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Run Allocation Module Pipeline

Source: R/run_allocation_module.R
run_allocation_module.Rd

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

cohort_level_data

Cohort-level input table with the following data requirement:

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

cohort_short

Character. Sex- and age-specific cohort code describing the production stage of the animals. Supported values include:

  • 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)

milk_production_fpcm_cohort

Numeric. Total fat-protein-corrected milk (FPCM) produced over the assessment period (kg/cohort/assessment period). Suggested standard fat, protein and lactose contents are 0.04, 0.033, and 0.048 respectively.

live_weight_cohort_at_slaughter

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

meat_production_live_weight_cohort

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

metabolic_energy_req_fibre_production

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 SHP and GTS and as metabolizable energy for CML.

cohort_stock_size

Numeric. Average population size in each of the 6 sex–age cohorts (# heads). (cohorts=FJ, FS, FA, MJ, MS, MA).

metabolic_energy_req_work

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.

herd_level_data

data.table. Herd-level input table (one row per herd_id) with the following data requirement:

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

live_weight_at_birth

Numeric. Live weight of the animal at birth (kg).

milk_protein_fraction_standard

Numeric. Standard protein content of milk, used to calculate Fat-protein-corrected milk (FPCM), (kg protein/kg milk). Suggested value = 0.033.

milk_fat_fraction_standard

Numeric. Standard fat content of milk, used to calculate Fat-protein-corrected milk (FPCM), (kg fat/kg milk). Suggested value = 0.04.

milk_lactose_fraction_standard

Numeric. Standard lactose content of milk, used to calculate Fat-protein-corrected milk (FPCM) , (kg lactose/kg milk). Suggested value = 0.048.

ratio_me_to_ne

Numeric. Ratio of metabolizable energy converted to net energy (fraction). Used for species_short = CML.

simulation_duration

Numeric. Length of the assessment period (days).

show_indicator

Logical. Whether to display progress indicators during simulation. Defaults to TRUE.

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).

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.

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

# \donttest{
# 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
)
#> 🕒 Computing allocation shares, please wait…
#> ✔ Allocation calculation complete.
head(results$allocation_long)
#> Key: <commodity_name>
#>    herd_id species_short              variable_name commodity_name
#>      <int>        <char>                     <char>         <char>
#> 1:       3           SHP                ch4_enteric          Fibre
#> 2:       3           SHP           ch4_manure_other          Fibre
#> 3:       3           SHP            ch4_ration_rice          Fibre
#> 4:       3           SHP co2_ration_crop_activities          Fibre
#> 5:       3           SHP      co2_ration_fertilizer          Fibre
#> 6:       3           SHP      co2_ration_luc_nopeat          Fibre
#>    commodity_type allocation_share
#>            <char>            <num>
#> 1:     Non-Edible        0.1122442
#> 2:     Non-Edible        0.1122442
#> 3:     Non-Edible        0.1122442
#> 4:     Non-Edible        0.1122442
#> 5:     Non-Edible        0.1122442
#> 6:     Non-Edible        0.1122442
# }