---
title: "WEFNC Nexus Analysis for Agricultural Systems"
author: "Lalit Kumar Rolaniya"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{WEFNC Nexus Analysis for Agricultural Systems}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
library(wefnexus)
```

## Introduction

The **wefnexus** package provides a comprehensive toolkit for analyzing
Water-Energy-Food-Nutrient-Carbon (WEFNC) nexus interactions in agricultural
production systems. This vignette demonstrates a complete workflow using a
conservation agriculture dataset from western Rajasthan, India.

## Load Sample Data

```{r data}
data(arid_pulse_nexus)
d <- arid_pulse_nexus
str(d)
```

## 1. Water Module

```{r water}
# Water Use Efficiency
wue <- water_use_efficiency(d$grain_yield, d$total_water)

# Crop Water Productivity
cwp <- crop_water_productivity(d$grain_yield, d$crop_et)

# Water Footprint (green + blue)
wf <- water_footprint(
  green_water = d$effective_rainfall,
  blue_water = d$irrigation_applied,
  yield = d$grain_yield
)
wf
```

## 2. Energy Module

```{r energy}
# Total energy output
e_out <- d$energy_output_grain + d$energy_output_straw

# Energy Use Efficiency
eue <- energy_use_efficiency(e_out, d$energy_input)

# Energy Return on Investment (EROI)
eroi_values <- eroi(e_out, d$energy_input)

# Net Energy Balance
ne <- net_energy(e_out, d$energy_input)

# Compare treatments
data.frame(Treatment = d$treatment, EUE = eue, EROI = eroi_values,
           Net_Energy = ne)
```

## 3. Food Module

```{r food}
# Harvest Index
bio_yield <- d$grain_yield + d$straw_yield
hi <- harvest_index(d$grain_yield, bio_yield)

# Protein Yield (assuming 22% protein in pulses)
py <- protein_yield(d$grain_yield, protein_content = 22)

data.frame(Treatment = d$treatment, HI = hi, Protein_kg_ha = py)
```

## 4. Nutrient Module

```{r nutrient}
# Partial Factor Productivity of N
pfp <- partial_factor_productivity(d$grain_yield, d$n_applied)

# Nutrient Harvest Index for N
nhi <- nutrient_harvest_index(d$grain_n_uptake, d$n_uptake)

data.frame(Treatment = d$treatment, PFP_N = pfp, NHI_N = nhi)
```

## 5. Carbon Module

```{r carbon}
# Carbon Footprint (IPCC AR6 GWP: CH4=27, N2O=273)
cf <- carbon_footprint(
  diesel_use = d$diesel_use[1],
  electricity_use = d$electricity_kwh[1],
  n_fertilizer = d$n_applied[1],
  p_fertilizer = d$p_applied[1],
  yield = d$grain_yield[1]
)
cf$breakdown

# Soil Carbon Stock
soc <- soil_carbon_stock(d$soc_pct, d$bulk_density, depth = 30)

# Global Warming Potential (example)
gwp100 <- global_warming_potential(co2 = 500, ch4 = 10, n2o = 2)
gwp20 <- global_warming_potential(co2 = 500, ch4 = 10, n2o = 2,
                                   time_horizon = "20yr")
```

## 6. Nexus Integration

```{r nexus}
# Full Nexus Summary
ns <- nexus_summary(
  yield = d$grain_yield,
  water_consumed = d$total_water,
  energy_input = d$energy_input,
  energy_output = e_out,
  n_applied = d$n_applied,
  n_uptake = d$n_uptake,
  carbon_emission = d$ghg_emission,
  treatment_names = d$treatment
)
ns[, c("treatment", "EROI", "nexus_index")]
```

### Radar Plot

```{r radar, fig.width=7, fig.height=6}
scores <- as.matrix(ns[, c("W_score", "E_score", "F_score",
                             "N_score", "C_score")])
nexus_radar(scores, treatment_names = d$treatment)
```

### Sustainability Scoring

```{r sustainability}
nss <- nexus_sustainability_score(
  water_score = ns$W_score,
  energy_score = ns$E_score,
  food_score = ns$F_score,
  nutrient_score = ns$N_score,
  carbon_score = ns$C_score
)
nss[, c("nexus_score", "category")]
```

## References

- Hoekstra, A.Y. et al. (2011). The Water Footprint Assessment Manual.
  Earthscan, London.
- Hall, C.A.S. et al. (2014). EROI of different fuels and the implications
  for society. Energy Policy, 64, 141-152.
- Dobermann, A. (2007). Nutrient use efficiency. In Fertilizer Best
  Management Practices, IFA, Paris.
- Forster, P. et al. (2021). IPCC AR6 WGI Chapter 7: The Earth's energy
  budget, climate feedbacks, and climate sensitivity.
- Lal, R. (2004). Carbon emission from farm operations. Environment
  International, 30(7), 981-990.