic_energy_req_maintenance().

For CTL, BFL, SHP and GTS, cact is computed as a weighted average of activity levels over the assessment period to account for variation in management and grazing intensity.

Specific coefficients by species and cohort:

CTL, BFL (NRC, 1996; AFRC, 1993):

• low_activity_fraction: cact = 0.17

• high_activity_fraction: cact = 0.36

CML (Wardeh, 2004):

• all activity levels: cact = 0.1

GTS (AFRC, 1993):

• low_activity_fraction: cact = 0.019

• high_activity_fraction: cact = 0.024

SHP (AFRC, 1993):

• low_activity_fraction: cact = 0.0107

• high_activity_fraction: cact = 0.024

PGS (NRC, 1998):

• all activity levels: cact = 0.125

This function is part of the run_metabolic_energy_req_module().

Value

Numeric. Energy required for activity, defined as the amount of energy needed to support animal movement and physical activity (MJ/head/day). Expressed as net energy for CTL, BFL, SHP, GTS and as metabolizable energy for CML and PGS.

References

NRC (1998). Nutrient Requirements of Swine, 10th Revised Edition. National Academies Press, Washington, DC.

NRC (1996). Nutrient Requirements of Beef Cattle, 7th Revised Edition. National Academies Press, Washington, DC.

AFRC (1993). Energy and Protein Requirements of Ruminants. An Advisory Manual Prepared by the AFRC Technical Committee on Responses to Nutrients. CAB International, Wallingford, UK.

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management, Equation 10.4; Table 10.5.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management, Equation 10.4; Table 10.5.

Wardeh, M. F. (2004). The nutrient requirements of the dromedary camel. Journal of Camel Science, 1(1):37-45. The Camel Applied Research and Development Network (CARDN), Arab Center for the Studies of Arid Zones and Dry Lands (ACSAD).

See Also

run_metabolic_energy_req_module, calc_metabolic_energy_req_maintenance, calc_avg_weights

Calculate metabolic energy requirements for fibre production

Description

Calculates the energy requirement for fibre production (MJ/head/day), defined as the additional energy required for the synthesis of animal fibre (e.g. wool or hair).

Usage

calc_metabolic_energy_req_fibre(
  species_short,
  cohort_short,
  fibre_yield_year = NA_real_
)

Arguments

Details

This component follows the IPCC Tier 2 partitioning approach and is applied only to fibre-producing species and relevant cohorts, which are assumed to be FA, FS, MA, and MS.

Species-specific approach:

• SHP and GTS (IPCC, 2006; IPCC, 2019):

  For sheep and goats, fibre production energy is calculated assuming a fixed net energy cost of 24 MJ per kilogram of fibre produced. Annual fibre production is converted to a daily requirement as:

  metabolic\_energy\_req\_fibre = \frac{24 \times fibre\_yield\_year}{365}

  where:

  • fibre\_yield\_year is annual fibre production (kg/head/year),

  • 24 is the net energy requirement per kilogram of fibre (MJ/kg fibre),

  • division by 365 converts annual production to a daily basis.

• CML (AFRC, 1998; Cannas et al., 2007):

  For camels, fibre energy requirements are first calculated on a net energy basis and then converted to metabolizable energy using a net-to-metabolizable energy efficiency coefficient:

  metabolic\_energy\_req\_fibre = \frac{24}{0.43} \times \frac{fibre\_yield\_year}{365}

  where:

  • 24 is the net energy requirement per kilogram of fibre (MJ/kg fibre),

  • 0.43 is the efficiency of conversion from metabolizable energy to net energy for fibre production (fraction),

  • fibre\_prod is annual fibre production per animal (kg/head/year),

  • 365 to convert annual production to a daily basis.

  The efficiency coefficient of 0.43 is adopted by analogy with goats, assuming a dietary metabolizability of approximately 0.55, following AFRC guidance and the synthesis by Cannas et al. (2007).

• Other species: Fibre production energy is assumed to be zero.

This function is part of the run_metabolic_energy_req_module().

Value

Numeric. Energy required for the synthesis of fibre for SHP, GTS and CML. Assumed to be 0 for other species. (MJ/head/day). Expressed as net energy for CTL, BFL, SHP, GTS and as metabolizable energy for CML and PGS (MJ/head/day).

References

AFRC (1998) The Nutrition of Goats. CAB International, Wallingford, UK.

AFRC (1993). Energy and Protein Requirements of Ruminants. An Advisory Manual Prepared by the AFRC Technical Committee on Responses to Nutrients. CAB International, Wallingford, UK.

Cannas, A., Atzori, A. S., Boe, F., & Teixeira, I. (2007). Energy and protein requirements of goats. In: Dairy sheep nutrition (pp. 31-49). CAB International, Wallingford, UK.

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories. Chapter 10: Emissions from Livestock and Manure Management, Equation 10.12.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories. Chapter 10: Emissions from Livestock and Manure Management, Equation 10.12.

See Also

run_metabolic_energy_req_module,

Calculate metabolic energy requirements for growth

Description

Calculates the energy requirement for growth by cohort (MJ/head/day), defined as the energy required for body tissue accretion, corresponding to the retained energy component of live weight gain.

Usage

calc_metabolic_energy_req_growth(
  species_short,
  cohort_short,
  live_weight_cohort_average = NA_real_,
  live_weight_cohort_final = NA_real_,
  live_weight_cohort_initial = NA_real_,
  live_weight_mature_stage = NA_real_,
  daily_weight_gain = NA_real_,
  offtake_rate = NA_real_,
  cohort_duration_days = NA_real_
)

Arguments

Details

This function follows the IPCC Tier 2 energy partitioning approach and applies species-specific equations for growth energy requirements.

In general, growth energy is computed only for growing cohorts (FJ, FS, MJ, MS); in this implementation, growth is set to 0 for adult cohorts (FA, MA).

Species-specific approach:

• CTL and BFL (NRC, 1996; IPCC, 2006; IPCC, 2019)

  Growth energy is computed using a growth coefficient cgro that differs between castrated and intact males. For male cohorts, cgro is calculated as a weighted average using offtake_rate, assuming that animals removed from the herd are castrated and animals remaining in the cohort are intact.

• SHP and GTS (Gibbs et al., 2002; AFRC, 1993; IPCC, 2006; IPCC, 2019)

  For sheep and goats, growth energy is calculated using a linear formulation with coefficients a and b (MJ/kg live weight). For male cohorts, the coefficients differ between castrated and intact males; the model computes a weighted average using offtake_rate, assuming that offtaken animals are castrated.

• CML (Al-Jassim, 2019)

  Growth energy is represented using a simplified linear relationship with daily weight gain.

• PGS (NRC, 1998)

  For pigs, growth is assumed to consist exclusively of protein tissue and fat tissue, and growth energy requirements are expressed as metabolizable energy (ME).

  The growth energy coefficient cgro (MJ/kg live weight) is calculated as:

  cgro = prot\_tissue\_frac \times meat\_protein \times meat\_protein\_energy + (1 - prot\_tissue\_frac) \times fat\_adipose\_tissue_frac \times meat\_fat\_energy

  Total metabolizable energy required for growth is then:

  metabolic\_energy\_req\_growth = daily\_weight\_gain \times cgro

  where:

  • cgro is the growth energy coefficient (MJ/kg live weight),

  • prot_tissue_frac = 0.65 is the fraction of protein tissue in daily weight gain,

  • meat_protein = 0.23 is the fraction of protein in protein tissue,

  • meat_protein_energy = 54.0 is the ME cost of protein deposition (MJ/kg protein),

  • fat_adipose_tissue_frac = 0.90 is the fraction of fat in adipose tissue,

  • meat_fat_energy = 52.3 is the ME cost of fat deposition (MJ/kg fat).

This function is part of the run_metabolic_energy_req_module().

Value

Numeric. Energy required for growth (i.e., weight gain) (MJ/head/day). Expressed as net energy for CTL, BFL, SHP, GTS and as metabolizable energy for CML and PGS.

References

Al-Jassim, R. (2019). Metabolisable energy and protein requirements of the Arabian camel (Camelus dromedarius). Journal of Camelid Science (12) 33-45

NRC (1998). Nutrient Requirements of Swine, 10th Revised Edition. National Academies Press, Washington, DC.

NRC (1996). Nutrient Requirements of Beef Cattle, 7th Revised Edition. National Academies Press, Washington, DC.

AFRC (1993). Energy and Protein Requirements of Ruminants. An Advisory Manual Prepared by the AFRC Technical Committee on Responses to Nutrients. CAB International, Wallingford, UK.

Gibbs, M.J., Conneely, D., Johnson, D., Lassey, K.R. and Ulyatt, M.J. (2002). CH4 emissions from enteric fermentation. In: Background Papers: IPCC Expert Meetings on Good Practice Guidance and Uncertainty Management in National Greenhouse Gas Inventories, p 297–320. IPCC-NGGIP, Institute for Global Environmental Strategies (IGES), Hayama, Kanagawa, Japan.

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management, Equation 10.6 and 10.7; Table 10.6.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management, Equation 10.6 and 10.7; Table 10.6.

See Also

run_metabolic_energy_req_module, calc_cohort_weights, calc_avg_weights, calc_daily_weight_gain

Calculate metabolic energy requirements for lactation

Description

Calculates the energy requirement for lactation by cohort (MJ/head/day), defined as the energy needed to support milk production by lactating females.

Usage

calc_metabolic_energy_req_lactation(
  species_short,
  cohort_short,
  lactating_females_fraction = NA_real_,
  milk_yield_day = NA_real_,
  milk_fat_fraction = NA_real_,
  non_productive_duration = NA_real_,
  pregnancy_duration = NA_real_,
  litter_size = NA_real_,
  death_rate_juvenile = NA_real_,
  live_weight_at_birth = NA_real_,
  live_weight_at_weaning = NA_real_,
  lactation_duration = NA_real_,
  parturition_rate = NA_real_
)

Arguments

Details

This approach follows the IPCC Tier 2 partitioning method and applies species-specific equations for lactation energy requirements as a function of the quantity of milk produced and a species-specific energy cost per unit of milk.

Requirements are calculated only for cohort = FA (adult females) and are scaled by the proportion of lactating animals (lactating_females_fraction) or reproducing females (parturition_rate) within the cohort.

Species-specific approach:

CTL, BFL, CML, SHP and GTS:

Total milk production includes:

• milk extracted for human consumption (milk_yield)

• milk consumed directly by offspring (milk_for_offspring)

In general form, lactation energy is computed as:

metabolic\_energy\_req\_lactation = (milk\_yield \times lactating\_females\_fraction + milk\_for\_offspring) \times energy\_milk

where:

energy_milk is a species-specific coefficient representing the net energy cost of producing one kilogram of milk (MJ/kg milk).

Species-specific values of energy_milk are:

• CTL, BFL: estimated as a function of milk fat content, 1.47 + 0.40 \times (milk\_fat\_fraction \times 100) (NRC, 1989),

• CML: 4.063 (Wardeh, 2004),

• SHP: 4.6 (AFRC, 1993),

• GTS: 3.0 (AFRC, 1998).

milk_for_offspring is the daily amount of milk required to rear offspring across the year (kg/day). It is calculated assuming that 5 kg of milk are required for each kilogram of live-weight gain up to weaning:

milk\_for\_offspring = \frac{parturition\_rate \times 5 \times (weaning\_weight - birth\_weight)}{365}

For SHP and GTS, milk_for_offspring is multiplied by litter_size to account for multiple offspring per birth.

PGS (NRC, 1998):

Lactation energy accounts only for the milk consumed directly by offspring (milk_for_offspring), adjusted by the fraction of the reproductive cycle spent in lactation (cadj):

\begin{aligned} metabolic\_energy\_req\_lactation &= litter\_size \times (1 - 0.5 \times death\_rate\_juvenile) \times \\ & \left( \frac{0.02059 \times (weaning\_weight - birth\_weight) \times 1000} {lactation\_duration} - \frac{0.3766}{0.67} \right) \times cadj \end{aligned}

where:

• 0.02059 is the coefficient for lactation energy requirement (MJ/g live weight),

• 0.3766 is the coefficient for sow weight loss during lactation (MJ/head/day),

• 0.67 is the efficiency of conversion of dietary intake to milk energy (fraction),

• cadj is the fraction of the reproductive cycle spent in lactation:

  cadj = \frac{lactation\_duration}{non\_productive\_duration + pregnancy\_duration + lactation\_duration}

This function is part of the run_metabolic_energy_req_module().

Value

Numeric. Energy required for lactation (MJ/head/day). Expressed as net energy for CTL, BFL, SHP, GTS and as metabolizable energy for CML and PGS.

References

AFRC (1998) The Nutrition of Goats. CAB International, Wallingford, UK.

AFRC (1993). Energy and Protein Requirements of Ruminants. An Advisory Manual Prepared by the AFRC Technical Committee on Responses to Nutrients. CAB International, Wallingford, UK.

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management, Equation 10.8-10.10.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management, Equation 10.8-10.10.

NRC (1998). Nutrient Requirements of Swine, 10th Revised Edition. National Academies Press, Washington, DC.

NRC (1989) Nutrient Requirements of Dairy Cattle, 6th Ed. . Washington, D.C. U.S.A: National Academy Press.

Wardeh, M. F. (2004). The nutrient requirements of the dromedary camel. Journal of Camel Science, 1(1):37-45. The Camel Applied Research and Development Network (CARDN), Arab Center for the Studies of Arid Zones and Dry Lands (ACSAD).

See Also

run_metabolic_energy_req_module

Calculate metabolic energy requirements for maintenance

Description

Calculates the energy requirement for maintenance by cohort (MJ/head/day), defined as the energy required to maintain basal physiological functions at equilibrium, with no net gain or loss of body energy.

Usage

calc_metabolic_energy_req_maintenance(
  species_short,
  cohort_short,
  live_weight_cohort_average,
  lactating_females_fraction = NA_real_,
  offtake_rate = NA_real_,
  age_first_parturition = NA_real_
)

Arguments

Details

This approach follows the IPCC Tier 2 partitioning method and applies:

metabolic\_energy\_req\_maintenance = cmain \times average\_weight^{0.75}

where cmain is a category-specific coefficient (MJ/day/kg^{0.75}) that reflects basal metabolic requirements and varies by species, physiological status, and sex.

For selected cohorts, cmain is computed as a weighted average to account for:

• CTL, BFL: lactating vs. non-lactating females

• CTL, BFL, SHP: intact vs. castrated males - Offtaken animals assumed castrated

• SHP: animals below vs. above one year of age

Specific coefficients by species and cohort:

CTL and BFL (NRC, 1996; AFRC, 1993):

• FA: cmain = 0.386 \times lactating\_females\_fraction + 0.322 \times (1 - lactating\_females\_fraction)

• FS, FJ, MJ: cmain = 0.322

• MA, MS: cmain = 0.322 \times offtake\_rate + 0.370 \times (1 - offtake\_rate)

CML (Wardeh, 2004):

• All cohorts: cmain = 0.435

GTS (AFRC, 1993):

• All cohorts: cmain = 0.315

SHP (AFRC, 1993):

• FA: cmain = 0.217

• FJ: cmain = 0.236

• FS: cmain = 0.236 \times (365/age\_first\_parturition) + 0.217 \times ((age\_first\_parturition - 365)/age\_first\_parturition)

• MA: cmain = 0.217 \times offtake\_rate + (0.217 \times 1.15) \times (1 - offtake\_rate)

• MJ: cmain = 0.236 \times offtake\_rate + (0.236 \times 1.15) \times (1 - offtake\_rate)

• MS: cmain = (0.217 \times offtake\_rate + (0.217 \times 1.15) \times (1 - offtake\_rate)) \times ((age\_first\_parturition - 365)/age\_first\_parturition) + (0.236 \times offtake\_rate + (0.236 \times 1.15) \times (1 - offtake\_rate)) \times (365/age\_first\_parturition)

PGS (NRC, 1998):

• All cohorts: cmain = 0.4435

This function is part of the run_metabolic_energy_req_module().

Value

Numeric. Energy required for maintenance, defined as the amount of energy needed to keep the animal at equilibrium such that body energy is neither gained nor lost. Expressed as net energy for CTL, BFL, SHP, GTS and as metabolizable energy for CML and PGS (MJ/head/day).

References

NRC (1998). Nutrient Requirements of Swine, 10th Revised Edition. National Academies Press, Washington, DC.

NRC (1996). Nutrient Requirements of Beef Cattle, 7th Revised Edition. National Academies Press, Washington, DC.

AFRC (1993). Energy and Protein Requirements of Ruminants. An Advisory Manual Prepared by the AFRC Technical Committee on Responses to Nutrients. CAB International, Wallingford, UK.

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories. Chapter 10: Emissions from Livestock and Manure Management, Equation 10.3; Table 10.4.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories. Chapter 10: Emissions from Livestock and Manure Management, Equation 10.3; Table 10.4.

Wardeh, M. F. (2004). The nutrient requirements of the dromedary camel. Journal of Camel Science, 1(1):37-45. The Camel Applied Research and Development Network (CARDN), Arab Center for the Studies of Arid Zones and Dry Lands (ACSAD).

See Also

run_metabolic_energy_req_module, calc_avg_weights

Calculate metabolic energy requirements for pregnancy

Description

Calculates the energy requirement for pregnancy by cohort (MJ/head/day) for pregnant females, defined as the additional energy needed to support gestation.

Usage

calc_metabolic_energy_req_pregnancy(
  species_short,
  cohort_short,
  metabolic_energy_req_maintenance = NA_real_,
  parturition_rate = NA_real_,
  litter_size = NA_real_,
  pregnancy_duration = NA_real_,
  non_productive_duration = NA_real_,
  lactation_duration = NA_real_,
  cohort_duration_days = NA_real_,
  offtake_rate = NA_real_
)

Arguments

Details

This component follows the IPCC Tier 2 partitioning framework and is applied only to female cohorts (FA and FS).

Pregnancy energy (metabolic_energy_req_pregnancy) represents the additional energy required to support gestation. Requirements are computed as a fraction of maintenance energy and are adjusted to reflect reproductive activity within the cohort:

• For FA, requirements are scaled by the annual parturition rate (parturition_rate) and (when applicable) by the fraction of the reproductive cycle spent in gestation (pregnancy_duration/(pregnancy_duration+lactation_duration+non_productive_duration)).

• For FS, only a fraction of animals is assumed to reach reproductive age within the cohort; requirements are therefore scaled by the proportion remaining in the cohort (1 - offtake\_rate) and by the share of the cohort duration spent pregnant (pregnancy_duration/cohort_duration_days).

General form

metabolic\_energy\_req\_pregnancy = metabolic\_energy\_req\_maintenance \times c_{preg} \times S

where

• c_{preg} is a species-specific pregnancy coefficient,

• S is a scaling term that depends on cohort (FA vs FS).

• metabolic\_energy\_req\_maintenance can be calculated using calc_metabolic_energy_req_maintenance()

Specific coefficients by species and cohort:

• CTL and BFL (IPCC, 2006, 2019): Pregnancy energy is approximated as 10\% of maintenance energy.

  • FA:

    \begin{aligned} metabolic\_energy\_req\_pregnancy &= 0.10 \times metabolic\_energy\_req\_maintenance \times parturition\_rate \times \\ & \frac{pregnancy\_duration}{365} \end{aligned}

  • FS:

    \begin{aligned} metabolic\_energy\_req\_pregnancy &= 0.10 \times metabolic\_energy\_req\_maintenance \times \\ & \frac{pregnancy\_duration}{cohort\_duration\_days} \times (1 - offtake\_rate) \end{aligned}

• CML (Wardeh, 2004): Pregnancy energy is estimated as 12\% of maintenance energy.

  • FA:

    metabolic\_energy\_req\_pregnancy = 0.12 \times metabolic\_energy\_req\_maintenance \times parturition\_rate

  • FS:

    metabolic\_energy\_req\_pregnancy = 0.12 \times metabolic\_energy\_req\_maintenance \times \frac{pregnancy\_duration}{cohort\_duration\_days} \times (1 - offtake\_rate)

• SHP and GTS (IPCC 2006; 2019): Pregnancy energy is calculated as a litter-size-dependent fraction of maintenance energy (c_{preg}).

  • FA:

    \begin{aligned} metabolic\_energy\_req\_pregnancy &= metabolic\_energy\_req\_maintenance \times c_{preg} \times parturition\_rate \times \\ & \frac{pregnancy\_duration}{365} \end{aligned}

    where c_{preg} is:

    c_{preg} = \left\{ \begin{array}{ll} 0.077 \times (2 - litter\_size) + 0.126 \times (litter\_size - 1), & 1 \le litter\_size \le 2 \\ 0.150, & litter\_size > 2 \end{array} \right.

  • FS: A single-birth coefficient is used (c_{preg}=0.077) and scaled by the proportion of reproductive individuals in the cohort:

    \begin{aligned} metabolic\_energy\_req\_pregnancy &= 0.12 \times metabolic\_energy\_req\_maintenance \times \\ & \frac{pregnancy\_duration}{cohort\_duration\_days} \times \\ & (1 - offtake\_rate) \end{aligned}

• PGS (NRC, 1998): Pregnancy energy is expressed using a gestation coefficient c_{gest} (MJ/piglet), with default c_{gest}=0.14985.

  • FA:

    \begin{aligned} metabolic\_energy\_req\_pregnancy &= c_{gest} \times litter\_size \times \\ & \frac{pregnancy\_duration}{ non\_productive\_duration + pregnancy\_duration + lactation\_duration } \end{aligned}

  • FS:

    \begin{aligned} metabolic\_energy\_req\_pregnancy &= c_{gest} \times litter\_size \times \\ & \frac{pregnancy\_duration}{cohort\_duration\_days} \times \\ & (1 - offtake\_rate) \end{aligned}

This function is part of the run_metabolic_energy_req_module().

Value

Numeric. Energy required for pregnancy for pregnant females (MJ/head/day). Expressed as net energy for CTL, BFL, SHP, GTS and as metabolizable energy for CML and PGS.

References

NRC (1998). Nutrient Requirements of Swine, 10th Revised Edition. National Academies Press, Washington, DC.

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories. Chapter 10: Emissions from Livestock and Manure Management, Equation 10.13; Table 10.7.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories. Chapter 10: Emissions from Livestock and Manure Management, Equation 10.13; Table 10.7.

Wardeh, M. F. (2004). The nutrient requirements of the dromedary camel. Journal of Camel Science, 1(1):37-45. The Camel Applied Research and Development Network (CARDN), Arab Center for the Studies of Arid Zones and Dry Lands (ACSAD).

See Also

run_metabolic_energy_req_module, calc_metabolic_energy_req_maintenance

Calculate metabolic energy requirements for work

Description

Calculates the energy requirement for work (MJ/head/day), defined as the additional energy required to support draught power and work-related physical activity.

Usage

calc_metabolic_energy_req_work(
  species_short,
  cohort_short,
  metabolic_energy_req_maintenance = NA_real_,
  draught_work_hours_female = NA_real_,
  draught_work_hours_male = NA_real_,
  draught_fraction_female = NA_real_,
  draught_fraction_male = NA_real_
)

Arguments

Details

This approach follows the IPCC Tier 2 partitioning method and applies species-specific coefficients for draught work.

This energy component is calculated only for adult cohorts ( FA and MA) of draught-capable species (CTL, BFL, and CML). It is scaled by the fraction of adult animals involved in draught work (draught_fraction_female, draught_fraction_male) and their average daily working time (draught_work_hours_female, draught_work_hours_male).

Species-specific approach:

CTL and BFL - (Bamualim & Kartiarso, 1985; IPCC, 2006; IPCC 2019). Draught work energy is expressed as a proportion of net energy for maintenance:

metabolic\_energy\_req\_work = 0.1 \times metabolic\_energy\_req\_maintenance \times work\_hours \times draught\_fraction

where:

• metabolic\_energy\_req\_maintenance is net energy required for maintenance (MJ/head/day) and can be calculated using calc_metabolic_energy_req_maintenance(),

• 0.1 represents a 10% increase in maintenance energy per hour of work,

• work\_hours is the mean number of hours worked per animal per day - draught_work_hours_female (for FA) and draught_work_hours_male (for MA) and,

• draught\_fraction is the fraction of adult animals performing draught work - draught_fraction_female (for FA) and draught_fraction_male (for MA)

CML - (Wilson, 1989) Draught work energy is calculated using a fixed metabolizable energy cost per hour of work:

metabolic\_energy\_req\_work = 4 \times work\_hours \times draught\_fraction

where:

• 4 is the metabolizable energy requirement for draught work (MJ/hour),

• work\_hours is the mean number of hours worked per animal per day - draught_work_hours_female (for FA) and draught_work_hours_male (for MA) and,

• draught\_fraction is the fraction of adult animals performing draught work - draught_fraction_female (for FA) and draught_fraction_male (for MA)

This function is part of the run_metabolic_energy_req_module().

Value

Numeric. Energy required for work, used to estimate the energy required for draught power for CTL, BFL and CML (MJ/head/day). Assumed to be 0 for other species. Expressed as net energy for CTL, BFL, SHP, GTS and as metabolizable energy for CML and PGS.

References

Bamualim A., Kartiarso (1985). Nutrition of draught animals with special reference to Indonesia. In: Draught Animal Power for Production. Australian Centre for International agricultural Research (ACIAR), Proceedings Series No. 10, ed. JW Copland. Canberra, A.C.T., Australia: ACIAR.

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management, Equation 10.11.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management, Equation 10.11.

Wilson (1989). The nutritional requirements of camel. In: Tisserand J.-L. (ed.). Séminaire sur la digestion, la nutrition et l'alimentation du dromadaire. Zaragoza : CIHEAM. (1989). p. 171-179 (Options Méditerranéennes : Série A. Séminaires Méditerranéens; n. 2)

See Also

run_metabolic_energy_req_module, calc_metabolic_energy_req_maintenance

Calculate milk energy requirements (for biophysical allocation)

Description

Calculates the energy required for milk production over the assessment period (MJ/cohort/assessment period), based on total fat- and protein-corrected milk (FPCM) produced by the cohort.

Usage

calc_milk_allocation_energy(
  milk_production_fpcm_cohort,
  milk_protein_fraction_standard,
  milk_fat_fraction_standard,
  milk_lactose_fraction_standard
)

Arguments

Details

This function provides the milk-related energy term used in a biophysical allocation framework to apportion emissions between milk and other co-products in multifunctional livestock production systems.

The approach implements the IDF (2022) standard, adapted from Thoma and Nemecek (2020), and is consistent with FAO LEAP livestock LCA guidelines (FAO, 2016a, 2016b, 2016c) and with ISO 14044:2006 (Section 4.3.4.2, Step 2).

In accordance with ISO 14044:2006, known biophysical relationships may be used to assign shared inputs and outputs of a production system to individual products or sub-units. In livestock systems, this includes apportioning shared feed and energy use according to physiological energy requirements such as lactation, growth, and maintenance. If the resulting process remains multifunctional, these energy terms may subsequently be used to derive allocation factors among co-products.

The milk_allocation_energy is calculated as follows:

energy\_allocation\_milk = energy\_standard \times milk\_production\_fpcm\_cohort

where:

• energy_standard is the energy content of standard milk, calculated internally based on standard fat, protein, and lactose contents following IDF (2022) (MJ/kg milk).

• milk_production_fpcm_cohort is the total fat- and protein-corrected milk (FPCM) produced over the assessment period (kg/assessment period). It can be computed using calc_milk_production (see also run_production_module).

This function is part of the run_allocation_module().

Value

Numeric. Energy required to produce total milk output by cohort (MJ/cohort/assessment period). Non-zero values are applicable only to milk-producing species and cohorts (species = CTL, BFL, CML, SHP, GTS; cohorts=FA). All other species–cohort combinations are assigned a value of 0.

References

ISO. (2006). Environmental management — Life cycle assessment — Requirements and guidelines (ISO 14044:2006). International Organization for Standardization, Geneva.

IDF. (2022). The IDF Global Carbon Footprint Standard for the Dairy Sector. Bulletin of the IDF No. 520/2022. International Dairy Federation, Brussels.

Thoma, G., and Nemecek, T. (2020). Allocation between milk and meat in dairy LCA: Critical discussion of the IDF’s standard methodology. In Proceedings of the 12th International Conference on Life Cycle Assessment of Food (LCAFood 2020) (pp. 83–89), 13–16 October, Berlin, Germany.

FAO. (2016a). Environmental performance of large ruminant supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

FAO. (2016b). Greenhouse gas emissions and fossil energy use from small ruminant supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

FAO. (2016c). Greenhouse gas emissions and fossil energy use from poultry supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

See Also

run_allocation_module, calc_milk_production, run_production_module

Calculate milk production

Description

Calculates total milk production for the producing cohort (FA) of milk-producing species (CML, CTL, BFL, SHP, GTS) over the assessment period and returns multiple production metrics: total milk mass, milk protein, and fat-protein-corrected milk (FPCM) (kg/cohort/assessment period).

Usage

calc_milk_production(
  species_short,
  cohort_short,
  milk_yield_day,
  simulation_duration,
  cohort_stock_size,
  lactating_females_fraction,
  milk_protein_fraction,
  milk_fat_fraction,
  milk_lactose_fraction,
  milk_protein_fraction_standard,
  milk_fat_fraction_standard,
  milk_lactose_fraction_standard
)

Arguments

Details

Milk production outputs are computed as follows:

• milk_production_mass_cohort is computed as:

  milk\_production = milk\_yield\_day \times simulation\_duration \times cohort\_stock\_size \times lactating\_females\_fraction

• milk_production_protein_cohort is computed as:

  milk\_protein\_production = milk\_production \times milk\_protein\_fraction

• milk_production_fpcm_cohort is computed using the ratio of energy content of actual versus standard milk:

  FPCM = milk\_production \times \frac{E_{milk}}{E_{standard}}

  where milk energy content (Mcal/kg) is computed as (IDF, 2022):

  E_{milk} = 0.0929 \times milk\_fat\_fraction + 0.0547 \times milk\_protein\_fraction + 0.0395 \times milk\_lactose\_fraction

  E_{standard} = 0.0929 \times milk\_fat\_fraction\_standard + 0.0547 \times milk\_protein\_fraction\_standard + 0.0395 \times milk\_lactose\_fraction\_standard

Non-zero milk outputs are only expected for adult female cohorts of milk-producing species.

This function is part of the run_production_module().

Value

A named list with:

milk_production_mass_cohort

Numeric. Total milk production produced over the assessment period (kg/cohort/assessment period).

milk_production_protein_cohort

Numeric. Total milk protein production produced over the assessment period (kg protein/cohort/assessment period).

milk_production_fpcm_cohort

Numeric. Total fat-protein-corrected milk (FPCM) produced over the assessment period (kg/cohort/assessment period).

References

International Dairy Federation (IDF). 2022. The IDF Global Carbon Footprint Standard for the Dairy Sector. Bulletin of the IDF No. 520/2022. International Dairy Federation (ed.), Brussels, Belgium. Equation 10.

See Also

run_production_module

Calculate direct Nitrous Oxide (N2O) emissions from manure management systems

Description

Calculates daily direct nitrous oxide (N2O) emissions from manure management using IPCC-based parameters and separates emissions from manure deposited on pasture, manure burned for fuel, and all other manure management systems.

Usage

calc_n2o_manure_direct(ratio_N2ON_to_N2O = 44/28, nitrogen_excretion, ...)

Arguments

Details

This calculation follows the Tier 2 methodology for direct nitrous oxide (N2O) emissions from manure management as defined in the IPCC Guidelines (Equation 10.25).

In the IPCC formulation, annual direct emissions are:

N2O_{D(mm)} = \frac{44}{28} \sum_{S} \left( N \times AWMS_S \times EF3_S \right)

where:

N2O_D(mm)

Direct N2O emissions from Manure Management.

44/28

Conversion factor from N2O–N to N2O.

N

Nitrogen excreted (kg N).

AWMS_S

Fraction of excreted nitrogen managed in manure management system S.

EF3_S

Direct emission factor for system S (kg N2O–N per kg N managed).

In this implementation, calculations are performed at daily, per-head resolution using nitrogen_excretion (kg N/head/day) - see also calc_nitrogen_excretion.

Daily emissions are computed as:

\begin{aligned} N2O &= nitrogen\_excretion \times ratio\_N2ON\_to\_N2O \times \\ & \sum \left( manure\_management\_system\_fraction \times n2o\_ef3 \right) \end{aligned}

This function is part of the run_emissions_manure_module().

Value

A named list with the following elements:

n2o_manure_pasture_direct

Numeric. Direct nitrous oxide (N2O) emissions from manure deposited on pasture (kg N2O/head/day).

n2o_manure_burned_direct

Numeric. Direct nitrous oxide (N2O) emissions from manure burned for fuel (kg N2O/head/day).

n2o_manure_other_direct

Numeric. Direct nitrous oxide (N2O) emissions from manure management systems, excluding emissions from manure deposited on pasture and burned for fuel (kg N2O/head/day).

n2o_manure_all_noburn_direct

Numeric. Direct nitrous oxide (N2O) emissions from manure management systems, excluding manure burned for fuel (kg N2O/head/day).

References

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management. Equation 10.25.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management. Equation 10.25.

See Also

run_emissions_manure_module

Examples

calc_n2o_manure_direct(
  ratio_N2ON_to_N2O = 44 / 28,
  nitrogen_excretion = 0.9,
  mms_burned = c(
    manure_management_system_fraction = 0.020,
    n2o_ef3  = 0
  ),
  mms_drylot = c(
    manure_management_system_fraction = 0.264,
    n2o_ef3  = 0.02
  ),
  mms_pasture = c(
    manure_management_system_fraction = 0.310,
    n2o_ef3  = 0.02
  ),
  mms_solid = c(
    manure_management_system_fraction = 0.406,
    n2o_ef3  = 0.005
  )
)

Calculate indirect Nitrous Oxide (N2O) emissions from manure leaching and runoff

Description

Calculates daily indirect nitrous oxide (N2O) emissions resulting from nitrogen leaching and runoff from manure management systems and separates emissions from manure deposited on pasture, manure burned for fuel, and all other manure management systems.

Usage

calc_n2o_manure_leaching(ratio_N2ON_to_N2O = 44/28, nitrogen_excretion, ...)

Arguments

Details

This calculation follows the Tier 2 methodology for indirect N2O emissions from manure management as defined in Equations 10.28 (IPCC, 2006), 10.27 (IPCC, 2019), and 10.29 (IPCC, 2006, 2019).

In the IPCC formulation, indirect emissions associated with nitrogen leaching and runoff are calculated as:

N2O_{L(mm)} = \frac{44}{28} \sum_{S} \left( N \times AWMS_S \times FracLeach_{S} \times EF5 \right)

where:

N2O_L(mm)

Indirect N2O emissions due to leaching and runoff from Manure Management.

44/28

Conversion factor from N2O–N to N2O.

N

Nitrogen excreted (kg N).

AWMS_S

Fraction of excreted nitrogen managed in manure management system S.

FracLeach_{S}

Fraction of nitrogen lost through leaching and runoff in manure management system S.

EF5

Emission factor for indirect N2O emissions from leaching and runoff (kg N2O–N per kg N leached or lost through runoff).

In this implementation, calculations are performed at daily, per-head resolution using nitrogen_excretion (kg N/head/day):

\begin{aligned} N_2O &= nitrogen\_excretion \times ratio\_N2ON\_to\_N2O \times \\ & \sum_{S} \left( manure\_management\_system\_fraction \times nitrogen\_fracleach \times n2o\_ef5 \right) \end{aligned}

This function is part of the run_emissions_manure_module().

Value

A named list with the following elements

n2o_manure_pasture_leach

Numeric. Indirect nitrous oxide (N2O) emissions resulting from leaching and runoff of manure nitrogen from manure deposited on pasture (kg N2O/head/day).

n2o_manure_burned_leach

Numeric. Indirect nitrous oxide (N2O) emissions resulting from leaching and runoff of manure nitrogen from manure burned for fuel (kg N2O/head/day).

n2o_manure_other_leach

Numeric. Indirect nitrous oxide (N2O) emissions resulting from leaching and runoff of manure nitrogen from manure management systems, excluding losses from manure deposited on pasture and manure burned for fuel (kg N2O/head/day).

n2o_manure_all_noburn_leach

Numeric. Indirect nitrous oxide (N2O) emissions resulting from leaching and runoff of manure nitrogen from manure management systems, excluding losses from manure burned for fuel (kg N2O/head/day).

References

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management. Equations 10.27; 10.29.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Volume 4, Chapter 10: Emissions from Livestock and Manure Management. Equations 10.28; 10.29.

See Also

run_emissions_manure_module

Examples

calc_n2o_manure_leaching(
  ratio_N2ON_to_N2O = 44 / 28,
  nitrogen_excretion = 0.9,
  mms_burned = c(
    manure_management_system_fraction = 0.020,
    n2o_ef5 = 0.011,
    nitrogen_fracleach = 0
  ),
  mms_drylot = c(
    manure_management_system_fraction = 0.264,
    n2o_ef5 = 0.011,
    nitrogen_fracleach = 0.035
  ),
  mms_pasture = c(
    manure_management_system_fraction = 0.310,
    n2o_ef5 = 0.011,
    nitrogen_fracleach = 0.24
  ),
  mms_solid = c(
    manure_management_system_fraction = 0.406,
    n2o_ef5 = 0.011,
    nitrogen_fracleach = 0.02
  )
)

Calculate total Nitrous Oxide (N2O) emissions from manure

Description

Aggregates direct and indirect nitrous oxide (N2O) emissions from manure, by manure management system group (deposited on pasture, burned for fuel, and all other systems). Indirect emissions include contributions from volatilization and from leaching and runoff.

Usage

calc_n2o_manure_total(
  n2o_manure_pasture_vol,
  n2o_manure_pasture_leach,
  n2o_manure_burned_vol,
  n2o_manure_burned_leach,
  n2o_manure_other_vol,
  n2o_manure_other_leach,
  n2o_manure_pasture_direct,
  n2o_manure_burned_direct,
  n2o_manure_other_direct
)

Arguments

Details

The following aggregations are applied:

n2o\_manure\_pasture\_indirect = n2o\_vol\_manure\_pasture + n2o\_leach\_manure\_pasture

n2o\_manure\_burned\_indirect = n2o\_vol\_manure\_burned + n2o\_leach\_manure\_burned

n2o\_manure\_other\_indirect = n2o\_vol\_manure\_other + n2o\_leach\_manure\_other

n2o\_manure\_pasture\_total = n2o\_manure\_pasture\_indirect + n2o\_manure\_pasture\_direct

n2o\_manure\_burned\_total = n2o\_manure\_burned\_indirect + n2o\_manure\_burned\_direct

n2o\_manure\_other\_total = n2o\_manure\_other\_indirect + n2o\_manure\_other\_direct

Value

A named list with:

n2o_manure_pasture_indirect

Numeric. Total indirect nitrous oxide (N2O) emissions from manure deposited on pasture. Includes emissions from atmospheric deposition of volatilised nitrogen (NH3 and NOx) and from leaching and runoff of manure nitrogen (kg N2O/head/day).

n2o_manure_burned_indirect

Numeric. Total indirect nitrous oxide (N2O) emissions originating from manure burned for fuel. Includes emissions from atmospheric deposition of volatilised nitrogen (NH3 and NOx) and from leaching and runoff of manure nitrogen (kg N2O/head/day).

n2o_manure_other_indirect

Numeric. Total indirect nitrous oxide (N2O) emissions originating from manure management systems, excluding manure deposited on pasture and manure burned for fuel. Includes emissions from atmospheric deposition of volatilised nitrogen (NH3 and NOx) and from leaching and runoff of manure nitrogen (kg N2O/head/day).

n2o_manure_pasture_total

Numeric. Total nitrous oxide (N2O) emissions from manure deposited on pasture. Includes direct emissions and indirect emissions from volatilisation, leaching, and runoff (kg N2O/head/day).

n2o_manure_burned_total

Numeric. Total nitrous oxide (N2O) emissions from manure burned for fuel. Includes direct emissions and indirect emissions from volatilisation, leaching, and runoff (kg N2O/head/day).

n2o_manure_other_total

Numeric. Total nitrous oxide (N2O) emissions from manure management systems, excluding manure deposited on pasture and manure burned for fuel. Includes direct emissions and indirect emissions from volatilisation, leaching, and runoff (kg N2O/head/day).

This function is part of the run_emissions_manure_module().

See Also

run_emissions_manure_module

Examples

calc_n2o_manure_total(
  n2o_manure_pasture_vol = 0.0129,
  n2o_manure_pasture_leach = 0.0012,
  n2o_manure_burned_vol = 0,
  n2o_manure_burned_leach = 0,
  n2o_manure_other_vol = 0.052,
  n2o_manure_other_leach = 0.00027,
  n2o_manure_pasture_direct = 0.009,
  n2o_manure_burned_direct = 0,
  n2o_manure_other_direct = 0.01033
)

Calculate indirect Nitrous Oxide (N2O) emissions from manure volatilization

Description

Calculates daily indirect nitrous oxide (N2O) emissions resulting from atmospheric deposition of volatilised nitrogen (NH3–N and NOx–N) from manure management systems and separates emissions from manure deposited on pasture, manure burned for fuel, and all other manure management systems.

Usage

calc_n2o_manure_volatilization(
  ratio_N2ON_to_N2O = 44/28,
  nitrogen_excretion,
  ...
)

Arguments

Details

This calculation follows the Tier 2 methodology for indirect N2O emissions from manure management as defined in the IPCC Guidelines in Equations 10.26 (IPCC, 2006, 2019), 10.27 (IPCC, 2006) and 10.28 (IPCC, 2019).

In the IPCC formulation, indirect emissions from atmospheric deposition of volatilised nitrogen are calculated as:

N2O_{G(mm)} = \frac{44}{28} \sum_{S} \left( N \times AWMS_S \times FracGas_{S} \times EF4 \right)

where:

N2O_G(mm)

Indirect N2O emissions due to volatilization of N from Manure Management.

44/28

Conversion factor from N2O-N to N2O.

N

Nitrogen excreted (kg N).

AWMS_S

Fraction of excreted nitrogen managed in manure management system S.

FracGas_{S}

Fraction of nitrogen volatilised as NH3–N and NOx–N in manure management system S.

EF4

Emission factor for indirect N2O emissions from atmospheric deposition (kg N2O-N per kg NH3–N + NOx–N).

In this implementation, calculations are performed at daily, per-head resolution using nitrogen_excretion (kg N/head/day):

\begin{aligned} N_2O &= nitrogen\_excretion \times ratio\_N2ON\_to\_N2O \times \\ & \sum_{S} \left( manure\_management\_system\_fraction \times nitrogen\_fracgas \times n2o\_ef4 \right) \end{aligned}

This function is part of the run_emissions_manure_module().

Value

A named list with the following elements:

n2o_manure_pasture_vol

Numeric. Indirect nitrous oxide (N2O) emissions resulting from atmospheric deposition of volatilised nitrogen (NH3 and NOx) from manure deposited on pasture (kg N2O/head/day).

n2o_manure_burned_vol

Numeric. Indirect nitrous oxide (N2O) emissions resulting from atmospheric deposition of volatilised nitrogen (NH3 and NOx) from manure burned for fuel (kg N2O/head/day).

n2o_manure_other_vol

Numeric. Indirect nitrous oxide (N2O) emissions resulting from atmospheric deposition of volatilised nitrogen (NH3 and NOx) from manure management systems, excluding manure deposited on pasture and manure burned for fuel (kg N2O/head/day).

n2o_manure_all_noburn_vol

Numeric. Indirect nitrous oxide (N2O) emissions resulting from atmospheric deposition of volatilised nitrogen (NH3 and NOx) from manure management systems, excluding losses from manure burned for fuel (kg N2O/head/day).

References

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management. Equation 10.26; 10.28.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management. Equation 10.26; 10.27.

See Also

run_emissions_manure_module

Examples

calc_n2o_manure_volatilization(
  ratio_N2ON_to_N2O = 44 / 28,
  nitrogen_excretion = 0.9,
  mms_burned = c(
    manure_management_system_fraction = 0.020,
    n2o_ef4 = 0.14,
    nitrogen_fracgas = 0
  ),
  mms_drylot = c(
    manure_management_system_fraction = 0.264,
    n2o_ef4 = 0.14,
    nitrogen_fracgas = 0.3
  ),
  mms_pasture = c(
    manure_management_system_fraction = 0.310,
    n2o_ef4 = 0.14,
    nitrogen_fracgas = 0.21
  ),
  mms_solid = c(
    manure_management_system_fraction = 0.406,
    n2o_ef4 = 0.14,
    nitrogen_fracgas = 0.45
  )
)

Calculate a ration component's contribution to nitrous oxide (N2O) emissions from crop residues decomposition

Description

Calculates the contribution of an individual feed component to nitrous oxide (N2O) emissions from crop residues decomposition in feed production, using feed-specific emission factors weighted by the component's share in the ration.

Usage

calc_n2o_ration_crop_residues(feed_ration_fraction, n2o_feed_crop_residues)

Arguments

Details

The contribution is computed as:

diet\_n2o\_feed\_crop\_residues = feed\_ration\_fraction \times n2o\_feed\_crop\_residues

This function is part of the run_emissions_ration_module().

Value

Numeric. Contribution of an individual feed component to the diet-level average nitrous oxide (N2O) emission factor from crop residues decomposition in feed production (g N2O/kg DM).

See Also

run_emissions_ration_module

Calculate a ration component's contribution to nitrous oxide (N2O) emissions from fertilizer use

Description

Calculates the contribution of an individual feed component to nitrous oxide (N2O) emissions from synthetic fertilizer in feed production, using feed-specific emission factors weighted by the component's share in the ration.

Usage

calc_n2o_ration_fertilizer(feed_ration_fraction, n2o_feed_fertilizer)

Arguments

Details

The contribution is computed as:

diet\_n2o\_feed\_fertilizer = feed\_ration\_fraction \times n2o\_feed\_fertilizer

This function is part of the run_emissions_ration_module().

Value

Numeric. Contribution of an individual feed component to the diet-level average nitrous oxide (N2O) emission factor from fertilizer use in feed production (g N2O/kg DM).

See Also

run_emissions_ration_module

Calculate a ration component's contribution to nitrous oxide (N2O) emissions from manure application and deposition

Description

Calculates the contribution of an individual feed component to nitrous oxide (N2O) emissions from manure application to or deposition on soil in feed production, using feed-specific emission factors weighted by the component's share in the ration.

Usage

calc_n2o_ration_manure(feed_ration_fraction, n2o_feed_manure_applied)

Arguments

Details

The contribution is computed as:

diet\_n2o\_feed\_manure\_applied = feed\_ration\_fraction \times n2o\_feed\_manure\_applied

This function is part of the run_emissions_ration_module().

Value

Numeric. Contribution of an individual feed component to the diet-level average nitrous oxide (N2O) emission factor from manure applied to or deposited on soil in feed production (g N2O/kg DM).

See Also

run_emissions_ration_module

Calculate daily nitrogen excretion

Description

Calculates daily nitrogen excretion per animal (kg N/head/day) as the difference between nitrogen intake and nitrogen retention.

Usage

calc_nitrogen_excretion(species_short, nitrogen_intake, nitrogen_retention)

Arguments

Details

Nitrogen excretion represents the fraction of consumed nitrogen that is not retained in animal tissues or products and is therefore excreted in urine and dung.

Nitrogen excretion is calculated as:

nitrogen\_excretion = nitrogen\_intake - nitrogen\_retention

where all quantities are expressed in kg N/head/day.

This quantity forms the basis for subsequent calculations of nitrous oxide (N2O) emissions from manure management under the IPCC Tier 2 methodology.

Value

Numeric. Daily nitrogen excretion (kg N/head/day).

References

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management. Equation 10.31A.

This function is part of the run_nitrogen_balance_module().

See Also

run_nitrogen_balance_module, calc_nitrogen_retention

Calculate daily nitrogen intake

Description

Calculates the daily nitrogen intake per head (kg N/head/day) as the product of feed dry matter intake (DMI) and diet nitrogen content.

Usage

calc_nitrogen_intake(ration_intake, ration_nitrogen)

Arguments

Details

This approach follows the IPCC Tier 2 approach and estimates ration_intake as follows:

nitrogen\_intake = dry\_matter\_intake \times diet\_nitrogen

This function is part of the run_nitrogen_balance_module().

Value

Numeric. Daily nitrogen intake (kg N/head/day).

References

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management. Equation 10.32.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management. Equation 10.32.

See Also

run_nitrogen_balance_module, calc_ration_intake, run_metabolic_energy_req_module, calc_ration_nitrogen_content, run_ration_quality_module

Calculate daily nitrogen retention

Description

Calculates daily nitrogen retention per animal by species and cohort (kg N/head/day). Nitrogen retention represents the portion of consumed nitrogen that is incorporated into animal products or body tissues.

Usage

calc_nitrogen_retention(
  species_short,
  cohort_short,
  milk_protein_fraction = NA_real_,
  milk_yield_day = NA_real_,
  daily_weight_gain = NA_real_,
  fibre_yield_year = NA_real_,
  litter_size = NA_real_,
  parturition_rate = NA_real_,
  live_weight_at_weaning = NA_real_,
  live_weight_at_birth = NA_real_,
  pregnancy_duration = NA_real_,
  cohort_duration_days = NA_real_
)

Arguments

Details

Species-specific nitrogen retention calculations are applied.

For CTL, BFL, SHP, GTS, and CML:

Nitrogen retained in products and tissues is computed consistent with the process described in the Technical paper from MPI (Ministry for Primary Industries (MPI), 2025), where nitrogen retention is calculated as the sum of:

• nitrogen secreted in milk,

• nitrogen retained in live weight gain (tissue),

• nitrogen retained in fibre (for fibre-producing species).

Coefficients for nitrogen content of deposited tissue, fibre, and milk are derived from Chapter 5 (Nitrogen Excretion) of the MPI Technical paper.

The following constants are used:

• Tissue nitrogen content (tissue_n)

  • CTL and BFL: 0.0326 kg N/kg live weight

  • SHP, GTS and CML: 0.026 kg N/kg live weight

• Fibre nitrogen content (fibre_n)

  • SHP, GTS and CML: 0.134 kg N/kg fibre

• Milk nitrogen content (milk_n):

  • CTL, BFL, SHP, GTS and CML: derived from milk_protein_fraction using a protein-to-nitrogen conversion factor of 6.25 kg protein/kg nitrogen

For PGS

Nitrogen retention is calculated following the IPCC (2019) Tier 2 equations for swine (Equations 10.33A and 10.33B).

Nitrogen retention includes nitrogen retained in:

• live weight gain (tissue),

• reproductive outputs (conceptus and weaned offspring).

In this implementation:

• Nitrogen content of live weight gain is assumed to be 0.025 kg N/kg live weight.

• Protein digestibility fraction is assumed to be 0.98 (dimensionless).

• For breeding cohorts, the reproductive component is represented by annual nitrogen retention in conceptus and weaned offspring, expressed as a daily average by distributing the annual value uniformly over the year (365 days).

• A constant factor of 0.806 (dimensionless) is applied to piglets' live weight gain to correct for their higher nitrogen content per unit of live weight gain, following IPCC (2019).

This function is part of the run_nitrogen_balance_module().

Value

Numeric. Daily nitrogen retention in animal body tissues and products (e.g., growth, pregnancy, milk...) (kg N/head/day)

References

Ministry for Primary Industries (MPI). (2025). Detailed methodologies for agricultural greenhouse gas emission calculation: Methodology for calculation of New Zealand’s agricultural greenhouse gas emissions (Version 11). MPI Technical Paper, Wellington, New Zealand. Chapter 5.

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management. Equation 10.33A, 10.33B.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management. Equation 10.33.

See Also

run_nitrogen_balance_module

Calculate one year of steady-state population dynamics

Description

Calculates one year of population dynamics under steady-state assumptions using demographic parameters and returns population size statistics and offtake results. The steady state is defined as a constant sex–age cohort structure over time, with population size potentially growing or declining at a constant rate.

Usage

calc_projected_population_size(
  herd_size_total,
  fecundity_female,
  fecundity_male,
  probability_death,
  probability_offtake,
  probability_growth,
  growth_rate_herd,
  herd_structure,
  cohort_share
)

Arguments

Value

A named list with:

cohort_stock_start

Numeric vector of length 6. Population size in each of the 6 sex–age cohorts at the start of the year (# heads). (cohorts= FJ, FS, FA, MJ, MS, MA)

cohort_stock_end_projected

Numeric vector of length 6. Population size in each of the 6 sex–age cohorts at the end of the year, projected using the steady-state growth rate (# heads). (cohorts= FJ, FS, FA, MJ, MS, MA)

cohort_stock_end_exact_simulated

Numeric vector of length 10. Population size in each of 10 sex–age cohort at the end of the year, based on a demographic daily simulation over 365 days (# heads) (cohorts= FB: Female Birth, FJ: Female Juvenile, FS: Female Sub-adult, FA: Female Adult, FC: Female Culling, MB: Male Birth, MJ: Male Juvenile, MS: Male Sub-adult, MA: Male Adult, MC: Male Culling)

cohort_stock_average

Numeric vector of length 6. Average population size in each of the 6 sex–age cohorts over the year (# heads). Estimated from cohort_stock_start and cohort_stock_end_projected (cohorts= FJ, FS, FA, MJ, MS, MA)

cohort_offtake_heads

Numeric vector of length 10. Total number of animals removed from the herd over the year, by 10 sex–age cohorts (heads/year) (cohorts= FB: Female Birth, FJ: Female Juvenile, FS: Female Sub-adult, FA: Female Adult, FC: Female Culling, MB: Male Birth, MJ: Male Juvenile, MS: Male Sub-adult, MA: Male Adult, MC: Male Culling)

This function is part of the run_demographic_herd_module().

See Also

run_demographic_herd_module()

Calculate diet ash contribution for a ration component

Description

Calculates the contribution of a single feed component to diet ash content by weighting feed ash content by its ration composition share.

Usage

calc_ration_ash(feed_ration_fraction, feed_ash)

Arguments

Details

The ash contribution is defined as:

ration\_ash = feed\_ration\_fraction \times feed\_ash / 100

Ash content is expressed as a percentage (g/100g DM); the result is a fraction.

This function is part of the run_ration_quality_module().

Value

Numeric. Contribution of the feed component to total diet ash content (kg ash/kg DM).

See Also

run_ration_quality_module

Calculate diet digestibility contribution for a ration component

Description

Applies species-specific digestibility parameters to a ration composition share to compute the contribution of a single feed component to total diet digestibility.

Usage

calc_ration_digestibility(
  species_short,
  feed_ration_fraction,
  feed_digestibility_fraction_ruminant = NA_real_,
  feed_digestibility_fraction_pigs = NA_real_
)

Arguments

Details

The digestibility contribution uses the animal-specific digestibility ratio:

• Ruminants (CTL, BFL, CML, SHP, GTS): feed_ration_fraction * feed_digestibility_fraction_ruminant

• Pigs (PGS): feed_ration_fraction * feed_digestibility_fraction_pigs

This function is part of the run_ration_quality_module().

Value

Numeric. Contribution of the feed component to total diet digestibility (fraction).

See Also

run_ration_quality_module

Calculate diet gross energy contribution for a ration component

Description

Computes the contribution of a single feed component to diet gross energy content by weighting feed gross energy by its ration composition share.

Usage

calc_ration_gross_energy(feed_ration_fraction, feed_gross_energy)

Arguments

Details

The gross energy contribution is defined as:

diet\_gross\_energy = feed\_ration\_fraction \times feed\_gross\_energy

This function is part of the run_ration_quality_module().

Value

Numeric. Contribution of the feed component to total diet gross energy content (MJ/kg DM).

See Also

run_ration_quality_module

Calculate daily ration intake in dry matter

Description

Calculates daily feed intake as dry matter intake (DMI) per animal (kg DM/head/day) from the animal's daily energy requirement and the diet energy density.

Usage

calc_ration_intake(
  species_short,
  metabolic_energy_req_total,
  ration_gross_energy,
  ration_metabolizable_energy
)

Arguments

Details

This function follows the IPCC Tier 2 framework. DMI is computed by dividing the appropriate daily energy requirement by the corresponding diet energy content (MJ/kg DM).

• Energy expressed as gross energy intake requirement - CTL, BFL, SHP, GTS:

  ration\_intake = \frac{metabolic\_energy\_req\_total}{ration\_gross\_energy}

• Energy expressed as metabolizable energy requirement - CML, PGS:

  ration\_intake = \frac{metabolic\_energy\_req\_total}{ration\_metabolizable\_energy}

This function is part of the run_metabolic_energy_req_module().

Value

Numeric. Average daily dry matter intake of feed (kg DM/head/day).

References

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Volume 4 (AFOLU), Chapter 10: Emissions from Livestock and Manure Management.

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Volume 4 (AFOLU), Chapter 10: Emissions from Livestock and Manure Management.

See Also

run_metabolic_energy_req_module, calc_total_metabolic_energy_req calc_ration_gross_energy calc_ration_metabolizable_energy

Calculate diet metabolizable energy contribution for a ration component

Description

Applies species-specific metabolizable energy parameters to a ration composition share to compute the contribution of a single feed component to total diet metabolizable energy content.

Usage

calc_ration_metabolizable_energy(
  species_short,
  feed_ration_fraction,
  feed_metabolizable_energy_ruminant = NA_real_,
  feed_metabolizable_energy_pigs = NA_real_
)

Arguments

Details

The metabolizable energy contribution uses the animal-specific parameter:

• Ruminants (CTL, BFL, CML, SHP, GTS): feed_ration_fraction * feed_metabolizable_energy_ruminant

• Pigs (PGS): feed_ration_fraction * feed_metabolizable_energy_pigs

This function is part of the run_ration_quality_module().

Value

Numeric. Contribution of the feed component to total diet metabolizable energy content (MJ/kg DM).

See Also

run_ration_quality_module

Calculate diet nitrogen contribution for a ration component

Description

Calculates the contribution of a single feed component to diet nitrogen content by weighting feed nitrogen content by its ration composition share.

Usage

calc_ration_nitrogen_content(feed_ration_fraction, feed_nitrogen_content)

Arguments

Details

The nitrogen contribution is defined as:

diet\_nitrogen = feed\_ration\_fraction \times feed\_nitrogen\_content

Value

Numeric. Contribution of the feed component to total diet nitrogen content (kg N/kg DM).

Calculate urinary energy fraction contribution for a ration component

Description

Applies species-specific urinary energy fractions to a ration composition share to compute the contribution of a feed component to urinary energy losses.

Usage

calc_ration_urinary_energy_fraction(
  species_short,
  feed_ration_fraction,
  feed_urinary_energy_ruminant = NA_real_,
  feed_urinary_energy_pigs = NA_real_
)

Arguments

Details

The urinary energy fraction contribution uses the animal-specific parameter:

• Ruminants (CTL, BFL, CML, SHP, GTS): feed_ration_fraction * feed_urinary_energy_ruminant

• Pigs (PGS): feed_ration_fraction * feed_urinary_energy_pigs

This function is part of the run_ration_quality_module().

Value

Numeric. Contribution of the feed component to the fraction of total diet gross energy that is excreted in urine (fraction).

See Also

run_ration_quality_module

Calculate the ratio of net energy available for growth in the diet (REG – Net Energy for Growth / Digestible Energy)

Description

Calculates the ratio of net energy available for growth to digestible energy consumed (fraction), which represents the efficiency with which digestible energy in the diet is converted into net energy retained as body tissue.

Usage

calc_reg_growth(species_short, ration_digestibility_fraction = NA_real_)

Arguments

Details

This component follows the IPCC Tier 2 partitioning approach and returns REG for ruminants (CTL, BFL, SHP, GTS) as:

net\_energy\_growth\_digestible\_energy\_ratio = 1.164 - 0.005160 \times diet\_digestibility\_fraction \times 100 + 0.00001308 \times (diet\_digestibility\_fraction \times 100)^2 - \frac{37.4}{diet\_digestibility\_fraction \times 100}

For Other species REG is not applicable and the function returns NA_real_.

This function is part of the run_metabolic_energy_req_module().

Value

Numeric. Ratio of net energy available for growth in the diet to digestible energy consumed (fraction).

References

Gibbs M.J., Johnson D.E. (1993) Livestock Emissions. In: International Methane Emissions. Washington, D.C., U.S.A: US Environmental Protection Agency, Climate Change Division.

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management, Equation 10.15.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management, Equation 10.15.

See Also

run_metabolic_energy_req_module, calc_ration_digestibility calc_total_metabolic_energy_req calc_ration_intake

Calculate ratio of net energy available for maintenance in the diet (REM - Net Energy for Maintenance / Digestible Energy)

Description

Calculates the ratio of net energy available in the diet for maintenance to digestible energy.

Usage

calc_rem_maintenance(species_short, ration_digestibility_fraction = NA_real_)

Arguments

Details

This component follows the IPCC Tier 2 partitioning approach and it returns the value for ruminants (CTL, BFL, SHP, GTS) calculated as follows:

net\_energy\_maintenance\_digestible\_energy\_ratio = 1.123 - 0.004092 \times (diet\_digestibility\_fraction \times 100) + 0.00001126 \times (diet\_digestibility\_fraction \times 100)^2 - \frac{25.4}{diet\_digestibility\_fraction \times 100}

For the Other species REM is not applicable and the function returns NA_real_.

This function is part of the run_metabolic_energy_req_module().

Value

Numeric. Ratio of net energy available for maintenance in the diet to digestible energy consumed (fraction).

References

Gibbs M.J., Johnson D.E. (1993) Livestock Emissions. In: International Methane Emissions. Washington, D.C., U.S.A: US Environmental Protection Agency, Climate Change Division.

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management, Equation 10.14.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management, Equation 10.14.

See Also

run_metabolic_energy_req_module, calc_ration_digestibility calc_total_metabolic_energy_req calc_ration_intake

Calculate steady-state population structure

Description

Calculates population dynamics over time until a steady state is reached. The steady state is defined as a constant sex–age cohort structure over time, with population size potentially growing or declining at a constant rate. Tracks sex–age cohort structure and population growth based on survival, offtake, and fecundity parameters.

Usage

calc_steady_state_structure(
  initial_herd_structure,
  max_simulation_years,
  min_lambda_change,
  fecundity_female,
  fecundity_male,
  probability_death,
  probability_offtake,
  probability_growth
)

Arguments

Value

A named list with:

days_to_steady_state

Numeric. Number of days required for the herd population structure to converge to a steady state, defined as the point at which successive iterations produce negligible changes in cohort proportions (days)

herd_structure

Named numeric vector of length 8. Final steady-state share of each of 8 sex-age cohorts (FB, FJ, FS, FA, MB, MJ, MS, MA) (fraction). Shares should sum to 1.

cohort_share

Named numeric vector of length 6. Final steady-state share of 6 grouped sex-age cohorts (FJ, FS, FA, MJ, MS, MA, where FJ = FB + FJ and MJ = MB + MJ) (fraction). Shares should sum to 1.

growth_rate_herd

Numeric. Annualized growth rate at which the herd reaches steady state (fraction)

This function is part of the run_demographic_herd_module().

See Also

run_demographic_herd_module()

Summarise offtake and stock Variation for a steady-state year

Description

Calculates annual offtake quantities and rates, as well as stock variation and their combined values across 6 sex-age classes based on steady-state population projections. The steady state is defined as a constant sex–age cohort structure over time, with population size potentially growing or declining at a constant rate.

Usage

calc_summary_offtake(
  cohort_stock_start,
  cohort_stock_end_projected,
  cohort_stock_average,
  cohort_offtake_heads,
  simulation_duration
)

Arguments

Value

A named list with:

stock_variation_heads

Numeric vector of length 6. Change in population size between the start and end of the year for each sex–age cohort (# heads) (cohorts= FJ, FS, FA, MJ, MS, MA).

offtake_heads

Numeric vector of length 6. Total number of animals removed via offtake over the year, aggregated to 6 sex–age cohorts (heads/year) (cohorts= FJ, FS, FA, MJ, MS, MA)

offtake_heads_assessment

Numeric vector of length 6. Total number of animals removed via offtake over the assessment period, aggregated to 6 sex–age cohorts (heads/assessment period) (cohorts= FJ, FS, FA, MJ, MS, MA)

offtake_rate_to_stock_start

Numeric vector of length 6. Offtake rate relative to the starting population size in each sex–age cohort (fraction) (cohorts= FJ, FS, FA, MJ, MS, MA)

offtake_rate_to_stock_average

Numeric vector of length 6. Offtake rate relative to the average population size in each sex–age cohort (fraction) (cohorts= FJ, FS, FA, MJ, MS, MA)

offtake_stock_variation_heads

Numeric vector of length 6. Sum of offtake and stock variation for each sex–age cohort over the year (# heads) (cohorts= FJ, FS, FA, MJ, MS, MA)

offtake_stock_plus_variation_rate_to_stock_start

Numeric vector of length 6. Offtake plus stock-variation rate relative to starting population size (fraction) (cohorts= FJ, FS, FA, MJ, MS, MA)

offtake_stock_plus_variation_rate_to_stock_average

Numeric vector of length 6. Offtake plus stock-variation rate relative to average population size (fraction) (cohorts= FJ, FS, FA, MJ, MS, MA)

This function is part of the run_demographic_herd_module().

See Also

run_demographic_herd_module()

Calculate total metabolic energy requirements

Description

Calculates the total daily energy requirement (MJ/head/day) by summing relevant energy partitions (maintenance, activity, lactation, work, pregnancy, growth, fibre, egg deposition).

Usage

calc_total_metabolic_energy_req(
  species_short,
  metabolic_energy_req_maintenance,
  metabolic_energy_req_activity,
  metabolic_energy_req_lactation,
  metabolic_energy_req_work,
  metabolic_energy_req_pregnancy,
  net_energy_maintenance_digestible_energy_ratio,
  metabolic_energy_req_growth,
  metabolic_energy_req_fibre_production,
  metabolic_energy_req_egg_deposition,
  net_energy_growth_digestible_energy_ratio,
  ration_digestibility_fraction
)

Arguments

Details

This component follows the IPCC Tier 2 partitioning approach and the calculation is computed differently depending on whether species energy requirements are expressed as net or metabolizable energy.

Species-specific approach:

• Energy requirements expressed as net energy (CTL, BFL, SHP, GTS)

  • CTL and BFL:

    metabolic\_energy\_req\_total = \frac{ \left( \frac{ metabolic\_energy\_req\_maintenance + metabolic\_energy\_req\_activity + metabolic\_energy\_req\_lactation + metabolic\_energy\_req\_work + metabolic\_energy\_req\_pregnancy }{REM} \right) + \left( \frac{metabolic\_energy\_req\_growth}{REG} \right) }{diet\_digestibility\_fraction}

  • SHP and GTS:

    metabolic\_energy\_req\_total = \frac{ \left( \frac{ metabolic\_energy\_req\_maintenance + metabolic\_energy\_req\_activity + metabolic\_energy\_req\_lactation + metabolic\_energy\_req\_pregnancy }{REM} \right) + \left( \frac{ metabolic\_energy\_req\_growth + metabolic\_energy\_req\_fibre }{REG} \right) }{diet_digestibility_fraction}

• Energy requirements expressed as metabolizable energy (CML, PGS)

  For these species, the total daily requirement is computed as the direct sum of relevant energy components (MJ/head/day).

  • CML:

    metabolic\_energy\_req\_total = metabolic\_energy\_req\_maintenance + metabolic\_energy\_req\_activity + metabolic\_energy\_req\_lactation + metabolic\_energy\_req\_work + metabolic\_energy\_req\_fibre\_production + metabolic\_energy\_req\_pregnancy + metabolic\_energy\_req\_growth

  • PGS:

    metabolic\_energy\_req\_total = metabolic\_energy\_req\_maintenance + metabolic\_energy\_req\_activity + metabolic\_energy\_req\_lactation + metabolic\_energy\_req\_pregnancy + metabolic\_energy\_req\_growth

This function is part of the run_metabolic_energy_req_module().

Value

Numeric. Total daily energy requirement (MJ/head/day). For CTL, BFL, SHP and GTS this is expressed as gross energy intake requirement (GE). For CML and PGS the function returns the summed daily metabolizable energy requirement.

References

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management, Equation 10.16.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management, Equation 10.16.

See Also

run_metabolic_energy_req_module, calc_metabolic_energy_req_maintenance calc_metabolic_energy_req_activity calc_metabolic_energy_req_growth calc_metabolic_energy_req_lactation calc_metabolic_energy_req_work calc_metabolic_energy_req_fibre calc_metabolic_energy_req_pregnancy calc_rem_maintenance calc_reg_growth calc_ration_intake

Calculate transition probabilities for sex-age classes

Description

Calculates hazard rates and daily transition probabilities (death, offtake, survival, and growth) across different sex-age cohorts. Converts annual inputs to daily hazards, then derives daily probabilities from those hazards.

Usage

calc_transition_probabilities(cohort_duration_days, offtake_rate, death_rate)

Arguments

Value

A named list with:

hazard_death

Numeric vector of length 6. Instantaneous mortality hazard rate for the 6 sex–age cohorts. Represents the risk of death per unit time (day) (cohorts= FJ, FS, FA, MJ, MS, MA)

hazard_offtake

Numeric vector of length 6. Instantaneous offtake hazard rate for the 6 sex-age cohorts. Represents the risk to leave the herd through planned removals per unit of time (day-1) (cohorts= FJ, FS, FA, MJ, MS, MA)

probability_death

Named numeric vector of length 10. Probability of animal dying within the model time interval for 10 cohorts (fraction). (cohorts= FB: Female Birth, FJ: Female Juvenile, FS: Female Sub-adult, FA: Female Adult, FC: Female Culling, MB: Male Birth, MJ: Male Juvenile, MS: Male Sub-adult, MA: Male Adult, MC: Male Culling)

probability_offtake

Named numeric vector of length 10. Probability that an animal will be removed from the herd within the model time interval for 10 cohorts (fraction). (cohorts= FB: Female Birth, FJ: Female Juvenile, FS: Female Sub-adult, FA: Female Adult, FC: Female Culling, MB: Male Birth, MJ: Male Juvenile, MS: Male Sub-adult, MA: Male Adult, MC: Male Culling)

probability_survival

Named numeric vector of length 10. Probability that an animal remains alive in the herd within the model time interval for 10 cohorts (fraction). (cohorts= FB: Female Birth, FJ: Female Juvenile, FS: Female Sub-adult, FA: Female Adult, FC: Female Culling, MB: Male Birth, MJ: Male Juvenile, MS: Male Sub-adult, MA: Male Adult, MC: Male Culling)

probability_growth

Named numeric vector of length 10. Probability of growing into the next age class for 10 cohorts (fraction) (cohorts= FB: Female Birth, FJ: Female Juvenile, FS: Female Sub-adult, FA: Female Adult, FC: Female Culling, MB: Male Birth, MJ: Male Juvenile, MS: Male Sub-adult, MA: Male Adult, MC: Male Culling)

This function is part of the run_demographic_herd_module().

See Also

run_demographic_herd_module()

Calculate Volatile Solids (VS)

Description

Calculates daily volatile solids (VS) excretion in manure (kg VS/head/day). VS represent the organic fraction of manure dry matter, including both biodegradable and non-biodegradable organic material. VS is a key intermediate variable required for estimating methane (CH4) emissions from manure management systems under IPCC methodologies.

Usage

calc_volatile_solids(
  ration_intake,
  ration_digestibility_fraction,
  ration_urinary_energy_fraction,
  ration_ash
)

Arguments

Details

The IPCC recommends estimating volatile solids (VS) excretion from feed intake and digestibility when country-specific average daily VS excretion rates are not available. The core relationship is provided in IPCC Equation 10.24 (Volatile solids excretion rates), which estimates daily VS excretion as a function of:

• Gross energy intake (gross_energy_intake, MJ/day)

• Digestibility of the diet (ration_digestibility_fraction)

• Urinary energy expressed as a fraction of GE (ration_urinary_energy_fraction)

• Ash content of the diet (ration_ash, fraction of dry matter)

• A conversion factor representing the average gross energy content of dry matter (18.45 MJ/kg DM)

The general structure of Eq. 10.24 partitions gross energy intake into digestible energy, urinary losses, and ash, and converts the remaining organic matter into volatile solids using the energy density of dry matter.

Implementation note. This function applies an algebraically simplified formulation from Equation 10.24 of IPCC.

In this implementation, the function takes ration_intake directly as an input. It can be calculated upstream with calc_ration_intake as a function of energy requirements and the energy content of the diet.

dry\_matter\_intake = \frac{gross\_energy\_intake}{diet\_gross\_energy}

This reflects the use of ration-specific energy content upstream and avoids assuming a fixed gross energy density of 18.45 MJ/kg DM, as in the IPCC default approach.

The volatile solids excretion is then calculated as:

volatile\_solids = dry\_matter\_intake \times (1 - diet\_digestibility\_fraction + urinary\_energy\_fraction) \times (1 - diet\_ash)

The resulting calculations are algebraically equivalent to the IPCC approach and fully consistent with Equation 10.24.

This function is part of the run_emissions_manure_module().

Value

Numeric. Total volatile solids (VS) excreted per animal per day, representing the organic material in livestock manure and consisting of both biodegradable and non-biodegradable fractions (kg VS/head/day).

References

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management. Equation 10.24.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management. Equation 10.24.

See Also

run_emissions_manure_module

Examples

calc_volatile_solids <- calc_volatile_solids(
  ration_intake = 5,
  ration_digestibility_fraction = 0.6,
  ration_urinary_energy_fraction = 0.04,
  ration_ash = 0.08
)

Calculate work energy requirements (for biophysical allocation)

Description

Calculates the energy required for animal work over the assessment period (MJ/cohort/assessment period), based on the daily energy requirement for work, cohort size, and assessment duration.

Usage

calc_work_allocation_energy(
  species_short,
  cohort_stock_size,
  metabolic_energy_req_work,
  simulation_duration,
  ratio_me_to_ne = NA_real_
)

Arguments

Details

This function provides the work-related energy term used in a biophysical allocation framework to apportion emissions between milk and other co-products in multifunctional livestock production systems.

The approach implements the IDF (2022) standard, adapted from Thoma and Nemecek (2020), and is consistent with FAO LEAP livestock LCA guidelines (FAO, 2016a, 2016b, 2016c) and with ISO 14044:2006 (Section 4.3.4.2, Step 2).

In accordance with ISO 14044:2006 (Section 4.3.4.2, Step 2), known processing or biophysical relationships may be used to assign shared inputs and outputs of a single production unit to individual products or sub-units. In livestock systems, this includes apportioning shared feed and energy use according to physiological energy requirements (e.g., net energy for lactation, growth, etc.). If the resulting process remains multifunctional, these energy terms may subsequently be used to derive allocation factors among co-products.

Total work-related energy is computed for species (CTL, BFL, CML) and cohorts (, FA, MA) assumed to be potentially involved in draught power generation.

The work_allocation_energy is calculated as follows:

energy\_allocation\_work = energy\_requirement\_work \times simulation\_duration \times cohort\_stock\_size

for cattle (CTL) and buffalo (BFL), and:

energy\_allocation\_work = \frac{energy\_requirement\_work \times simulation\_duration \times cohort\_stock\_size} {ratio\_me\_to\_ne}

for camels (CML).

where metabolic_energy_req_work can be computed using calc_metabolic_energy_req_work (see also run_metabolic_energy_req_module).

This function is part of the run_allocation_module().

Value

Numeric. Energy required to provide all draught power (traction/work) by cohort (MJ/cohort/assessment period). Non-zero values are expected only for draught or work-producing species (CTL, BFL CML).

References

ISO. (2006). Environmental management — Life cycle assessment — Requirements and guidelines (ISO 14044:2006). International Organization for Standardization, Geneva.

IDF. (2022). The IDF Global Carbon Footprint Standard for the Dairy Sector. Bulletin of the IDF No. 520/2022. International Dairy Federation, Brussels.

Thoma, G., and Nemecek, T. (2020). Allocation between milk and meat in dairy LCA: Critical discussion of the IDF’s standard methodology. In Proceedings of the 12th International Conference on Life Cycle Assessment of Food (LCAFood 2020) (pp. 83–89), 13–16 October, Berlin, Germany.

FAO. (2016a). Environmental performance of large ruminant supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

FAO. (2016b). Greenhouse gas emissions and fossil energy use from small ruminant supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

FAO. (2016c). Greenhouse gas emissions and fossil energy use from poultry supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

See Also

run_allocation_module, calc_metabolic_energy_req_work, run_metabolic_energy_req_module

Valid cohort short codes

Description

All sex- and age-class cohort codes recognised by GLEAM. Derived from gleam_cohorts_names.

Usage

gleam_cohorts

Format

A character vector of length 6.

Female cohort codes (complement of male in gleam_cohorts)

Description

Female cohort codes (complement of male in gleam_cohorts)

Usage

gleam_cohorts_female

Format

A character vector of length 3.

Male cohort codes (M-prefix)

Description

Male cohort codes (M-prefix)

Usage

gleam_cohorts_male

Format

A character vector of length 3.

Cohort code -> full name mapping

Description

Maps each cohort short code to its descriptive name (sex and age class). gleam_cohorts is derived from this as the vector of codes.

Usage

gleam_cohorts_names

Format

A named character vector of length 6.

Emissions variable metadata

Description

All direct and indirect emission sources handled by the allocation and aggregation modules. Each element contains emissions_source (the column name in cohort-level data) and label (the string used in the aggregated long-form output).

Usage

gleam_emissions_meta

Format

An object of class list of length 19.

Details

The emissions_source values from this list are the canonical set passed to assign_allocation_shares() in the allocation module and used to pivot the aggregation output. Adding or renaming an emission source here automatically updates both modules.

Feed-related emission sources

Description

Emission variables expressed per kg dry matter intake (g/kg DM). Passed to calc_cohort_totals() to apply ration_intake scaling. All other emissions use cohort_stock_size * simulation_duration only.

Usage

gleam_feed_emissions_meta

Format

A list of lists with emissions_source and label.

Feed intake variable metadata

Description

One entry: dry-matter intake from the ration quality module.

Usage

gleam_feed_meta

Format

An object of class list of length 1.

Details

Each element contains:

feed_source

Column name in cohort-level data.

label

Human-readable label used in aggregated output.

unit

Physical unit of the variable.

Nitrogen balance variable metadata

Description

Intake, retention, and excretion from the nitrogen balance module.

Usage

gleam_nitrogen_balance_meta

Format

An object of class list of length 3.

Details

Each element contains nitrogen_balance_source, label, unit.

Emission sources excluded from commodity allocation

Description

These pasture and burn emission sources are not allocated to individual commodities (they remain as herd-level totals). Referenced by both run_allocation_module and any downstream reporting logic.

Usage

gleam_non_allocated_emissions

Format

An object of class character of length 6.

Production variable metadata

Description

Milk, meat, and fibre production outputs from the production module.

Usage

gleam_production_meta

Format

An object of class list of length 8.

Details

Each element contains production_source, label, unit, commodity_name, and commodity_type.

Valid species short codes

Description

All livestock species supported by GLEAM. Derived from gleam_species_names.

Usage

gleam_species

Format

A character vector of length 6.

Milk-producing species

Description

Species for which milk production, lactation energy requirements, and ruminant-style digestibility parameters apply. Includes ruminants plus Camels.

Usage

gleam_species_milk_producers

Format

A character vector of length 5.

Species code -> full name mapping

Description

Maps each species short code to its full common name. Used for display and documentation. gleam_species is derived from this as the vector of codes.

Usage

gleam_species_names

Format

A named character vector of length 6.

Species with non-zero enteric CH4 and N excretion

Description

All supported species. Used for enteric methane emission calculations and nitrogen excretion models. (Legacy alias; equivalent to gleam_species.)

Usage

gleam_species_non_poultry

Format

A character vector of length 6.

Ruminant species (four-stomach, NE-based energy system)

Description

Cattle, Buffalo, Sheep, Goats. Energy requirements are expressed as net energy (NE) and converted to gross energy (GE) via digestibility ratios. Camels use metabolizable energy (ME) instead.

Usage

gleam_species_ruminants

Format

A character vector of length 4.

Run Aggregation Module Pipeline

Description

This function generates final herd-level results by aggregating key cohort-level outputs, scaling variables over the assessment duration, allocating emissions to commodities, and converting methane (CH4) and nitrous oxide (N2O) emissions to CO2-equivalents (CO2eq) using selected 100-year Global Warming Potential (GWP-100) factors.

Usage

run_aggregation_module(
  cohort_level_data,
  allocation_herd_long,
  simulation_duration = 365,
  global_warming_potential_set = "AR6",
  show_indicator = TRUE
)

Arguments

Details

This function represents the final step of the Global Livestock Environmental Assessment Model (GLEAM) computational pipeline run_gleam() and performs the following calculation sequence:

1. Cohort-level variables are reshaped from wide to long format.

2. Variables are classified into "Feed", "NitrogenBalance", "Production", and "Emissions".

3. Cohort totals are calculated using calc_cohort_totals(). Production variables are retained as provided, whereas emissions, feed, and nitrogen balance variables are scaled using cohort stock size and simulation duration.

4. Cohort totals are aggregated to herd level within each herd_id x species_short x variable_type x variable_name group.

5. Herd-level emissions are merged with commodity allocation shares from allocation_herd_long.

6. Emissions are allocated to commodities using calc_allocated_emissions().

7. Gas type is identified from the emission variable name as "CH4", "N2O", or "CO2".

8. Allocated CH4, N2O, and CO2 emissions are converted to CO2-equivalents (CO2eq) using calc_co2eq() and the selected GWP-100 option.

9. Final output tables are produced summarizing herd-level results for emissions, feed, production, and nitrogen balance variables.

Value

A named list with the following elements:

results_emissions

A data.table containing herd-level emissions scaled to the assessment duration and allocated to commodities. Includes gas type, allocation shares, commodity metadata, GWP factors, and emissions expressed both as allocated gas mass (kg gas) and as CO2-equivalents (kg CO2eq).

results_feed

A data.table containing herd-level feed variables, aggregated at herd level and scaled to the assessment duration.

results_production

A data.table containing herd-level production variables aggregated from cohort-level values over the assessment duration.

results_nitrogen

A data.table containing herd-level nitrogen balance variables aggregated from cohort-level values and scaled to the assessment duration.

See Also

run_gleam(), calc_cohort_totals(), calc_cohort_to_herd_aggregation(), calc_allocated_emissions(), calc_co2eq(), run_allocation_module()

Examples

# Load cohort-level aggregation input
aggregation_chrt_dt <- data.table::fread(system.file(
  "extdata/run_modules_examples/aggregation_input_chrt_data.csv",
  package = "gleam"
))

# Load allocation shares (herd-level, long format)
allocation_long <- data.table::fread(system.file(
  "extdata/run_modules_examples/aggregation_allocation_input_data.csv",
  package = "gleam"
))

# Run aggregation
results <- run_aggregation_module(
  cohort_level_data = aggregation_chrt_dt,
  allocation_herd_long = allocation_long,
  simulation_duration = 365,
  global_warming_potential_set = "AR6"
)

Run Allocation Module Pipeline

Description

Calculates biophysical allocation shares for livestock commodities by computing cohort-level energy requirements for meat, milk, fibre, work, and eggs, aggregating these terms to herd level, and assigning allocation shares to emission sources.

Usage

run_allocation_module(
  cohort_level_data,
  herd_level_data,
  simulation_duration = 365,
  show_indicator = TRUE
)

Arguments

Details

This function implements the allocation pipeline used to derive biophysical allocation shares for livestock commodities in multifunctional production systems.

The approach follows the IDF standard for the dairy sector, adapted for livestock systems in which emissions are apportioned among multiple products according to their physiological energy requirements. In accordance with ISO 14044:2006, known biophysical relationships may be used to assign shared inputs and outputs of a production system to individual products or sub-units.

This function represents the intermediate allocation module of the Global Livestock Environmental Assessment Model (GLEAM) computational pipeline run_gleam() and performs the following calculation sequence:

1. Calculation of cohort-level energy allocation terms for meat, milk, fibre, work, and eggs using calc_meat_allocation_energy, calc_milk_allocation_energy, calc_fibre_allocation_energy, calc_work_allocation_energy, and calc_eggs_allocation_energy.

2. Aggregation of cohort-level energy terms to herd level using calc_cohort_to_herd_aggregation.

3. Calculation of herd-level allocation shares for commodities using calc_allocation_shares.

4. Reshaping of allocation shares to long format and assignment of shares to emission sources using assign_allocation_shares.

Commodity-specific allocation shares represent the fraction of total herd-level energy requirements attributable to each commodity. These shares are then used to assign emissions to meat, milk, fibre, work, eggs, or the residual category "None".

Emissions from manure burned for fuel and manure deposited on pasture are not allocated to livestock commodities. These flows are assigned fully to "None" in accordance with the rules implemented in assign_allocation_shares.

Value

A named list of two data.table objects:

cohort_allocation_inputs

A data.table with the original cohort-level input columns plus the following new variables:

milk_allocation_energy

Numeric. Energy required to produce total milk output by cohort (MJ/cohort/assessment period).

meat_allocation_energy

Numeric. Energy required by a given sex–age cohort for total meat output by cohort during the assessment period, equal to the energy needed to produce all live-weight gain to reach the target slaughter weight (MJ/cohort/assessment period).

fibre_allocation_energy

Numeric. Energy required to produce all fibre output by cohort (MJ/cohort/assessment period).

work_allocation_energy

Numeric. Energy required to provide all draught power (traction/work) by cohort (MJ/cohort/assessment period).

egg_allocation_energy

Numeric. Energy required for egg production over the assessment period (MJ/cohort/assessment period). Currently set to 0.

allocation_long

A herd-level data.table in long format with one row per herd, commodity, and emission source combination, containing the following columns:

herd_id

Character. Unique identifier for the herd, repeated for each cohort belonging to the same herd.

species_short

Character. Code identifying the livestock species. Supported values include:

• PGS: pigs

• CML: camels

• CTL: cattle

• BFL: buffalo

• SHP: sheep

• GTS: goats

variable_name

Character. Names of emission variables to which allocation should be applied (e.g.,"ch4_enteric", "ch4_manure_pasture", "ch4_manure_burned","ch4_manure_other", "n2o_manure_pasture_direct", "n2o_manure_burned_direct","n2o_manure_other_direct", "n2o_manure_burned_indirect","n2o_manure_pasture_indirect", "n2o_manure_other_indirect", "co2_ration_fertilizer", "co2_ration_pesticides", "co2_ration_crop_activities", "co2_ration_luc_nopeat", "co2_ration_luc_peat", "n2o_ration_fertilizer", "n2o_ration_manure_applied", "n2o_ration_crop_residues", "ch4_ration_rice")

commodity_name

Character. List of commodity categories to which emissions may be allocated. List=c("None","Milk","Meat","Fibre","Work","Eggs")

commodity_type

Character. Commodity (commodity_name) grouping, either "Edible" or "Non-Edible".

allocation_share

Numeric. Allocation share assigned to the commodity for the corresponding emission source (fraction).

References

ISO. (2006). Environmental management — Life cycle assessment — Requirements and guidelines (ISO 14044:2006). International Organization for Standardization, Geneva.

IDF. (2022). The IDF Global Carbon Footprint Standard for the Dairy Sector. Bulletin of the IDF No. 520/2022. International Dairy Federation, Brussels.

Thoma, G., and Nemecek, T. (2020). Allocation between milk and meat in dairy LCA: Critical discussion of the IDF’s standard methodology. In Proceedings of the 12th International Conference on Life Cycle Assessment of Food (LCAFood 2020) (pp. 83–89), 13–16 October, Berlin, Germany.

FAO. (2016a). Environmental performance of large ruminant supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

FAO. (2016b). Greenhouse gas emissions and fossil energy use from small ruminant supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

FAO. (2016c). Greenhouse gas emissions and fossil energy use from poultry supply chains: Guidelines for assessment. Livestock Environmental Assessment and Performance (LEAP) Partnership. FAO, Rome, Italy.

See Also

run_gleam, calc_milk_production, calc_meat_production, run_production_module, calc_meat_allocation_energy, calc_milk_allocation_energy, calc_fibre_allocation_energy, calc_work_allocation_energy, calc_eggs_allocation_energy, calc_cohort_to_herd_aggregation, calc_allocation_shares, assign_allocation_shares

Examples

# Load allocation inputs (cohort and herd-level)
allocation_chrt_dt <- data.table::fread(system.file(
  "extdata/run_modules_examples/allocation_input_chrt_data.csv",
  package = "gleam"
))
allocation_hrd_dt <- data.table::fread(system.file(
  "extdata/run_modules_examples/allocation_input_hrd_data.csv",
  package = "gleam"
))
results <- run_allocation_module(
cohort_level_data = allocation_chrt_dt,
herd_level_data = allocation_hrd_dt
)
head(results$allocation_long)

Run Demographic Herd Module Pipeline

Description

This function takes herd- and cohort-level demographic inputs and estimates a steady-state sex–age herd structure compatible with downstream calculations in the Global Livestock Environmental Assessment Model (GLEAM) computational pipeline run_gleam(). In addition to cohort population sizes, it derives population growth rates, and offtake numbers. The steady state is defined as a constant sex–age cohort structure over time, with population size potentially growing or declining at a constant rate.

Usage

run_demographic_herd_module(
  cohort_level_data,
  herd_level_data,
  initial_herd_structure = c(FJ = 100, FS = 50, FA = 30, MJ = 100, MS = 50, MA = 30),
  max_simulation_years = 100,
  min_lambda_change = 1e-09,
  show_indicator = TRUE,
  simulation_duration = 365
)

Arguments

Details

The function operates under a steady-state assumption: demographic parameters are constant over time, so the population converges to a stable cohort composition and a constant annual growth rate. Once this regime is reached, the model computes cohort population sizes (start/end/average), cohort shares, and offtake totals.

A key feature of this implementation is that it applies demography at a daily resolution. Annual mortality and offtake inputs are converted into daily hazards and daily transition probabilities under competing risks (death vs. offtake vs. survival).

Conceptually, this corresponds to the steady-state demographic approach implemented in Dynmod STEADY1 (Lesnoff, 2013), adapted here to a daily time-step formulation within an R workflow and fully integrated into the GLEAM computational pipeline.

Model structure

The population is divided by sex (female/male) and age class (juvenile/subadult/adult), represented by six cohorts:

• FJ, FS, FA (female juvenile, subadult, adult)

• MJ, MS, MA (male juvenile, subadult, adult)

Only adult females (FA) contribute to reproduction. Births are distributed between females and males using birth_fraction_female. Reproduction is assumed to be distributed over time (no birth pulse). Daily fecundity rates are computed in calc_fecundity_rates.

Dynamics and parameters

Herd dynamics result from:

• births (driven by parturition_rate and litter_size)

• natural deaths (driven by death_rate)

• removals by offtake (driven by offtake_rate)

• cohort aging / growth transitions (driven by cohort_duration_days)

As in Dynmod, offtake_rate is interpreted as a net removal rate for the cohort (e.g. slaughter), while death_rate represents natural mortality excluding offtake.

Competing risks and conversion to daily probabilities

Mortality and offtake are treated as competing risks within each cohort: at any time an animal can survive, die, or be offtaken.Annual inputs are converted to daily hazards and then daily transition probabilities in calc_transition_probabilities.

Internally, the model:

1. Converts annual mortality (death_rate) into a daily mortality hazard.

2. Solves for the daily offtake hazard such that the implied offtake probability matches offtake_rate under competing risks.

3. Computes daily probabilities of death, offtake, and survival from the hazards.

Steady state

Under constant parameters, the cohort structure converges to a stable composition and a stable population growth rate. This function seeks that steady state by iterating the demographic system (see calc_steady_state_structure) starting from initial_herd_structure until changes in cohort-specific growth rates of sex–age cohort proportions (\lambda) fall below min_lambda_change, or until max_simulation_years is reached.

Projection of population size

The steady-state solution obtained here provides:

• cohort shares used to scale herd-level population sizes,

• a stable annual herd growth rate,

• internally consistent death, offtake, and survival probabilities.

These outputs are subsequently used to project one year of population dynamics (calc_projected_population_size) and to summarise annual offtake and stock variation (calc_summary_offtake).

Value

A named list with two elements:

cohort_level_results

A data.table with one row per herd and cohort containing all original cohort_level_data columns plus the following simulation results:

• cohort_stock_size - Numeric vector of length 6. Average population size in each of the 6 sex–age cohorts (# heads) (cohorts = (FJ, FS, FA, MJ, MS, MA)). This corresponds to cohort_stock_start returned by calc_projected_population_size, as it reflects the size of the population by cohort while preserving the total population size (herd_size_total) provided in the inputs.

• offtake_heads - Numeric vector of length 6. Total number of animals removed via offtake over the year, aggregated to 6 sex–age cohorts (heads/year) (cohorts = FJ, FS, FA, MJ, MS, MA).

• offtake_heads_assessment - Numeric vector of length 6. Total number of animals removed via offtake over the assessment period, aggregated to 6 sex–age cohorts (heads/assessment period) (cohorts = FJ, FS, FA, MJ, MS, MA).

herd_level_results

A data.table with one row per herd containing all original herd_level_data columns plus the following herd-level simulation results:

• growth_rate_herd - Numeric. Annualized growth rate at which the herd size reaches steady state (fraction).

References

Lesnoff, M. (2013). DYNMOD: A spreadsheet interface for demographic projections of tropical livestock populations, User's manual. CIRAD, Montpellier, France.

See Also

calc_fecundity_rates, calc_transition_probabilities, calc_steady_state_structure, calc_projected_population_size, calc_summary_offtake

Examples

# Load herd simulation inputs (cohort- and herd-level)
herd_simulation_chrt_dt <- data.table::fread(system.file(
  "extdata/run_modules_examples/herd_simulation_input_chrt_data.csv",
  package = "gleam"
))
herd_simulation_hrd_dt <- data.table::fread(system.file(
  "extdata/run_modules_examples/herd_simulation_input_hrd_data.csv",
  package = "gleam"
))

# Run herd simulation
results <- run_demographic_herd_module(
  cohort_level_data = herd_simulation_chrt_dt,
  herd_level_data = herd_simulation_hrd_dt,
  simulation_duration = 200
)

# Access results
print(results$cohort_level_results)
print(results$herd_level_results)

Run Enteric Methane (CH4) Emissions Module Pipeline

Description

Calculates daily enteric methane emissions by cohort (kg CH4/head/day) using a Tier 2 IPCC approach, by applying species-, cohort- and diet-specific methane conversion factors (ym).

Usage

run_emissions_enteric_module(cohort_level_data, show_indicator = TRUE)

Arguments

Details

This function represents the intermediate module of the Global Livestock Environmental Assessment Model (GLEAM) computational pipeline run_gleam() to estimate enteric methane emissions and performs the following calculation sequence:

1. If ch4_mitigation_factor is not provided in the input data, it is set to 1 (no mitigation).

2. The methane conversion factor (ym) is computed using calc_conversion_factor_ym.

3. Daily enteric methane emissions are computed using calc_ch4_enteric.

Value

A data.table with the original input columns plus the following new variables:

ch4_mitigation_factor

Added by the function if not provided as input.

ch4_conversion_factor_ym

Numeric. Methane (CH4) conversion factor (ym), representing the percentage of gross energy of the feed ration that is converted to CH4 (percentage).

ch4_enteric

Numeric. Average daily enteric methane (CH4) emissions (kg CH4/head/day).

References

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories. Chapter 10: Emissions from Livestock and Manure Management, Equation 10.21.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories. Chapter 10: Emissions from Livestock and Manure Management, Equation 10.21.

See Also

run_gleam, calc_conversion_factor_ym, calc_ch4_enteric

Examples

# Load example input (6 herd_ids, cohort-level; only required columns)
input_path <- system.file(
  "extdata/run_modules_examples/emissions_enteric_input_chrt_data.csv",
  package = "gleam"
)
emissions_enteric_input_chrt_data <- data.table::fread(input_path)
results <- run_emissions_enteric_module(
cohort_level_data = emissions_enteric_input_chrt_data
)

Run Emissions from Manure Module Pipeline

Description

Calculates methane (CH4) and nitrous oxide (N2O) emissions at cohort-level from manure management systems (MMS).

Usage

run_emissions_manure_module(
  cohort_level_data,
  manure_management_system_fraction,
  manure_management_system_factors,
  show_indicator = TRUE
)

Arguments

Details

This function represents the intermediate module of the Global Livestock Environmental Assessment Model (GLEAM) computational pipeline run_gleam() to estimate emissions from manure management systems (MMS) and orchestrates a cohort-level implementation of the IPCC manure management methodology.

The following calculation sequence is applied:

1. VS excretion is computed from nutritional parameters of the feed ration (digestibility, urinary energy, and ash) using a simplified formulation of Equation 10.24 (IPCC 2006, 2019) - calc_volatile_solids

2. Methane (CH4) emissions from manure management are computed from VS and MMS-specific factors (MCF and B0) and reported by MMS group (pasture, burned, and other), consistently with Equation 10.23 (IPCC, 2006, 2019) - calc_ch4_manure

3. Direct nitrous oxide (N2O) emissions from manure management are computed from nitrogen excretion and MMS-specific EF3 values, and reported by MMS group, consistently with Equation 10.25 (IPCC, 2006, 2019) - calc_n2o_manure_direct

4. Indirect N2O emissions are computed as the sum of:

   • volatilisation-driven N2O using MMS-specific nitrogen losses (FracGas) and EF4, consistently with Equations 10.26 (IPCC, 2006, 2019), 10.27 (IPCC, 2006), and 10.28 (IPCC, 2019) - calc_n2o_manure_volatilization

   • leaching/runoff-driven N2O using MMS-specific nitrogen losses (FracLeach) and EF5, consistently with Equations 10.28 (IPCC, 2006), 10.27 (IPCC, 2019), and 10.29 (IPCC, 2006, 2019) - calc_n2o_manure_leaching

5. Total N2O emissions are aggregated by MMS group (pasture, burned, other) - calc_n2o_manure_total

The approach corresponds to a Tier 2 implementation as:

• VS is derived from ration-level inputs rather than using fixed daily excretion defaults, and

• emissions are allocated across MMS categories using herd/cohort MMS fractions and MMS-specific parameters.

Value

cohort_level_data data.table. Input cohort table with added manure emissions columns:

volatile_solids

Numeric. Total volatile solids (VS) excreted per animal per day, representing the organic material in livestock manure and consisting of both biodegradable and non-biodegradable fractions (kg VS/head/day).

ch4_manure_pasture

Numeric. Methane (CH4) emissions from manure deposited on pasture (kg CH4/head/day).

ch4_manure_burned

Numeric. Methane (CH4) emissions from manure burned for fuel (kg CH4/head/day).

ch4_manure_other

Numeric. Methane (CH4) emissions from manure management systems, excluding emissions from manure deposited on pasture and burned for fuel (kg CH4/head/day).

ch4_manure_all_noburn

Numeric. Methane (CH4) emissions from manure management systems, excluding manure burned for fuel (kg CH4/head/day).

n2o_manure_pasture_direct

Numeric. Direct nitrous oxide (N2O) emissions from manure deposited on pasture (kg N2O/head/day).

n2o_manure_burned_direct

Numeric. Direct nitrous oxide (N2O) emissions from manure burned for fuel (kg N2O/head/day).

n2o_manure_other_direct

Numeric. Direct nitrous oxide (N2O) emissions from manure management systems, excluding emissions from manure deposited on pasture and burned for fuel (kg N2O/head/day).

n2o_manure_all_noburn_direct

Numeric. Direct nitrous oxide (N2O) emissions from manure management systems, excluding emissions from manure burned for fuel (kg N2O/head/day).

n2o_manure_pasture_vol

Numeric. Indirect nitrous oxide (N2O) emissions resulting from atmospheric deposition of volatilised nitrogen (NH3 and NOx) from manure deposited on pasture (kg N2O/head/day).

n2o_manure_burned_vol

Numeric. Indirect nitrous oxide (N2O) emissions resulting from atmospheric deposition of volatilised nitrogen (NH3 and NOx) from manure burned for fuel (kg N2O/head/day).

n2o_manure_other_vol

Numeric. Indirect nitrous oxide (N2O) emissions resulting from atmospheric deposition of volatilised nitrogen (NH3 and NOx) from manure management systems, excluding manure deposited on pasture and manure burned for fuel (kg N2O/head/day).

n2o_manure_all_noburn_vol

Numeric. Indirect nitrous oxide (N2O) emissions resulting from atmospheric deposition of volatilised nitrogen (NH3 and NOx) from manure management systems, excluding losses from manure burned for fuel (kg N2O/head/day).

n2o_manure_pasture_leach

Numeric. Indirect nitrous oxide (N2O) emissions resulting from leaching and runoff of manure nitrogen from manure deposited on pasture (kg N2O/head/day).

n2o_manure_burned_leach

Numeric. Indirect nitrous oxide (N2O) emissions resulting from leaching and runoff of manure nitrogen from manure burned for fuel (kg N2O/head/day).

n2o_manure_other_leach

Numeric. Indirect nitrous oxide (N2O) emissions resulting from leaching and runoff of manure nitrogen from manure management systems, excluding losses from manure deposited on pasture and manure burned for fuel (kg N2O/head/day).

n2o_manure_all_noburn_leach

Numeric. Indirect nitrous oxide (N2O) emissions resulting from leaching and runoff of manure nitrogen from manure management systems, excluding losses from manure burned for fuel (kg N2O/head/day).

n2o_manure_pasture_indirect

Numeric. Total indirect nitrous oxide (N2O) emissions from manure deposited on pasture. Includes emissions from atmospheric deposition of volatilised nitrogen (NH3 and NOx) and from leaching and runoff of manure nitrogen (kg N2O/head/day).

n2o_manure_burned_indirect

Numeric. Total indirect nitrous oxide (N2O) emissions originating from manure burned for fuel. Includes emissions from atmospheric deposition of volatilised nitrogen (NH3 and NOx) and from leaching and runoff of manure nitrogen (kg N2O/head/day).

n2o_manure_other_indirect

Numeric. Total indirect nitrous oxide (N2O) emissions originating from manure management systems, excluding manure deposited on pasture and burned for fuel. Includes emissions from atmospheric deposition of volatilised nitrogen (NH3 and NOx) and from leaching and runoff of manure nitrogen.

n2o_manure_pasture_total

Numeric. Total nitrous oxide emissions from manure deposited on pasture. Includes direct emissions and indirect emissions from volatilisation, leaching, and runoff (kg N2O/head/day).

n2o_manure_burned_total

Numeric. Total nitrous oxide emissions (N2O) from manure burned for fuel. Includes direct emissions and indirect emissions from volatilisation, leaching, and runoff (kg N2O/head/day).

n2o_manure_other_total

Numeric. Total nitrous oxide (N2O) emissions from manure management systems, excluding manure deposited on pasture and manure burned for fuel. Includes direct emissions and indirect emissions from volatilisation, leaching, and runoff (kg N2O/head/day).

Manure management system (MMS) reference

A complete list of MMS names, definitions, and associated emission factors can be accessed in the GLEAM Data Explorer.

References

IPCC. (2019). 2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Volume 4, Chapter 10: Emissions from Livestock and Manure Management. Equations 10.23, 10.24, 10.25, 10.26, 10.27, 10.28, and 10.29.

IPCC. (2006). 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Volume 4, Chapter 10: Emissions from Livestock and Manure Management. Equations 10.23, 10.24, 10.25, 10.26, 10.27, 10.28, and 10.29.

See Also

run_gleam, calc_volatile_solids, calc_ch4_manure, calc_n2o_manure_direct, calc_n2o_manure_volatilization, calc_n2o_manure_leaching, calc_n2o_manure_total

Examples

# Load emissions manure inputs (cohort-level and system lookups)
emissions_manure_input_chrt_data <- data.table::fread(system.file(
  "extdata/run_modules_examples/emissions_manure_input_chrt_data.csv",
  package = "gleam"
))
manure_management_system_factors <- data.table::fread(system.file(
  "extdata/run_modules_examples/manure_management_system_factors.csv",
  package = "gleam"
))
manure_management_system_fraction <- data.table::fread(system.file(
  "extdata/run_modules_examples/manure_management_system_fraction.csv",
  package = "gleam"
))

results <- run_emissions_manure_module(
  cohort_level_data = emissions_manure_input_chrt_data,
  manure_management_system_fraction = manure_management_system_fraction,
  manure_management_system_factors = manure_management_system_factors
)

Run Emissions from Feed Production Module Pipeline

Description

Computes cohort-level average greenhouse gas (GHG) emission factors from feed production by weighting emission factors of individual feed components by diet composition. Returns diet-level average GHG emission factors by gas and emission source for each cohort.

Usage

run_emissions_ration_module(
  rations_share,
  feed_emissions,
  show_indicator = TRUE
)

Arguments

Details

This function represents the intermediate module of the Global Livestock Environmental Assessment Model (GLEAM) computational pipeline run_gleam() to estimate emissions from feed production used in the animal's ration. The function joins rations_share with feed_emissions by feed_id, uses species_short directly, and computes ration-weighted emission factors by cohort.

The following calculation sequence is applied:

1. Merge ration shares with emission factors at the feed-component level using merge on feed_id (left join: all.x = TRUE).

2. Compute feed-component contributions (row-wise) for each emission source by multiplying the ration share of each feed component (feed_ration_fraction) by the corresponding feed emission factor. Each contribution is computed using the specific helper below (called with by = .I):

   • CO2 fertilizer: calc_co2_ration_fertilizer

   • CO2 pesticides: calc_co2_ration_pesticides

   • CO2 crop operations: calc_co2_ration_crop_activities

   • CO2 land-use change (no peat): calc_co2_ration_luc_nopeat

   • CO2 land-use change (peat): calc_co2_ration_luc_peat

   • N2O fertilizer: calc_n2o_ration_fertilizer

   • N2O manure applied: calc_n2o_ration_manure

   • N2O crop residues: calc_n2o_ration_crop_residues

   • CH4 rice cultivation: calc_ch4_ration_rice

3. Aggregate to cohort-level diet emission factors by summing feed-component contributions across all feeds within each group (herd_id, species_short, cohort_short).

For each emission source, cohort-level dietary emission factors are computed as:

\mathrm{diet\_ef} = \sum_{i=1}^{n} \left( \mathrm{feed\_ration\_fraction}_{i} \times \mathrm{feed\_ef}_{i} \right)

Value

data.table. Cohort-level emission factors summarized by herd_id, species_short, and cohort_short with the following columns:

co2_ration_fertilizer

Numeric. Diet-level average carbon dioxide (CO2) emission factor from fertilizer manufacture in feed production (g CO2/kg DM).

co2_ration_pesticides

Numeric. Diet-level average carbon dioxide (CO2) emission factor from pesticide manufacture in feed production (g CO2/kg DM).

co2_ration_crop_activities

Numeric. Diet-level average carbon dioxide (CO2) emission factor from on-field agricultural activities in feed production (g CO2/kg DM).

co2_ration_luc_nopeat

Numeric. Diet-level average carbon dioxide (CO2) emission factor from land-use change (excluding peatland drainage) in feed production (g CO2/kg DM).

co2_ration_luc_peat

Numeric. Diet-level average carbon dioxide (CO2) emission factor from peatland drainage in feed production (g CO2/kg DM).

n2o_ration_fertilizer

Numeric. Diet-level average nitrous oxide (N2O) emission factor from fertilizer use in feed production (g N2O/kg DM).

n2o_ration_manure_applied

Numeric. Diet-level average nitrous oxide (N2O) emission factor from manure applied to or deposited on soil in feed production (g N2O/kg DM).

n2o_ration_crop_residues

Numeric. Diet-level average nitrous oxide (N2O) emission factor from crop residues decomposition in feed production (g N2O/kg DM).

ch4_ration_rice

Numeric. Diet-level average methane (CH4) emission factor from rice cultivation in feed production (g CH4/kg DM).

See Also

run_gleam, calc_co2_ration_fertilizer, calc_co2_ration_pesticides, calc_co2_ration_crop_activities, calc_co2_ration_luc_nopeat, calc_co2_ration_luc_peat, calc_n2o_ration_fertilizer, calc_n2o_ration_manure, calc_n2o_ration_crop_residues, calc_ch4_ration_rice

Examples

# Load cleaned example input from the package and compute the calculation of feed emission factors

# Load table with ration shares
rations_share <- data.table::fread(system.file(
  "extdata/run_modules_examples/feed_rations_share_chrt.csv",
  package = "gleam"
))

# Load table with feed emission factors
feed_emissions <- data.table::fread(system.file(
  "extdata/run_modules_examples/feed_emission_factors.csv",
  package = "gleam"
))

# Run the code
result <- run_emissions_ration_module(
  rations_share = rations_share,
  feed_emissions = feed_emissions
)

Run the full Global Livestock Environmental Assessment Model (GLEAM) Pipeline

Description

Runs the full GLEAM pipeline from master herd and cohort inputs through all modules: herd (optional), weights, ration quality, energy requirements, manure emissions, enteric fermentation, nitrogren balance, feed emissions, allocation, and aggregation.

Common identifiers: Several input tables share the following identifier columns. Their supported values are listed once here and referenced throughout.

species_short — Character. Species code:

• CTL: Cattle

• BFL: Buffalo

• SHP: Sheep

• GTS: Goats

• PGS: Pigs

• CML: Camels

cohort_short — Character. Sex- and age-specific cohort code:

• FA: adult females (from age at first parturition)

• FS: sub-adult females (from weaning to age at first parturition)

• FJ: juvenile females (from birth to weaning)

• MA: adult males (from age at first breeding)

• MS: sub-adult males (from weaning to age at first breeding)

• MJ: juvenile males (from birth to weaning)

Usage

run_gleam(
  has_herd_structure = FALSE,
  cohort_level_data,
  herd_level_data,
  feed_rations,
  feed_params,
  feed_emissions,
  manure_management_system_fraction,
  manure_management_system_factors,
  simulation_duration = 365,
  global_warming_potential_set = "AR6",
  show_indicator = TRUE
)

Arguments