title: "AgriDataTools: Automated Biometrical & Genetic Analysis in R"
author: "Faheem Khan"
date: "r Sys.Date()"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{AgriDataTools: Automated Biometrical & Genetic Analysis in R}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
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knitr::opts_chunk_options(
  collapse = TRUE,
  comment = "#>",
  fig.width = 7,
  fig.height = 5
)
Introduction
The AgriDataTools package provides an integrated analytics and visualization hub specifically designed for plant breeders, agronomists, and quantitative geneticists. It streamlines biometrical trial workflows—including Analysis of Variance (ANOVA), Mean Comparisons, Principal Component Analysis (PCA), Hierarchical Cluster Analysis, and Path Coefficient Evaluation.

This vignette demonstrates the end-to-end execution of AgriDataTools using the built-in multi-trait agricultural screening dataset gv_data.

1. Environment Initialization and Data Loading
We begin by loading the package and inspecting the built-in wheat phenotypic trial dataset gv_data.

Code snippet


library(AgriDataTools)

# Load sample trial dataset
data(gv_data, package = "AgriDataTools")

# Inspect dataset structure
head(gv_data)
The dataset contains evaluation data across multiple replications and genotypes for primary agronomic characters:

PH: Plant Height

SL: Spike Length

PL: Peduncle Length

NOT: Number of Tillers

NOSS: Number of Spikelets per Spike

TGW: Thousand Grain Weight

GYPM: Grain Yield per Meter

2. Phenotypic Traits Analysis & Mean Performance
To evaluate single-trait phenotypic performance, we perform Analysis of Variance (ANOVA) followed by Least Significant Difference (LSD) mean ranking using compute_lsd().

Code snippet


# Define trait vector and replications
traits <- c("PH", "SL", "PL", "NOT", "NOSS", "TGW", "GYPM")
reps <- length(unique(gv_data$Replication))

# Fit ANOVA model for Plant Height (PH)
fit <- aov(PH ~ Genotype + Replication, data = gv_data)
m_anova <- list(
  anova_table = data.frame(
    Source = c("Genotype", "Replication", "Error"),
    Df = summary(fit)[[1]]$Df,
    MS = summary(fit)[[1]][[3]]
  )
)

# Compute LSD Mean Comparisons
lsd_res <- compute_lsd(
  data = gv_data, 
  trait = "PH", 
  anova_result = m_anova, 
  replications = reps
)

# Display Ranked Means Table
print(lsd_res$ranked_means)
3. Correlation & Path Coefficient Analysis
Understanding trait interrelationships and direct/indirect impacts on yield components is crucial for selection indexing.

Code snippet


# Compute Phenotypic Correlation Matrix
corr_res <- compute_correlation(
  data = gv_data, 
  traits = traits, 
  reporting_level = 0
)

# Perform Path Coefficient Analysis on Yield (GYPM)
path_res <- compute_path_analysis(
  correlation_payload = corr_res,
  response_trait = "GYPM",
  reporting_level = 0
)

# Inspect Direct Effects
print(path_res)
4. Multivariate Pattern Discovery (PCA & Clustering)
To group germplasm lines based on multi-trait variance, we apply Principal Component Analysis (PCA) and Hierarchical Clustering.

Code snippet


# Execute PCA Analysis Engine
pca_res <- analyze_pca(
  data = gv_data, 
  traits = traits
)

# Execute Hierarchical Cluster Engine (k = 4 groups)
cl_res <- analyze_clustering(
  data = gv_data, 
  traits = traits, 
  k = 4
)
5. Integrated Publication Graphics Rendering
The core graphical engine plot_agri_graphics() unifies all statistical diagnostic modules into publication-ready plots.

Code snippet


# 1. Mean Performance Barchart
plot_agri_graphics(
  type = "mean", 
  payload = lsd_res, 
  trait_name = "Plant Height"
)

# 2. Residual Diagnostics Plot
fit_lm <- lm(PH ~ Genotype, data = gv_data)
res_payload <- list(
  residuals = residuals(fit_lm), 
  fitted_values = fitted(fit_lm)
)
plot_agri_graphics(
  type = "residual", 
  payload = res_payload, 
  trait_name = "Residuals"
)

# 3. Path Analysis Direct Effects Plot
plot_agri_graphics(
  type = "path", 
  payload = path_res, 
  trait_name = "Grain Yield per Meter (GYPM)"
)
Conclusion
The AgriDataTools computational suite bridges raw phenotypic data processing and publication-ready biometrical visual diagnostics in R. For full function signature descriptions, consult the package manual (help(package = "AgriDataTools")).