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afsetools: Agro-Food System and Environment Tools

This package provides coefficients, classifications, and functions for assessing environmental impacts of agro-food systems and tracing them through global supply chains.

Overview

afsetools contains:

  • 73 data objects: Biomass coefficients, codes, classifications, and conversion factors from harmonized datasets
  • 35+ functions: NPP calculation, impact allocation, supply chain tracing, biological N fixation, GHG emissions, and more
  • Workflow functions: Complete footprint calculation pipelines
  • Standardized visualizations: Color palettes and plotting themes for consistent figures

Installation 

# Install from GitHub
# install.packages("devtools")
devtools::install_github("eduaguilera/afsetools")

Documentation

Function Reference: All functions are documented with roxygen2. You can read more about the package’s functionalities from the documentation at the reference page.

After installation, you can also use R’s built-in help system:

# Get help for any function
?load_general_data
?calculate_footprints
?Calc_NPP_potentials

# See all package functions
help(package = "afsetools")

Data Objects: For detailed information about the 73+ data objects loaded by load_general_data(), see DATA_REFERENCE.md.

Quick Start 

library(afsetools)

# Load all coefficients and classification data (73 objects)
load_general_data()

# Now you have access to:
# - Biomass_coefs: Conversion factors for DM, N, C, energy
# - GWP: Global warming potentials for greenhouse gases  
# - BNF: Biological nitrogen fixation parameters
# - items_full, regions_full: Harmonized nomenclatures
# - And 60+ more data objects

# Calculate NPP from climate data
npp <- Calc_NPP_potentials(climate_data)

# Calculate crop NPP components
crop_npp <- Calculate_crop_NPP(crop_data, harvest_index)

# Trace impacts through supply chains
footprints <- calculate_footprints(
  CBS = commodity_balance_sheets,
  Primary_all = primary_production,
  Impact_prod = production_impacts,
  Crop_NPPr_NoFallow = crop_npp,
  trade_mode = "gt"  # or "dtm" for bilateral trade
)

# Access results
primary_fp <- footprints$FP_prim
final_fp <- footprints$FP_final

Main Functions

Data Loading

NPP Calculation

  • Calc_NPP_potentials(): Calculate potential NPP using Miami, NCEAS, and Rosenzweig models
  • Calculate_crop_NPP(): Calculate crop NPP components (product, residue, root biomass)
  • Calc_NPP_DM_C_N(): Convert NPP to dry matter, carbon, and nitrogen
  • Calc_CropNPP_components(): Complete cropland NPP including weed biomass

Impact Tracing

Comprehensive Workflow

  • calculate_footprints(): Complete footprint calculation pipeline from primary production to final products
  • extract_luh2(): Extract carbon stock and area data from Land-Use Harmonization 2 (LUH2) dataset

Analysis Functions

Utilities

Visualization

Package Data

After calling load_general_data(), you’ll have access to:

Nomenclatures and Classifications (35 objects): - items_full, items_prod_full, items_cbs: Item codes and names - regions_full, regions_full_uISO3: Country codes and regional aggregations - Cats, Cats_proc: Product categories - Primary_double, Secondary_double: Multi-product processes - And 25+ more classification tables

Biomass Coefficients (17 objects): - Biomass_coefs: Main coefficient table (DM, N, C, energy content, etc.) - Root_ref: Reference root biomass - Weed_NPP_Scaling: Weed biomass scaling factors - Residue_Shares: Crop residue management shares - Fallow_cover: Fallow land cover fractions - And 12+ more coefficient tables

Global Warming Potentials (7 objects): - GWP: GWP values for different gases and time horizons - GWP_100: 100-year GWP values - And 5 more GWP-related objects

Biological N Fixation (3 objects): - BNF: Nitrogen fixation parameters - Names_BNF: BNF nomenclature - Ndfa_ref: Reference Ndfa values

Constants (6 scalars): - Residue_kgC_kgDM_W, Root_kgC_kgDM_W: Carbon content of weeds - Residue_kgN_kgDM_W, Root_kgN_kgDM_W: Nitrogen content of weeds - Root_Shoot_ratio_W: Root:shoot ratio for weeds - Rhizod_kgN_kgRootN_W: Rhizodeposition N coefficient

Color Palettes and Vectors: - Total_color, SOM_color, GHG_color, N_color, P_color, Land_color, Water_color, Energy_color - Month_names, Month_numbers: Month utilities

Data Files

The package bundles standardized input data in inst/extdata/:

  • Codes_coefs.xlsx: 48 sheets with codes, coefficients, and classifications
  • Biomass_coefs.xlsx: Biomass conversion coefficients
  • BNF.xlsx: Biological nitrogen fixation parameters
  • GWP.xlsx: Global warming potentials

These are automatically loaded by load_general_data().

Example Workflow 

library(afsetools)
library(dplyr)

# 1. Load all data
load_general_data()

# 2. Prepare your input data
# (CBS, Primary_all, Impact_prod, Crop_NPPr_NoFallow)

# 3. Calculate complete footprints
results <- calculate_footprints(
  CBS = my_cbs_data,
  Primary_all = my_primary_data,
  Impact_prod = my_impact_data,
  Crop_NPPr_NoFallow = my_crop_npp,
  trade_mode = "gt"
)

# 4. Analyze results
library(ggplot2)

results$FP_final %>%
  filter(Impact == "GHG", Year == 2020) %>%
  ggplot(aes(x = area, y = Impact_u, fill = Product_group)) +
  geom_bar(stat = "identity") +
  theme_new() +
  labs(title = "GHG Footprint by Product Group, 2020")

Citation

If you use this package in your research, please cite:

Aguilera, E., et al. (2025). afsetools: Agro-Food System and Environment Tools. R package version 0.1.0. https://github.com/eduaguilera/afsetools

This package provides the foundational tools used by:

  • Spain_Hist: Historical environmental footprints of Spanish agro-food system

License

MIT © Eduardo Aguilera

Author

Eduardo Aguilera ()
ORCID: 0000-0002-0429-0883

Contributing

Contributions are welcome! Please see CONTRIBUTING.md for guidelines.

Development

To contribute to this package:

# Clone the repository
git clone https://github.com/eduaguilera/afsetools.git
cd afsetools

# Install development dependencies
devtools::install_dev_deps()

# Run tests
devtools::test()

# Check package
devtools::check()