Package 'gleam'

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()

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()

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

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

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

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
  )
)

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

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

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

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

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

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).

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(),

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()

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()

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

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

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

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)

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

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

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

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

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

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

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,

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

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

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

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:

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