BKBreed

Colourful Biometrical Analysis for Plant Breeding and Genetics

Available on CRAN: install.packages("BKBreed")

BKBreed is a small, accurate R package that runs the everyday analyses of a plant-breeding programme in one call each — and returns a publication-ready, stunningly colourful ggplot2 figure for every result through a single verb: bk_plot().

It was built to be different from the existing agricultural-statistics packages (e.g. agricolae, AgroR, metan, aridagri): those are broad and console-first; BKBreed is genetics-focused, figure-first, and covers the augmented (unreplicated) designs that balanced-only packages cannot.

What it does

Domain	Function	Signature figure
Randomised Block Design	`bk_rbd()`	ranked genotype means + CD letters
Factorial RBD	`bk_frbd()`	interaction line plot
Augmented Alpha-Lattice / RCBD	`bk_augmented()`	adjusted-means lollipop vs check line
Genetic variability (GCV, PCV, h², GA)	`bk_variability()`	GCV vs PCV bars + heritability
Genotypic & phenotypic correlation	`bk_correlation()`	diverging correlation heatmap
Path-coefficient analysis	`bk_path()`	direct/indirect effect matrix
Line × Tester combining ability	`bk_lxt()`	GCA effect bars + SCA heatmap
Griffing diallel (Method 2, Model I)	`bk_diallel()`	GCA effect bars + SCA heatmap
Mahalanobis D² divergence	`bk_diversity()`	D² principal-coordinate clusters
G×E stability (Eberhart-Russell + AMMI)	`bk_stability()`	AMMI-2 biplot & E-R plot

Every function also returns a tidy result object with a formatted print() method (ANOVA tables with SS/MS/F/p, SE, CD, CV%, letter groupings).

Install

# from CRAN (recommended)
install.packages("BKBreed")

# or the development version from GitHub
# # remotes::install_github("bkpraveenars-del/BKBreed")
install.packages("BKBreed", repos = c('https://bkpraveenars-del.r-universe.dev', 'https://cloud.r-project.org'))

Dependencies: ggplot2 (required); ggrepel, patchwork (optional, for nicer labels). R ≥ 4.0. No compiled code — no Rtools needed.

60-second tour

library(BKBreed)

## 1. RBD — one call gives ANOVA + CD + letters + a colour figure
rbd <- bk_rbd(bk_data("rbd"), trait = "grain_yield",
              gen = "genotype", rep = "rep")
rbd            # formatted ANOVA + ranked means
bk_plot(rbd)   # ranked colour bars with SE and letter groups

## 2. Genetic variability across several traits
traits <- c("grain_yield","plant_height","tillers","panicle_len","test_weight")
bk_plot(bk_variability(bk_data("rbd"), traits, "genotype", "rep"))

## 3. Correlation heatmap (genotypic)
bk_plot(bk_correlation(bk_data("rbd"), traits, "genotype", "rep"))

## 4. Path analysis on yield
bk_plot(bk_path(bk_data("rbd"),
        c("plant_height","tillers","panicle_len","test_weight"),
        dependent = "grain_yield", gen = "genotype", rep = "rep"))

## 5. D² divergence clusters
bk_plot(bk_diversity(bk_data("rbd"), traits, "genotype", "rep"))

## 6. Augmented alpha-lattice (unreplicated test entries + checks)
bk_plot(bk_augmented(bk_data("augmented"), "grain_yield", "genotype",
                     block = "block", rep = "rep",
                     checks = paste0("CHK-", 1:4)))

## 7. Multi-location stability — AMMI-2 biplot
bk_plot(bk_stability(bk_data("mlt"), "grain_yield",
        gen = "genotype", env = "environment", rep = "rep"))

Run everything and save all figures as PNG:

source(system.file("examples", "run_all.R", package = "BKBreed"))

Bundled example data

bk_data("rbd") pearl-millet multi-trait RBD · bk_data("frbd") N × variety factorial · bk_data("augmented") augmented alpha-lattice (4 checks + 20 test entries) · bk_data("mlt") 10 genotypes × 5 environments · bk_data("lxt") 5 lines × 3 testers · bk_data("diallel") 6-parent half diallel.

Methods & conventions

Variability uses the Singh & Chaudhary formulation (σ²g = (Mg − Me)/r, σ²p = σ²g + Me).
Correlations use analysis-of-covariance mean cross-products.
Augmented analysis estimates block effects by intra-block least squares from the checks and reports the four classical Federer standard errors. For exact BLUPs on strongly unbalanced data, pair with a mixed-model package.
Stability follows Eberhart & Russell (1966) and Gauch's AMMI.

Citation

If you use BKBreed in your research, please cite it:

Praveen Kumar B. K. (2026). BKBreed: Colourful Biometrical Analysis for Plant Breeding and Genetics. R package version 0.3.2. https://CRAN.R-project.org/package=BKBreed DOI: 10.5281/zenodo.21716452

In R: citation("BKBreed")

License

GPL-3. Author: Dr. Praveen Kumar B. K., Department of Genetics and Plant Breeding, Agriculture University, Jodhpur, India.