wefnexus 1.1.0

This release is dedicated to the memory of co-authors Dr. Monika Punia and Dr. Hemant Poonia.

New features

• nexus_analysis() runs the full WEFNC workflow on replicated (plot-level) field data in one call: plot-level indicators, ANOVA, composite nexus index from treatment means, and TOPSIS ranking.
• nexus_anova() gives treatment means with letter groups (Fisher’s LSD), SEm, CD and CV for CRD and RCBD experiments, as a table ready for a manuscript. Means are least-squares means (block-adjusted when plots are missing), every pair is tested with its own standard error, and letters use the insert-and-absorb algorithm of Piepho (2004), so they stay exact with unequal replication and beyond 26 groups.
• nexus_weights() derives objective dimension weights by the entropy, CRITIC or PCA method, as an alternative to equal weights.
• nexus_topsis() ranks treatments by TOPSIS on raw indicators, handling lower-is-better indicators such as carbon footprint directly.
• energy_budget() converts physical input quantities (diesel, fertilizer, labour hours, seed, chemicals) and outputs to energy, with direct, indirect, renewable and non-renewable shares and efficiency indicators.
• New datasets: energy_coefficients (editable table of 20 energy equivalents) and arid_pulse_trial (6 treatments x 3 replications, RCBD).
• nexus_rank_compare() ranks treatments eight ways (composite index and TOPSIS, each with equal, entropy, CRITIC and PCA weights) and reports Kendall’s W, a consensus ranking and Spearman correlations between rankings, so the robustness of a recommendation can be shown.
• Publication-ready ggplot2 figures: plot() methods for nexus_anova (means with error bars and letter groups), energy_budget (stacked input energy by item, direct/indirect or renewable/non-renewable), topsis_result, rank_compare and nexus_analysis; and plot_tradeoff() for the trade-off matrix with significance stars.
• nexus_tradeoff() now attaches correlation-test p-values and pair counts as attributes (attr(x, "p_values"), attr(x, "n")).
• nexus_radar_gg() gains facet = TRUE (one panel per treatment, with the mean profile as a reference) and a colours argument; nexus_heatmap_gg() gains colours.
• All plots now use a colour-blind-checked palette and a single-hue sequential scale for scores, replacing the red-green defaults. Radar charts start at the top and run clockwise.
• nexus_summary() gains nutrient_metric ("pfp" or "iue") for legumes grown without fertilizer N, carbon_basis ("emission" or "intensity"), and accepts a weighting method name in weights. The output adds IUE_kg_kgN and rank columns and stores the weights used.
• carbon_footprint() and ghg_emission() gain ef_n2o so the 2019 IPCC disaggregated factors (0.005 dry, 0.016 wet climates) can be used; ghg_emission() also gains ef_ch4_paddy.
• All functions now default to verbose = getOption("wefnexus.verbose", TRUE), so options(wefnexus.verbose = FALSE) silences messages globally.

Bug fixes

• ghg_emission() added biogenic CO2 from residue burning to the total and left out burning CH4 and N2O. Burning now follows IPCC (2006, Vol. 4, Ch. 2): combustion factor 0.8 and emission factors of 2.7 g CH4 and 0.07 g N2O per kg dry matter burnt; biogenic CO2 is reported but only counted with include_burn_co2 = TRUE. The single-observation output gains counted and an attr(, "total_CO2eq"), and vector inputs of any argument are recycled.

• global_warming_potential(time_horizon = "20yr") used 81 for CH4 and overrode user-supplied values. It now uses the AR6 20-year value for non-fossil methane (79.7, consistent with 27 at 100 years) and keeps any gwp_ch4 or gwp_n2o you supply. The AR5 note is corrected.

• soil_carbon_stock() returned values 10 times too low. SOC (percent) x bulk density (Mg/m3) x depth (cm) is already Mg C/ha, but an extra factor of 0.1 was applied, so the result was in kg C/m2 while labelled Mg C/ha. Stocks and any sequestration rates derived from them should be recalculated.

• nexus_heatmap_gg() placed the values of the last treatment against the label of the first (rows were reversed relative to their labels). The base-graphics nexus_heatmap() was not affected.

• nutrient_use_efficiency() returned a fixed nutrient harvest index of 0.75 for every input. It now computes NHI from the new grain_uptake argument and returns NA when that is not supplied.

• water_footprint() multiplied the footprint by area, although water

  (mm) and yield (kg/ha) are both per hectare. area is now deprecated and ignored, with a warning when a value other than 1 is given.

• nexus_summary() required n_uptake but never used it, and failed when N applied was zero. Both are fixed.

• ghg_emission() returned a single tillage value for vector input; it is now repeated for each observation.

• carbon_footprint() no longer divides by zero in source shares when the total footprint is zero.

• nexus_index() now warns when scores fall outside 0 to 1, checks that score vectors have matching lengths, and rejects negative weights.

• crop_water_stress_index() now cites Jackson et al. (1981) for the evapotranspiration form of the index.

• carbon_footprint() no longer fails when yield is a vector and the other inputs are single values.

• soil_carbon_stock() now rejects a coarse fragment fraction of 1 or more.

• nexus_summary() warns when every treatment receives the same N, since PFP is then proportional to yield and yield would carry double weight.

• nexus_weights() CRITIC weights no longer change when a constant indicator is present; nexus_topsis() rejects all-zero weights; nexus_heatmap_gg(), nexus_radar_gg() and nexus_heatmap() check that labels match the score matrix; energy_budget() warns about missing quantities and rejects unknown categories in the coefficient table.

• nutrient_balance() no longer fails when an input is zero (for example no K applied); the output-to-input ratio is NA for that nutrient.

• The reference DOI for Lal (2004) in carbon_footprint() pointed to an unrelated article; corrected to 10.1016/j.envint.2004.03.005. All other DOIs were checked against Crossref.

Changed defaults

• carbon_footprint() grid electricity factor updated from 0.82 to 0.727 kg CO2/kWh (Central Electricity Authority, CO2 Baseline Database v20, 2023-24). Use ef_electricity = 0.82 to reproduce earlier results.

Documentation

• nexus_rank_compare() reports the chi-square statistic for reference only: the rankings share the same data, so W is read descriptively.

• Help-page formulas corrected to match the code (no change in results) for energy_profitability(), crop_yield_index(), production_efficiency_index(), nutrient_harvest_index(), carbon_footprint(), carbon_sustainability_index(), food_productivity_index(), specific_energy() and nexus_sustainability_score().

• Vignette extended with energy budgeting, objective weighting, TOPSIS, ranking robustness, figures and the replicated-trial workflow.

• README function counts corrected (59 exported functions).

wefnexus 1.0.0

Initial CRAN release

Water Module (7 functions)

• water_use_efficiency() - WUE (kg/ha/mm)
• water_productivity() - Physical and economic WP (kg/m3)
• water_footprint() - Green, blue, grey WF decomposition
• irrigation_efficiency() - Conveyance, application, overall, consumptive
• crop_water_stress_index() - CWSI bounded 0-1
• crop_water_productivity() - CWP (kg/m3) from ET
• depleted_fraction() - Basin-level water allocation metric

Energy Module (10 functions)

• energy_input() - 15-component energy input aggregation
• energy_output() - Grain + straw energy with customizable coefficients
• energy_use_efficiency() - EUE ratio
• eroi() - Energy Return on Investment with interpretation
• energy_productivity() - Yield per MJ input
• energy_intensity() - MJ per kg yield
• specific_energy() - MJ/ha/day for duration comparisons
• net_energy() - Energy balance (output minus input)
• energy_profitability() - Economic return per MJ
• human_energy_profitability() - Labour energy amplification ratio

Food Module (8 functions)

• food_productivity_index() - Composite yield-protein-calorie index
• crop_yield_index() - Relative to check treatment
• harvest_index() - Economic to biological yield ratio
• land_equivalent_ratio() - Intercropping advantage (LER)
• system_productivity_index() - Multi-crop system equivalent
• caloric_yield() - kcal/ha output
• protein_yield() - kg protein/ha
• production_efficiency_index() - Yield per unit cost

Nutrient Module (8 functions)

• agronomic_efficiency() - AE (kg yield increase/kg nutrient)
• physiological_efficiency() - PE (yield/uptake increase)
• recovery_efficiency() - RE (uptake increase/applied)
• partial_factor_productivity() - PFP (total yield/applied)
• internal_utilization_efficiency() - IUE (yield/total uptake)
• nutrient_harvest_index() - NHI (grain/total plant nutrient)
• nutrient_balance() - N-P-K input-output balance sheet
• nutrient_use_efficiency() - Comprehensive single-call NUE report

Carbon Module (7 functions)

• carbon_footprint() - Source-wise CF with IPCC AR6 GWP defaults
• carbon_efficiency() - Yield per kg CO2-eq
• carbon_sustainability_index() - CSI with sequestration offset
• ghg_emission() - N2O/CH4/CO2 estimation (IPCC Tier 1)
• soil_carbon_stock() - SOC stock (Mg C/ha)
• carbon_sequestration_rate() - Annual SOC change
• global_warming_potential() - GWP with AR6 values (100yr and 20yr)

Nexus Integration (8 functions)

• normalize_minmax() - Min-max 0-1 scaling with inverse option
• normalize_zscore() - Z-score standardization
• nexus_index() - Weighted composite WEFNC index
• nexus_tradeoff() - Correlation-based trade-off matrix
• nexus_radar() - Spider/web chart visualization
• nexus_heatmap() - Treatment x dimension heatmap
• nexus_sustainability_score() - Categorized sustainability assessment
• nexus_summary() - One-call complete nexus analysis from raw data

Dataset

• arid_pulse_nexus - 6 CA treatments x 26 variables from western Rajasthan

Technical Notes

• GWP defaults updated to IPCC AR6: CH4 = 27, N2O = 273 (100-yr)
• India-specific grid electricity EF: 0.82 kg CO2/kWh (CEA 2023)
• All functions use verbose = TRUE parameter (CRAN compliant)
• All @return tags present in documentation
• No cat()/print() outside if(verbose) blocks
• All examples executable (no \dontrun)