Help for package NUETON

Type:

Package

Title:

Nitrogen Use Efficiency Toolkit on Numerics

Version:

0.2.0

Description:

A comprehensive toolkit for calculating and visualizing Nitrogen Use Efficiency (NUE) indicators in agricultural research. The package implements 23 parameters categorized into fertilizer-based, plant-based, soil-based, isotope-based, ecology-based, and system-based indicators based on Congreves et al. (2021) <doi:10.3389/fpls.2021.637108>. Key features include vectorized calculations for paired-plot experimental designs, batch processing capabilities for handling large datasets, and built-in visualization tools using 'ggplot2'. Designed to streamline the workflow from raw agronomic data to publication-ready metrics and plots.

License:

GPL-3

Encoding:

UTF-8

Imports:

dplyr, ggplot2, magrittr, rlang

RoxygenNote:

7.3.3

Config/testthat/edition:

NeedsCompilation:

Packaged:

2025-12-17 09:21:04 UTC; shubhamlove

Author:

Shubham Love [aut, cre]

Maintainer:

Shubham Love <shubhamlove2101@gmail.com>

Repository:

CRAN

Date/Publication:

2025-12-17 23:20:23 UTC

NUETON: Nitrogen Use Efficiency Toolkit on Numerics

Description

The NUETON package provides a comprehensive suite of tools for calculating Nitrogen Use Efficiency (NUE) indicators from agricultural experimental data. It includes vector-based calculations for 23 different parameters, batch processing capabilities, and automated visualization tools.

Getting Started

The quickest way to learn the package is to run the included demo script, which demonstrates the batch processing and visualization features on a built-in dataset.

# Run the master walkthrough
demo("nueton_walkthrough", package = "NUETON")

Key Functions

calculate_nue_batch: Automatically calculates all 23 indicators from a dataframe.
plot_nue_compare: Visualizes the results with error bars.
AE, NRE, NUEsoil: Individual parameter calculators.

Author(s)

Maintainer: Shubham Love shubhamlove2101@gmail.com

Calculate Agronomic Efficiency (AE)

Description

The contribution of fertilizer N towards yield, compared to a non-fertilized control. Formula: AE = (YieldF - Yield0) / FertN

Usage

AE(YieldF, Yield0, FertN)

Arguments

YieldF

A numeric vector for yield in fertilized conditions.

Yield0

A numeric vector of non-fertilized control yield values.

FertN

A numeric value or vector for fertilizer N input.

Value

A numeric vector of AE values.

Examples

YieldF <- c(10, 12, 15)
Yield0 <- c(5, 5, 5)
FertN <- 50
AE(YieldF, Yield0, FertN)

Calculate Internal Efficiency (IE)

Description

The fraction of plant tissue N that is contained in the yield component. Formula: IE = YieldNF / PlantNf

Usage

IE(YieldNF, PlantNf)

Arguments

YieldNF

A numeric vector for yield N in fertilized conditions.

PlantNf

A numeric vector for plant N in fertilized conditions.

Value

A numeric vector of IE values.

Examples

YieldNF <- c(80, 90, 100)
PlantNf <- c(3.5, 4.0, 4.2)
IE(YieldNF, PlantNf)

Calculate N Balance Intensity (NBI)

Description

The difference between fertilizer N applied and the N removed as yield (N Surplus). Formula: NBI = FertN - YieldN

Usage

NBI(YieldN, FertN)

Arguments

YieldN

A numeric vector of the N removed as yield.

FertN

A numeric value or vector for fertilizer N input.

Value

A numeric vector of NBI values.

Examples

YieldN <- c(80, 90, 100)
FertN <- 50
NBI(YieldN, FertN)

Calculate N Harvest Index (NHI)

Description

The percent of plant tissue N that is contained in the yield component. Formula: NHI = YieldF / PlantNf

Usage

NHI(YieldF, PlantNf)

Arguments

YieldF

A numeric vector of final yield values.

PlantNf

A numeric vector for total plant tissue N.

Value

A numeric vector of NHI values.

Examples

YieldF <- c(10, 12, 15)
PlantNf <- c(2.5, 3.0, 3.2)
NHI(YieldF, PlantNf)

Calculate Nitrogen Productivity (NP)

Description

The ratio of the relative growth rate to the concentration of N in plant tissues. Formula: NP = GR / PlantN

Usage

NP(GR, PlantN)

Arguments

GR

A numeric vector for Plant relative growth rate.

PlantN

A numeric vector for plant N concentration.

Value

A numeric vector of NP values.

Examples

GR <- c(0.5, 0.6)
PlantN <- c(2.0, 2.2)
NP(GR, PlantN)

Calculate Fertilizer N Recovery Efficiency (NRE)

Description

The percentage of fertilizer N that is taken up by the plant. Formula: NRE = ((PlantNf - PlantN0) / FertN) * 100

Usage

NRE(PlantNf, PlantN0, FertN)

Arguments

PlantNf

A numeric vector of plant N in fertilized conditions.

PlantN0

A numeric vector of plant N in control conditions.

FertN

A numeric value or vector for fertilizer N input.

Value

A numeric vector of NRE percentages.

Examples

PlantNf <- c(3.5, 4.0, 4.2)
PlantN0 <- c(2.0, 2.0, 2.0)
FertN <- 50
NRE(PlantNf, PlantN0, FertN)

Calculate Isotope-Based Recovery Efficiency (NRE15)

Description

The percent recovery of fertilizer-N in plant and/or soil components. Formula: NRE15 = (TNdfF / FertN) * 100

Usage

NRE15(TNdfF, FertN)

Arguments

TNdfF

Total N derived from Fertilizer (vector).

FertN

Fertilizer N input (numeric vector or single value).

Value

A numeric vector of NRE15 percentages.

Examples

TNdfF <- c(5.5, 6.0, 4.8)
FertN <- 50
NRE15(TNdfF, FertN)

Calculate NUE of a Food Chain (NUEFC)

Description

The N balance of the entire food chain system. Formula: NUEFC = Ncon / Ni

Usage

NUEFC(Ncon, Ni)

Arguments

Ncon

The value of N available for consumption.

Ni

Sum total of new N input.

Value

A numeric vector of NUEFC values.

Examples

Ncon <- c(40, 45)
Ni <- c(100, 110)
NUEFC(Ncon, Ni)

Calculate NUE Balance

Description

The fraction of N inputs that are removed from the system. Formula: NUEbal = No / Ni

Usage

NUEbal(No, Ni)

Arguments

No

Sum total of N outputs.

Ni

Sum total of N inputs.

Value

A numeric vector of NUEbal values.

Examples

No <- c(50, 60)
Ni <- c(100, 110)
NUEbal(No, Ni)

Calculate NUE Crop

Description

The fraction of fertilizer N that is utilized and allocated to yield N. Formula: NUEcrop = YieldN / FertN

Usage

NUEcrop(YieldN, FertN)

Arguments

YieldN

A numeric vector of the N removed as yield.

FertN

A numeric value or vector for fertilizer N input.

Value

A numeric vector of NUEcrop values.

Examples

YieldN <- c(80, 90, 100)
FertN <- 50
NUEcrop(YieldN, FertN)

Calculate NUE Soil

Description

The biomass production per unit of available N. Formula: NUEsoil = PlantBM / (FertN + SoilN)

Usage

NUEsoil(PlantBM, SoilN, FertN)

Arguments

PlantBM

A numeric vector of plant biomass.

SoilN

A numeric value or vector for soil N content.

FertN

A numeric value or vector for fertilizer N input.

Value

A numeric vector of NUEsoil values.

Examples

PlantBM <- c(100, 120, 130)
SoilN <- c(20, 20, 20)
FertN <- 50
NUEsoil(PlantBM, SoilN, FertN)

Calculate NUE Yield

Description

The contribution of N supplied from the soil that is allocated to yield. Formula: NUEyield = NUpE * NUtE

Usage

NUEyield(NUpE, NUtE)

Arguments

NUpE

N Uptake Efficiency value or vector.

NUtE

N Utilization Efficiency value or vector.

Value

A numeric vector of NUEyield values.

Examples

NUpE <- c(40, 50)
NUtE <- c(20, 25)
NUEyield(NUpE, NUtE)

Calculate N Uptake Efficiency (NUpE)

Description

The percentage of available soil N that is utilized by the plant. Formula: NUpE = (PlantN / (FertN + SoilN)) * 100

Usage

NUpE(PlantN, SoilN, FertN)

Arguments

PlantN

A numeric vector of values for plant N content.

SoilN

A numeric value or vector for soil N content.

FertN

A numeric value or vector for fertilizer N input.

Value

A numeric vector of NUpE percentages.

Examples

PlantN <- c(3.0, 3.5, 3.8)
SoilN <- c(20, 20, 20)
FertN <- 50
NUpE(PlantN, SoilN, FertN)

Calculate N Utilization Efficiency (NUtE)

Description

The contribution of fertilizer N from the plant tissues towards the yield component. Formula: NUtE = Yield / PlantN

Usage

NUtE(Yield, PlantN)

Arguments

Yield

A numeric vector of yield values.

PlantN

A numeric vector for plant tissue N.

Value

A numeric vector of NUtE values.

Examples

Yield <- c(10, 12, 15)
PlantN <- c(2.5, 3.0, 3.2)
NUtE(Yield, PlantN)

Calculate N derived from Fertilizer (NdfF)

Description

The percentage of plant or soil N that is derived from the fertilizer. Formula: NdfF = (Plant15N / Fert15N) * 100

Usage

NdfF(Plant15N, Fert15N)

Arguments

Plant15N

A vector of 15N atom percent excess in plant or soil.

Fert15N

15N atom percent excess of fertilizer N.

Value

A numeric vector of NdfF percentages.

Examples

Plant15N <- c(0.4, 0.5)
Fert15N <- 2.5
NdfF(Plant15N, Fert15N)

Calculate Physiological Efficiency (PE)

Description

The contribution of fertilizer N from the plant tissues towards the yield component. Formula: PE = (YieldF - Yield0) / (PlantNf - PlantN0)

Usage

PE(YieldF, Yield0, PlantNf, PlantN0)

Arguments

YieldF

A numeric vector of final yield values.

Yield0

A numeric vector of non-fertilized control yield values.

PlantNf

A numeric vector of plant N at the end of the experiment.

PlantN0

A numeric vector of plant N at the beginning/control.

Value

A numeric vector of PE values.

Examples

YieldF <- c(12, 13, 14)
Yield0 <- c(10, 10, 10)
PlantNf <- c(3.5, 4.0, 4.2)
PlantN0 <- c(2.0, 2.0, 2.0)
PE(YieldF, Yield0, PlantNf, PlantN0)

Calculate Partial Factor Productivity (PFP)

Description

The expression of yield per unit of fertilizer N applied. Formula: PFP = YieldF / FertN

Usage

PFP(YieldF, FertN)

Arguments

YieldF

A numeric vector of final yield values.

FertN

A numeric value or vector for fertilizer N input.

Value

A numeric vector of PFP values.

Examples

YieldF <- c(10, 12, 15)
FertN <- 50
PFP(YieldF, FertN)

Calculate Partial N Balance (PNB)

Description

The expression of plant N content per unit of fertilizer N applied. Formula: PNB = PlantNf / FertN

Usage

PNB(PlantNf, FertN)

Arguments

PlantNf

A numeric vector of Plant N content in fertilized conditions.

FertN

A numeric value or vector for fertilizer N input.

Value

A numeric vector of PNB values.

Examples

PlantNf <- c(3.5, 4.0, 4.2)
FertN <- 50
PNB(PlantNf, FertN)

Calculate Total N derived from Fertilizer (TNdfF)

Description

The total quantity of plant or soil N that is derived from fertilizer. Formula: TNdfF = (NdfF/100) * (PlantN or SoilN)

Usage

TNdfF(NdfF, PlantN = NULL, SoilN = NULL)

Arguments

NdfF

N derived from Fertilizer expressed as a percentage (0-100).

PlantN

Optional numeric vector for plant N content.

SoilN

Optional numeric vector for soil N content.

Value

A numeric vector of TNdfF values.

Examples

NdfF <- c(15, 20)
PlantN <- c(3.0, 3.5)

# Case 1: Using Plant N
TNdfF(NdfF, PlantN = PlantN)

# Case 2: Using Soil N (must specify SoilN explicitly)
SoilN <- c(100, 120)
TNdfF(NdfF, SoilN = SoilN)

Calculate Virtual N Factor (VNF)

Description

The portion of N released to the environment not contained in food. Formula: VNF = Nrec / Ncon

Usage

VNF(Nrec, Ncon)

Arguments

Nrec

N used to produce food item that ends up recycled.

Ncon

N in food item that is consumed.

Value

A numeric vector of VNF values.

Examples

Nrec <- c(10, 12)
Ncon <- c(40, 45)
VNF(Nrec, Ncon)

Calculate All NUE Indicators (Batch Processing)

Description

Automatically detects available data columns and calculates all 23 NUE indicators.

Usage

calculate_nue_batch(
  data,
  yield_f = "YieldF",
  yield_0 = "Yield0",
  fert_n = "FertN",
  plant_n_f = "PlantNf",
  plant_n_0 = "PlantN0",
  yield_n = "YieldN",
  soil_n = "SoilN",
  plant_bm = "PlantBM",
  plant_15n = "Plant15N",
  fert_15n = "Fert15N",
  gr = "GR",
  n_con = "Ncon",
  n_rec = "Nrec",
  n_loss = "Nloss",
  n_in = "Ni",
  n_out = "No",
  delta_soil_n = "delSoilN",
  mrt = "MRT"
)

Arguments

data

A dataframe containing experimental data.

yield_f

Column name for Fertilized Yield. Default: "YieldF"

yield_0

Column name for Control Yield. Default: "Yield0"

fert_n

Column name for Fertilizer N input. Default: "FertN"

plant_n_f

Column name for Plant N (fertilized). Default: "PlantNf"

plant_n_0

Column name for Plant N (control). Default: "PlantN0"

yield_n

Column name for N removed as yield. Default: "YieldN"

soil_n

Column name for Soil N. Default: "SoilN"

plant_bm

Column name for Plant Biomass. Default: "PlantBM"

plant_15n

Column name for Plant 15N excess. Default: "Plant15N"

fert_15n

Column name for Fertilizer 15N excess. Default: "Fert15N"

gr

Column name for Plant Growth Rate. Default: "GR"

n_con

Column name for N available for consumption. Default: "Ncon"

n_rec

Column name for N recycled. Default: "Nrec"

n_loss

Column name for N lost from system. Default: "Nloss"

n_in

Column name for Total N Input (System). Default: "Ni"

n_out

Column name for Total N Output (System). Default: "No"

delta_soil_n

Column name for Change in Soil N. Default: "delSoilN"

mrt

Column name for Mean Residency Time. Default: "MRT"

Value

A dataframe with new columns appended for every calculable metric.

Examples

# Create a simple dataset
df <- data.frame(
  YieldF = c(3.5, 4.2, 5.0),
  Yield0 = c(2.0, 2.5, 3.0),
  FertN = c(10, 10, 10)
)

# Run the batch calculator
result <- calculate_nue_batch(df)

# View calculated AE column
print(result$AE)

Calculate Ecological NUE (ecoNUE)

Description

The product of N productivity and mean residency time (MRT). Formula: ecoNUE = NP * MRT

Usage

ecoNUE(NP, MRT)

Arguments

NP

Nitrogen Productivity Value.

MRT

Mean Residency Time value.

Value

A numeric vector of ecoNUE values.

Examples

NP <- c(10, 12)
MRT <- c(4, 5)
ecoNUE(NP, MRT)

Plot NUE Comparison

Description

Creates a bar chart comparing NUE metrics across different groups (e.g., Treatments or Sites). Includes error bars (Standard Error).

Usage

plot_nue_compare(data, x_var, y_var)

Arguments

data

A dataframe containing the results.

x_var

The column name to group by (e.g., "Treatment", "Year").

y_var

The NUE metric to plot (e.g., "AE", "NRE").

Value

A ggplot object.

Examples

# Create dummy data
df <- data.frame(
  Treat = c("A", "A", "B", "B"),
  AE = c(10, 12, 20, 22)
)

# Plot
plot_nue_compare(df, x_var = "Treat", y_var = "AE")

Calculate N Balance Index of a System (sNBI)

Description

The accumulation or reduction of soil N over a set time. Formula: sNBI = Ni - No - delSoilN

Usage

sNBI(Ni, No, delSoilN)

Arguments

Ni

Sum total of N inputs (vector or value).

No

Sum total of N outputs (vector or value).

delSoilN

Change in total soil N value.

Value

A numeric vector of sNBI values.

Examples

Ni <- c(100, 120)
No <- c(80, 90)
delSoilN <- c(5, -2)
sNBI(Ni, No, delSoilN)

Calculate NUE of a System (sNUE)

Description

The fraction of system N outputs that are captured as N yield. Formula: sNUE = YieldN / (YieldN + Nloss)

Usage

sNUE(YieldN, Nloss)

Arguments

YieldN

Observed crop yield N.

Nloss

N lost from the system.

Value

A numeric vector of sNUE values.

Examples

YieldN <- c(80, 90, 100)
Nloss <- c(20, 25, 20)
sNUE(YieldN, Nloss)