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Calculate daily nitrogen retention

Source: R/core_model_nitrogen_balance.R
calc_nitrogen_retention.Rd

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

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_protein_fraction

Numeric. Milk protein fraction (kg protein / kg milk). Required only for species = CML, CTL, BFL, SHP, and GTS.

milk_yield_day

Numeric. Average milk yield per milk-producing animal during the assessment duration (kg/head/day). This value is calculated as the total quantity of milk produced for human consumption by milk-producing animals during the assessment period, divided by the number of milk-producing animals, and the length of the assessment period (days). Required only for species = CML, CTL, BFL, SHP, and GTS.

daily_weight_gain

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

fibre_yield_year

Numeric. Annual production yield of fibre, such as wool, cashmere, mohair (kg/head/year). Required only for species = CML, SHP, and GTS.

litter_size

Numeric. Average number of offspring born per parturition (# offsprings/parturition). This value can be calculated as the total number of offspring born divided by the total number of parturitions during the year.

parturition_rate

Numeric. Average annual number of parturitions per female animal (# parturitions/adult female/year). A herd-level reproductive performance indicator calculated as the total number of parturitions (deliveries) occurring during a year divided by the number of adult females potentially able to give birth during that year.

live_weight_at_weaning

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

live_weight_at_birth

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

pregnancy_duration

Numeric. Duration of pregnancy period (days).

cohort_duration_days

Numeric. Amount of time that each animal spends in a specific cohort (days).

Value

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

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().

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