Run Emissions from Feed Production Module Pipeline

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

rations_share

data.table. Cohort-level feed ration composition shares with the following minimum 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)

feed_id

Character. Unique identifier for the feed component, used to join feed ration data with feed parameter tables.

feed_name

Character. Feed component name (optional, for readability and reporting). If provided, it should uniquely identify the same feed component as feed_id.

feed_ration_fraction

Numeric. Proportion of a specific feed component in the total ration, expressed as its fraction of diet dry matter intake (fraction). Within each herd_id and cohort, proportions should sum to 1.

feed_emissions

data.table. Emission factors of individual feed components with the following data requirement:

feed_id: Character. Unique identifier for the feed component, used to join feed ration data with feed parameter tables.
feed_name: Character. Feed component name (optional, for readability and reporting). If provided, it should uniquely identify the same feed component as feed_id.
co2_feed_fertilizer: Numeric. Carbon dioxide (CO2) emission factor of a feed component, representing CO2 emissions from fertilizer manufacture in feed production, expressed per kilogram of dry matter intake (g CO2/kg DM).
co2_feed_pesticides: Numeric. Carbon dioxide (CO2) emission factor of a feed component, representing CO2 emissions from pesticide manufacture in feed production, expressed per kilogram of dry matter intake (g CO2/kg DM).
co2_feed_crop_activities: Numeric. Carbon dioxide (CO2) emission factor of a feed component, representing CO2 emissions from on-field agricultural activities in feed production, expressed per kilogram of dry matter intake (kg CO2/kg DM).
co2_feed_luc_nopeat: Numeric. Carbon dioxide (CO2) emission factor of a feed component, representing CO2 emissions from land-use change in feed production (excluding peatland drainage), expressed per kilogram of dry matter intake (g CO2/kg DM).
co2_feed_luc_peat: Numeric. Carbon dioxide (CO2) emission factor of a feed component, representing CO2 emissions from peatland drainage in feed production, expressed per kilogram of dry matter intake (g CO2/kg DM).
n2o_feed_fertilizer: Numeric. Nitrous oxide (N2O) emission factor of a feed component, representing N2O emissions from fertilizer use in feed production, expressed per kg of dry matter intake (g N2O/kg DM).
n2o_feed_manure_applied: Numeric. Nitrous oxide (N2O) emission factor of a feed component, representing N2O emissions from manure applied to or deposited on soil in feed production, expressed per kg of dry matter intake (g N2O/kg DM).
n2o_feed_crop_residues: Numeric. Nitrous oxide (N2O) emission factor of a feed component, representing N2O emissions from crop residues decomposition in feed production, expressed per kg of dry matter intake (g N2O/kg DM).
ch4_feed_rice: Numeric. Methane (CH4) emission factor of a feed component, representing CH4 emissions from rice cultivation in feed production, expressed per kg of dry matter intake (g CH4/kg DM).

show_indicator

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

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).

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:

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

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

Examples

# \donttest{
# 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
)
#> 🕒 Aggregating feed emissions, please wait…
#> ✔ Feed emissions aggregation complete.
# }

Usage

Arguments

Value

Details

See also

Examples