# Introduction to Dairy Life Cycle Assessment

## Overview

The dairy industry plays a crucial role in global food security, but it also contributes significantly to greenhouse gas emissions. Understanding and quantifying the environmental impact of dairy production is essential for sustainable development and climate change mitigation.

The cowfootR package provides a comprehensive toolkit for calculating dairy farm carbon footprints following internationally recognized standards, specifically the International Dairy Federation (IDF) 2022 guidelines and IPCC 2019 methodologies.

## How to Use This Vignette

This vignette is designed as a step-by-step tutorial for new users of cowfootR. It introduces the concepts of dairy life cycle assessment (LCA) and demonstrates how to calculate greenhouse gas emissions for a single farm.

You can: - Read it sequentially as a guided example, or - Jump directly to the sections of interest (e.g., emissions, intensities, or visualization).

All examples use simplified, hypothetical data intended for learning purposes.

## Theoretical Background

### Life Cycle Assessment in Dairy Production

Life Cycle Assessment (LCA) is a systematic approach to evaluating the environmental impacts of a product or service throughout its entire life cycle. In dairy production, LCA helps quantify greenhouse gas emissions from various sources within the farm system.

### Key Emission Sources in Dairy Systems

Dairy farm emissions primarily originate from five main sources:

1. Enteric Fermentation: Methane (CH₄) produced during digestion in ruminants
2. Manure Management: CH₄ and nitrous oxide (N₂O) from manure storage and treatment
3. Soil Emissions: N₂O from nitrogen fertilizers and excreta deposition
4. Energy Use: Carbon dioxide (CO₂) from fossil fuel combustion and electricity
5. Purchased Inputs: Embodied emissions in feeds, fertilizers, and materials

### System Boundaries

System boundaries define which processes are included in the assessment:

- Farm Gate: Includes on-farm emissions only
- Cradle-to-Farm Gate: Includes upstream production of inputs
- Partial: Custom selection of emission sources

### Functional Units and Intensity Metrics

Results are expressed using functional units that allow meaningful comparisons:

- kg CO₂eq per kg FPCM: Fat and Protein Corrected Milk intensity
- kg CO₂eq per hectare: Land use intensity
- Absolute emissions: Total farm emissions in kg CO₂eq per year

## Getting Started with cowfootR

### Installation

    # Install from CRAN (when available)
    install.packages("cowfootR")

    # Or install development version from GitHub
    # devtools::install_github("yourusername/cowfootR")

### Loading the Package

    library(cowfootR)

### Input Data Structure

Most `cowfootR` functions expect farm information either as: - Individual numeric arguments (e.g. number of animals, litres of milk), or - A structured list containing farm characteristics.

In this vignette, we use a simple list (`farm_data`) to keep all farm-related information together. This approach improves readability and makes it easier to reuse the same data across multiple calculation steps.

Most emission functions return a list containing: - Total emissions for that source (kg CO₂eq) - A breakdown by gas or process - Metadata describing the calculation method

### Basic Workflow

The typical cowfootR workflow involves four main steps:

1. Define system boundaries
2. Calculate emissions by source
3. Aggregate total emissions
4. Calculate intensity metrics

## Data Requirements: Required vs Optional

### Required Data

The following information is required to run the core cowfootR functions and perform a basic farm-level carbon footprint assessment:

- Herd size and composition
- Annual milk production
- Total farm area
- Major nitrogen inputs (fertilizer or excreta)

### Optional but Recommended Data

Providing additional farm-specific information improves the accuracy and interpretability of results:

- Detailed feed quantities and composition
- Animal productivity parameters (e.g. milk yield per cow)
- Energy use disaggregated by source
- Soil type and climate characteristics
- Allocation of land use by category

If some optional data are not available, cowfootR applies default values based on IPCC and IDF guidance. However, users are encouraged to provide farm-specific data whenever possible.

Let’s walk through a simple example:

## Example: Basic Farm Assessment

### Step 1: Define System Boundaries

    # Define farm-gate boundaries (most common approach)
    boundaries <- set_system_boundaries("farm_gate")
    boundaries
    #> $scope
    #> [1] "farm_gate"
    #>
    #> $include
    #> [1] "enteric" "manure"  "soil"    "energy"  "inputs"

### Step 2: Basic Farm Data

For this example, we’ll use data from a typical dairy farm:

    # Farm characteristics
    farm_data <- list(
      # Herd composition
      dairy_cows = 100,
      heifers = 30,
      calves = 25,

      # Production
      milk_litres = 600000, # Annual milk production
      milk_yield_per_cow = 6000, # kg/cow/year

      # Farm area
      total_area_ha = 120,
      productive_area_ha = 110,

      # Inputs
      concentrate_kg = 180000, # Annual concentrate use
      n_fertilizer_kg = 1500, # Nitrogen fertilizer
      diesel_litres = 8000, # Annual diesel consumption
      electricity_kwh = 35000 # Annual electricity use
    )

    farm_data
    #> $dairy_cows
    #> [1] 100
    #>
    #> $heifers
    #> [1] 30
    #>
    #> $calves
    #> [1] 25
    #>
    #> $milk_litres
    #> [1] 6e+05
    #>
    #> $milk_yield_per_cow
    #> [1] 6000
    #>
    #> $total_area_ha
    #> [1] 120
    #>
    #> $productive_area_ha
    #> [1] 110
    #>
    #> $concentrate_kg
    #> [1] 180000
    #>
    #> $n_fertilizer_kg
    #> [1] 1500
    #>
    #> $diesel_litres
    #> [1] 8000
    #>
    #> $electricity_kwh
    #> [1] 35000

### Step 3: Calculate Emissions by Source

Now we calculate emissions from each source using the individual calculation functions:

#### Enteric Fermentation

Enteric fermentation is typically the largest source of emissions in dairy systems. The function `calc_emissions_enteric()` estimates methane emissions from ruminal fermentation based on animal numbers, productivity, and the selected IPCC Tier.

In this example, we use Tier 2 to incorporate milk yield into the calculation.

    # Calculate enteric methane emissions
    enteric_emissions <- calc_emissions_enteric(
      n_animals = farm_data$dairy_cows,
      cattle_category = "dairy_cows",
      avg_milk_yield = farm_data$milk_yield_per_cow,
      tier = 2, # Use Tier 2 for more accurate results
      boundaries = boundaries
    )

    enteric_emissions
    #> $source
    #> [1] "enteric"
    #>
    #> $category
    #> [1] "dairy_cows"
    #>
    #> $production_system
    #> [1] "mixed"
    #>
    #> $ch4_kg
    #> [1] 9429.19
    #>
    #> $co2eq_kg
    #> [1] 256474
    #>
    #> $units_ch4
    #> [1] "kg CH4 yr-1"
    #>
    #> $units_co2eq
    #> [1] "kg CO2eq yr-1"
    #>
    #> $emission_factors
    #> $emission_factors$emission_factor_ch4
    #> [1] 94.292
    #>
    #> $emission_factors$ym_percent
    #> [1] 6.5
    #>
    #> $emission_factors$gwp_ch4
    #> [1] 27.2
    #>
    #> $emission_factors$method_used
    #> [1] "Tier 2"
    #>
    #>
    #> $inputs
    #> $inputs$n_animals
    #> [1] 100
    #>
    #> $inputs$avg_body_weight
    #> [1] 550
    #>
    #> $inputs$avg_milk_yield
    #> [1] 6000
    #>
    #> $inputs$dry_matter_intake
    #> NULL
    #>
    #> $inputs$feed_inputs
    #> NULL
    #>
    #> $inputs$tier
    #> [1] 2
    #>
    #>
    #> $methodology
    #> [1] "IPCC Tier 2 (GE-based where possible)"
    #>
    #> $standards
    #> [1] "IPCC 2019 Refinement, IDF 2022"
    #>
    #> $date
    #> [1] "2026-01-13"
    #>
    #> $per_animal
    #> $per_animal$ch4_kg
    #> [1] 94.292
    #>
    #> $per_animal$co2eq_kg
    #> [1] 2564.741
    #>
    #> $per_animal$milk_intensity_kg_co2eq_per_kg_milk
    #> [1] 0.4275

#### Manure Management

Manure management emissions include both methane (CH₄) and nitrous oxide (N₂O) released during manure storage, handling, and application. The function `calc_emissions_manure()` estimates these emissions based on the number of animals, manure management system, and the selected IPCC Tier.

Here, a pasture-based manure system is assumed, which is common in extensive and mixed dairy systems.

    # Calculate manure management emissions
    manure_emissions <- calc_emissions_manure(
      n_cows = farm_data$dairy_cows,
      manure_system = "pasture", # Typical for extensive systems
      tier = 2,
      include_indirect = TRUE,
      boundaries = boundaries
    )

    manure_emissions
    #> $source
    #> [1] "manure"
    #>
    #> $system
    #> [1] "pasture"
    #>
    #> $tier
    #> [1] 2
    #>
    #> $climate
    #> [1] "temperate"
    #>
    #> $ch4_kg
    #> [1] 2139.32
    #>
    #> $n2o_direct_kg
    #> [1] 314.29
    #>
    #> $n2o_indirect_kg
    #> [1] 57.75
    #>
    #> $n2o_total_kg
    #> [1] 372.04
    #>
    #> $co2eq_kg
    #> [1] 159755.4
    #>
    #> $units
    #> $units$ch4_kg
    #> [1] "kg CH4 yr-1"
    #>
    #> $units$n2o_kg
    #> [1] "kg N2O yr-1"
    #>
    #> $units$co2eq_kg
    #> [1] "kg CO2eq yr-1"
    #>
    #>
    #> $emission_factors
    #> $emission_factors$ef_ch4
    #> [1] NA
    #>
    #> $emission_factors$ef_n2o_direct
    #> [1] 0.02
    #>
    #> $emission_factors$gwp_ch4
    #> [1] 27.2
    #>
    #> $emission_factors$gwp_n2o
    #> [1] 273
    #>
    #>
    #> $inputs
    #> $inputs$n_cows
    #> [1] 100
    #>
    #> $inputs$n_excreted
    #> [1] 100
    #>
    #> $inputs$manure_system
    #> [1] "pasture"
    #>
    #> $inputs$include_indirect
    #> [1] TRUE
    #>
    #> $inputs$avg_body_weight
    #> [1] 600
    #>
    #> $inputs$diet_digestibility
    #> [1] 0.65
    #>
    #> $inputs$retention_days
    #> NULL
    #>
    #> $inputs$system_temperature
    #> NULL
    #>
    #>
    #> $methodology
    #> [1] "IPCC Tier 2 (VS_B0_MCF calculation)"
    #>
    #> $standards
    #> [1] "IPCC 2019 Refinement, IDF 2022"
    #>
    #> $date
    #> [1] "2026-01-13"
    #>
    #> $per_cow
    #> $per_cow$ch4_kg
    #> [1] 21.3932
    #>
    #> $per_cow$n2o_kg
    #> [1] 3.720357
    #>
    #> $per_cow$co2eq_kg
    #> [1] 1597.553
    #>
    #> $per_cow$units
    #> $per_cow$units$ch4_kg
    #> [1] "kg CH4 yr-1"
    #>
    #> $per_cow$units$n2o_kg
    #> [1] "kg N2O yr-1"
    #>
    #> $per_cow$units$co2eq_kg
    #> [1] "kg CO2eq yr-1"
    #>
    #>
    #>
    #> $tier2_details
    #> $tier2_details$vs_kg_per_day
    #> [1] 32.4
    #>
    #> $tier2_details$b0_used
    #> [1] 0.18
    #>
    #> $tier2_details$mcf_used
    #> [1] 1.5

#### Soil Emissions

Soil-related emissions are mainly associated with nitrous oxide (N₂O) released from nitrogen inputs to agricultural soils. The function `calc_emissions_soil()` estimates direct and indirect soil N₂O emissions resulting from synthetic fertilizers and animal excreta deposited on pasture.

This example uses generalized assumptions for soil type and climate, which can be refined when site-specific information is available.

    # Calculate soil N2O emissions
    soil_emissions <- calc_emissions_soil(
      n_fertilizer_synthetic = farm_data$n_fertilizer_kg,
      n_excreta_pasture = farm_data$dairy_cows * 100, # Estimated N excretion
      area_ha = farm_data$total_area_ha,
      soil_type = "well_drained",
      climate = "temperate",
      include_indirect = TRUE,
      boundaries = boundaries
    )

    soil_emissions
    #> $source
    #> [1] "soil"
    #>
    #> $units
    #> $units$n2o_kg
    #> [1] "kg N2O yr-1"
    #>
    #> $units$co2eq_kg
    #> [1] "kg CO2eq yr-1"
    #>
    #>
    #> $soil_conditions
    #> $soil_conditions$soil_type
    #> [1] "well_drained"
    #>
    #> $soil_conditions$climate
    #> [1] "temperate"
    #>
    #>
    #> $nitrogen_inputs
    #> $nitrogen_inputs$synthetic_fertilizer_kg_n
    #> [1] 1500
    #>
    #> $nitrogen_inputs$organic_fertilizer_kg_n
    #> [1] 0
    #>
    #> $nitrogen_inputs$excreta_pasture_kg_n
    #> [1] 10000
    #>
    #> $nitrogen_inputs$crop_residues_kg_n
    #> [1] 0
    #>
    #> $nitrogen_inputs$total_kg_n
    #> [1] 11500
    #>
    #>
    #> $emissions_breakdown
    #> $emissions_breakdown$direct_n2o_kg
    #> [1] 180.714
    #>
    #> $emissions_breakdown$indirect_volatilization_n2o_kg
    #> [1] 33.786
    #>
    #> $emissions_breakdown$indirect_leaching_n2o_kg
    #> [1] 40.661
    #>
    #> $emissions_breakdown$total_indirect_n2o_kg
    #> [1] 74.446
    #>
    #> $emissions_breakdown$total_n2o_kg
    #> [1] 255.161
    #>
    #>
    #> $co2eq_kg
    #> [1] 69658.88
    #>
    #> $emission_factors
    #> $emission_factors$ef_direct
    #> [1] 0.01
    #>
    #> $emission_factors$ef_volatilization
    #> [1] 0.01
    #>
    #> $emission_factors$ef_leaching
    #> [1] 0.0075
    #>
    #> $emission_factors$gwp_n2o
    #> [1] 273
    #>
    #> $emission_factors$factors_source
    #> [1] "IPCC-style defaults (temperate, well_drained)"
    #>
    #>
    #> $methodology
    #> [1] "Tier 1-style (direct + indirect)"
    #>
    #> $standards
    #> [1] "IPCC 2019 Refinement, IDF 2022"
    #>
    #> $date
    #> [1] "2026-01-13"
    #>
    #> $per_hectare_metrics
    #> $per_hectare_metrics$n_input_kg_per_ha
    #> [1] 95.8
    #>
    #> $per_hectare_metrics$n2o_kg_per_ha
    #> [1] 2.126
    #>
    #> $per_hectare_metrics$co2eq_kg_per_ha
    #> [1] 580.49
    #>
    #> $per_hectare_metrics$emission_intensity_kg_co2eq_per_kg_n
    #> [1] 6.06
    #>
    #>
    #> $source_contributions
    #> $source_contributions$synthetic_fertilizer_pct
    #> [1] 13
    #>
    #> $source_contributions$organic_fertilizer_pct
    #> [1] 0
    #>
    #> $source_contributions$excreta_pasture_pct
    #> [1] 87
    #>
    #> $source_contributions$crop_residues_pct
    #> [1] 0
    #>
    #> $source_contributions$direct_emissions_pct
    #> [1] 70.8
    #>
    #> $source_contributions$indirect_emissions_pct
    #> [1] 29.2

#### Energy Use

Energy-related emissions originate from the combustion of fossil fuels and the use of electricity on the farm. The function `calc_emissions_energy()` estimates carbon dioxide (CO₂) emissions from diesel and electricity consumption, using country- or region-specific emission factors when available.

In this example, electricity emissions are calculated using national grid factors for Uruguay.

    # Calculate energy-related emissions
    energy_emissions <- calc_emissions_energy(
      diesel_l = farm_data$diesel_litres,
      electricity_kwh = farm_data$electricity_kwh,
      country = "UY", # Uruguay electricity grid
      boundaries = boundaries
    )

    energy_emissions
    #> $source
    #> [1] "energy"
    #>
    #> $units
    #> $units$co2_kg
    #> [1] "kg CO2 yr-1"
    #>
    #> $units$co2eq_kg
    #> [1] "kg CO2eq yr-1"
    #>
    #> $units$diesel_l
    #> [1] "L yr-1"
    #>
    #> $units$petrol_l
    #> [1] "L yr-1"
    #>
    #> $units$lpg_kg
    #> [1] "kg yr-1"
    #>
    #> $units$natural_gas_m3
    #> [1] "m3 yr-1"
    #>
    #> $units$electricity_kwh
    #> [1] "kWh yr-1"
    #>
    #>
    #> $fuel_emissions
    #> $fuel_emissions$diesel_co2_kg
    #> [1] 21360
    #>
    #> $fuel_emissions$petrol_co2_kg
    #> [1] 0
    #>
    #> $fuel_emissions$lpg_co2_kg
    #> [1] 0
    #>
    #> $fuel_emissions$natural_gas_co2_kg
    #> [1] 0
    #>
    #> $fuel_emissions$electricity_co2_kg
    #> [1] 2800
    #>
    #> $fuel_emissions$units
    #> $fuel_emissions$units$co2_kg
    #> [1] "kg CO2 yr-1"
    #>
    #>
    #>
    #> $direct_co2eq_kg
    #> [1] 24160
    #>
    #> $upstream_co2eq_kg
    #> [1] 0
    #>
    #> $co2eq_kg
    #> [1] 24160
    #>
    #> $emission_factors
    #> $emission_factors$diesel_kg_co2_per_l
    #> [1] 2.67
    #>
    #> $emission_factors$petrol_kg_co2_per_l
    #> [1] 2.31
    #>
    #> $emission_factors$lpg_kg_co2_per_kg
    #> [1] 3
    #>
    #> $emission_factors$natural_gas_kg_co2_per_m3
    #> [1] 2
    #>
    #> $emission_factors$electricity_kg_co2_per_kwh
    #> [1] 0.08
    #>
    #> $emission_factors$electricity_country
    #> [1] "UY"
    #>
    #>
    #> $inputs
    #> $inputs$diesel_l
    #> [1] 8000
    #>
    #> $inputs$petrol_l
    #> [1] 0
    #>
    #> $inputs$lpg_kg
    #> [1] 0
    #>
    #> $inputs$natural_gas_m3
    #> [1] 0
    #>
    #> $inputs$electricity_kwh
    #> [1] 35000
    #>
    #> $inputs$include_upstream
    #> [1] FALSE
    #>
    #>
    #> $methodology
    #> [1] "IPCC 2019 emission factors"
    #>
    #> $standards
    #> [1] "IPCC 2019 Refinement, IDF 2022"
    #>
    #> $date
    #> [1] "2026-01-13"
    #>
    #> $energy_metrics
    #> $energy_metrics$electricity_share_pct
    #> [1] 11.6
    #>
    #> $energy_metrics$fossil_fuel_share_pct
    #> [1] 88.4
    #>
    #> $energy_metrics$co2_intensity_kg_per_mwh
    #> [1] 80

#### Purchased Inputs

Purchased inputs include emissions embodied in externally produced goods such as concentrates, fertilizers, and other materials used on the farm. The function `calc_emissions_inputs()` accounts for these upstream emissions using average emission factors.

This component is particularly relevant when system boundaries extend beyond the farm gate to include upstream processes.

    # Calculate emissions from purchased inputs
    input_emissions <- calc_emissions_inputs(
      conc_kg = farm_data$concentrate_kg,
      fert_n_kg = farm_data$n_fertilizer_kg,
      region = "global", # Use global emission factors
      boundaries = boundaries
    )

    input_emissions
    #> $source
    #> [1] "inputs"
    #>
    #> $units
    #> $units$co2eq_kg
    #> [1] "kg CO2eq yr-1"
    #>
    #> $units$conc_kg
    #> [1] "kg yr-1"
    #>
    #> $units$fert_n_kg
    #> [1] "kg N yr-1"
    #>
    #> $units$plastic_kg
    #> [1] "kg yr-1"
    #>
    #> $units$feed_kg
    #> [1] "kg DM yr-1"
    #>
    #> $units$transport_km
    #> [1] "km"
    #>
    #> $units$ef_conc
    #> [1] "kg CO2e per kg"
    #>
    #> $units$ef_fert
    #> [1] "kg CO2e per kg N"
    #>
    #> $units$ef_plastic
    #> [1] "kg CO2e per kg"
    #>
    #> $units$ef_feed
    #> [1] "kg CO2e per kg DM"
    #>
    #> $units$ef_truck
    #> [1] "kg CO2e per (kg*km)"
    #>
    #>
    #> $emissions_breakdown
    #> $emissions_breakdown$concentrate_co2eq_kg
    #> [1] 126000
    #>
    #> $emissions_breakdown$fertilizer_co2eq_kg
    #> [1] 9900
    #>
    #> $emissions_breakdown$plastic_co2eq_kg
    #> [1] 0
    #>
    #> $emissions_breakdown$feeds_co2eq_kg
    #>  grain_dry  grain_wet     ration byproducts   proteins       corn        soy
    #>          0          0          0          0          0          0          0
    #>      wheat
    #>          0
    #>
    #> $emissions_breakdown$total_feeds_co2eq_kg
    #> [1] 0
    #>
    #> $emissions_breakdown$transport_adjustment_co2eq_kg
    #> [1] 0
    #>
    #>
    #> $co2eq_kg
    #> [1] 135900
    #>
    #> $total_co2eq_kg
    #> [1] 135900
    #>
    #> $region
    #> [1] "global"
    #>
    #> $emission_factors_used
    #> $emission_factors_used$concentrate
    #> $emission_factors_used$concentrate$value
    #> [1] 0.7
    #>
    #> $emission_factors_used$concentrate$unit
    #> [1] "kg CO2e per kg"
    #>
    #>
    #> $emission_factors_used$fertilizer
    #> $emission_factors_used$fertilizer$value
    #> [1] 6.6
    #>
    #> $emission_factors_used$fertilizer$type
    #> [1] "mixed"
    #>
    #> $emission_factors_used$fertilizer$unit
    #> [1] "kg CO2e per kg N"
    #>
    #>
    #> $emission_factors_used$plastic
    #> $emission_factors_used$plastic$value
    #> [1] 2.5
    #>
    #> $emission_factors_used$plastic$type
    #> [1] "mixed"
    #>
    #> $emission_factors_used$plastic$unit
    #> [1] "kg CO2e per kg"
    #>
    #>
    #> $emission_factors_used$feeds
    #> $emission_factors_used$feeds$grain_dry
    #> $emission_factors_used$feeds$grain_dry$value
    #> [1] 0.4
    #>
    #> $emission_factors_used$feeds$grain_dry$unit
    #> [1] "kg CO2e per kg DM"
    #>
    #>
    #> $emission_factors_used$feeds$grain_wet
    #> $emission_factors_used$feeds$grain_wet$value
    #> [1] 0.3
    #>
    #> $emission_factors_used$feeds$grain_wet$unit
    #> [1] "kg CO2e per kg DM"
    #>
    #>
    #> $emission_factors_used$feeds$ration
    #> $emission_factors_used$feeds$ration$value
    #> [1] 0.6
    #>
    #> $emission_factors_used$feeds$ration$unit
    #> [1] "kg CO2e per kg DM"
    #>
    #>
    #> $emission_factors_used$feeds$byproducts
    #> $emission_factors_used$feeds$byproducts$value
    #> [1] 0.15
    #>
    #> $emission_factors_used$feeds$byproducts$unit
    #> [1] "kg CO2e per kg DM"
    #>
    #>
    #> $emission_factors_used$feeds$proteins
    #> $emission_factors_used$feeds$proteins$value
    #> [1] 1.8
    #>
    #> $emission_factors_used$feeds$proteins$unit
    #> [1] "kg CO2e per kg DM"
    #>
    #>
    #> $emission_factors_used$feeds$corn
    #> $emission_factors_used$feeds$corn$value
    #> [1] 0.45
    #>
    #> $emission_factors_used$feeds$corn$unit
    #> [1] "kg CO2e per kg DM"
    #>
    #>
    #> $emission_factors_used$feeds$soy
    #> $emission_factors_used$feeds$soy$value
    #> [1] 2.1
    #>
    #> $emission_factors_used$feeds$soy$unit
    #> [1] "kg CO2e per kg DM"
    #>
    #>
    #> $emission_factors_used$feeds$wheat
    #> $emission_factors_used$feeds$wheat$value
    #> [1] 0.52
    #>
    #> $emission_factors_used$feeds$wheat$unit
    #> [1] "kg CO2e per kg DM"
    #>
    #>
    #>
    #> $emission_factors_used$transport
    #> $emission_factors_used$transport$ef_truck
    #> [1] 1e-04
    #>
    #> $emission_factors_used$transport$unit
    #> [1] "kg CO2e per (kg*km)"
    #>
    #> $emission_factors_used$transport$transport_km
    #> [1] 0
    #>
    #>
    #> $emission_factors_used$region_source
    #> [1] "global"
    #>
    #>
    #> $inputs_summary
    #> $inputs_summary$concentrate_kg
    #> [1] 180000
    #>
    #> $inputs_summary$fertilizer_n_kg
    #> [1] 1500
    #>
    #> $inputs_summary$plastic_kg
    #> [1] 0
    #>
    #> $inputs_summary$total_feeds_kg
    #> [1] 0
    #>
    #> $inputs_summary$feed_breakdown_kg
    #> $inputs_summary$feed_breakdown_kg$grain_dry
    #> [1] 0
    #>
    #> $inputs_summary$feed_breakdown_kg$grain_wet
    #> [1] 0
    #>
    #> $inputs_summary$feed_breakdown_kg$ration
    #> [1] 0
    #>
    #> $inputs_summary$feed_breakdown_kg$byproducts
    #> [1] 0
    #>
    #> $inputs_summary$feed_breakdown_kg$proteins
    #> [1] 0
    #>
    #> $inputs_summary$feed_breakdown_kg$corn
    #> [1] 0
    #>
    #> $inputs_summary$feed_breakdown_kg$soy
    #> [1] 0
    #>
    #> $inputs_summary$feed_breakdown_kg$wheat
    #> [1] 0
    #>
    #>
    #>
    #> $contribution_analysis
    #> $contribution_analysis$concentrate_pct
    #> [1] 92.7
    #>
    #> $contribution_analysis$fertilizer_pct
    #> [1] 7.3
    #>
    #> $contribution_analysis$plastic_pct
    #> [1] 0
    #>
    #> $contribution_analysis$feeds_pct
    #> [1] 0
    #>
    #> $contribution_analysis$transport_pct
    #> [1] 0
    #>
    #>
    #> $uncertainty
    #> NULL
    #>
    #> $methodology
    #> [1] "Regional emission factors with optional uncertainty analysis"
    #>
    #> $standards
    #> [1] "IDF 2022; generic LCI sources"
    #>
    #> $date
    #> [1] "2026-01-13"

### Step 4: Aggregate Total Emissions

After calculating emissions for each individual source, the function `calc_total_emissions()` aggregates all components into a single result. The output includes total farm emissions and a breakdown by source, which is useful for identifying the main contributors to the carbon footprint.

    # Combine all emission sources
    total_emissions <- calc_total_emissions(
      enteric_emissions,
      manure_emissions,
      soil_emissions,
      energy_emissions,
      input_emissions
    )

    total_emissions
    #> Carbon Footprint - Total Emissions
    #> ==================================
    #> Total CO2eq: 645948.3 kg CO2eq yr-1
    #> Number of sources: 5
    #>
    #> Breakdown by source:
    #>   energy : 24160 kg CO2eq yr-1
    #>   enteric : 256474 kg CO2eq yr-1
    #>   inputs : 135900 kg CO2eq yr-1
    #>   manure : 159755.4 kg CO2eq yr-1
    #>   soil : 69658.88 kg CO2eq yr-1
    #>
    #> Calculated on: 2026-01-13

### Step 5: Calculate Intensity Metrics

While absolute emissions provide information on the total environmental impact of a farm, intensity metrics relate emissions to production or land use. These metrics allow comparisons between farms of different sizes or production levels.

#### Milk Intensity

    # Calculate emissions per kg of milk (FPCM)
    milk_intensity <- calc_intensity_litre(
      total_emissions = total_emissions,
      milk_litres = farm_data$milk_litres,
      fat = 3.8, # Typical fat content
      protein = 3.2 # Typical protein content
    )

    milk_intensity
    #> Carbon Footprint Intensity
    #> ==========================
    #> Intensity: 1.08 kg CO2eq/kg FPCM
    #>
    #> Production data:
    #>  Raw milk (L): 6e+05 L
    #>  Raw milk (kg): 618,000 kg
    #>  FPCM (kg): 597,977 kg
    #>  Fat content: 3.8 %
    #>  Protein content: 3.2 %
    #>
    #> Total emissions: 645,948 kg CO2eq
    #> Calculated on: 2026-01-13

#### Area Intensity

    # Calculate emissions per hectare
    area_intensity <- calc_intensity_area(
      total_emissions = total_emissions,
      area_total_ha = farm_data$total_area_ha,
      area_productive_ha = farm_data$productive_area_ha,
      area_breakdown = list(
        pasture_permanent = 80,
        pasture_temporary = 20,
        crops_feed = 15,
        infrastructure = 5
      )
    )

    area_intensity
    #> Carbon Footprint Area Intensity
    #> ===============================
    #> Intensity (total area): 5382.9 kg CO2eq/ha
    #> Intensity (productive area): 5872.26 kg CO2eq/ha
    #>
    #> Area summary:
    #>  Total area: 120 ha
    #>  Productive area: 110 ha
    #>  Land use efficiency: 91.7%
    #>
    #> Land use breakdown:
    #>  pasture permanent: 80.0 ha (66.7%) -> 430632 kg CO2eq
    #>  pasture temporary: 20.0 ha (16.7%) -> 107658 kg CO2eq
    #>  crops feed: 15.0 ha (12.5%) -> 80744 kg CO2eq
    #>  infrastructure: 5.0 ha (4.2%) -> 26914 kg CO2eq
    #>
    #> Total emissions: 645,948 kg CO2eq
    #> Calculated on: 2026-01-13

## Visualizing Results

The primary goal of cowfootR is to calculate greenhouse gas emissions and intensity metrics following standardized methodologies. The package does not aim to provide a comprehensive visualization framework.

Instead, cowfootR outputs are designed to be easily extracted and converted into standard R objects (such as numeric vectors, lists, or data frames), which can then be visualized using external packages like ggplot2.

The examples below illustrate how users can manually transform cowfootR results into data frames for exploratory visualization and reporting.

### Emission Source Breakdown

    # Create a data frame for plotting
    emission_breakdown <- data.frame(
      Source = names(total_emissions$breakdown),
      Emissions = as.numeric(total_emissions$breakdown)
    )

    # Create pie chart
    ggplot(emission_breakdown, aes(x = "", y = Emissions, fill = Source)) +
      geom_col(width = 1) +
      coord_polar("y", start = 0) +
      theme_void() +
      labs(
        title = "Farm Emissions by Source",
        subtitle = paste("Total:", round(total_emissions$total_co2eq), "kg CO₂eq/year")
      ) +
      theme(
        plot.title = element_text(hjust = 0.5),
        plot.subtitle = element_text(hjust = 0.5)
      )

### Intensity Comparison

    # Create comparison chart
    intensity_data <- data.frame(
      Metric = c(
        "Milk Intensity\n(kg CO₂eq/kg FPCM)",
        "Area Intensity\n(kg CO₂eq/ha)"
      ),
      Value = c(
        milk_intensity$intensity_co2eq_per_kg_fpcm,
        area_intensity$intensity_per_productive_ha
      ),
      Benchmark = c(1.2, 8000) # Typical benchmark values
    )

    ggplot(intensity_data, aes(x = Metric)) +
      geom_col(aes(y = Value), fill = "steelblue", alpha = 0.7) +
      geom_point(aes(y = Benchmark), color = "red", size = 3) +
      geom_text(aes(y = Benchmark, label = "Benchmark"),
        color = "red", vjust = -0.5
      ) +
      labs(
        title = "Farm Intensity Metrics",
        y = "Value",
        x = ""
      ) +
      theme_minimal()

## Understanding the Results

### Interpreting Emission Factors

- Enteric fermentation typically represents 40-60% of total farm emissions
- Purchased inputs (especially protein feeds) can be 20-40% of emissions
- Soil N₂O usually contributes 5-15% of total emissions
- Energy use is generally the smallest component (2-8%)

### Benchmarking Performance

The calculated intensities can be compared against regional or global benchmarks:

- Excellent performance: < 1.0 kg CO₂eq/kg FPCM
- Good performance: 1.0-1.3 kg CO₂eq/kg FPCM
- Average performance: 1.3-2.0 kg CO₂eq/kg FPCM
- Poor performance: > 2.0 kg CO₂eq/kg FPCM

### Common Issues

1. Missing data: The package provides reasonable defaults, but farm-specific data improves accuracy
2. Unit consistency: Ensure all inputs use the correct units (kg, litres, hectares)
3. System boundaries: Be consistent about what’s included/excluded
4. Temporal boundaries: Use annual data for meaningful comparisons

## Next Steps

This vignette introduced the basic concepts of dairy life cycle assessment and demonstrated a complete single-farm workflow using cowfootR.

To continue exploring the package, users may refer to the following vignettes and functions:

- Single Farm Analysis
  A detailed walkthrough of individual emission calculation functions (`calc_emissions_*()`), including assumptions and optional arguments.

- Batch Processing Workflow
  How to process multiple farms simultaneously using structured input data and Excel templates.

- Understanding IPCC Methodology Tiers
  Guidance on choosing between Tier 1 and Tier 2 approaches and understanding their implications for data requirements and accuracy.

- Complete Parameter Reference Guide
  A comprehensive overview of all available functions, arguments, and default values used throughout the package. ## Key Takeaways

1. cowfootR follows internationally recognized LCA standards (IDF 2022, IPCC 2019)
2. The modular approach allows flexible assessment of different emission sources
3. Results should be interpreted in context of farm system and regional benchmarks
4. Data quality significantly affects accuracy - collect farm-specific data when possible
5. The package provides both absolute emissions and intensity metrics for comprehensive analysis

For questions, bug reports, or contributions, visit the cowfootR GitHub repository or contact the development team.