Mandala for R

Purpose-built mixed model analysis for breeding programs, simplified for R.

Why Mandala?

Field Trial Focus

Purpose-built for agricultural experiments. Supports RCBD, alpha-lattice, row-column, and multi-environment trial designs out of the box.

Spatial Analysis

AR1×AR1 correlation structures and P-spline smoothing (pspline2D) with interactive variogram diagnostics for field heterogeneity.

Simple Syntax

Clean, intuitive formula interface. Specify fixed and random effects clearly—no steep learning curve required.

Heritability & BLUPs

Unified heritability estimates (Cullis, Piepho methods) and easy extraction of BLUPs/BLUEs for selection decisions.

Genomic Prediction

GBLUP with relationship matrices via GM(), cross-validation workflows, and high-level mandala_gp() wrapper for genomic selection.

Factor-Analytic G×E

Model complex genotype-by-environment interactions with FA() models, biplots, environment correlations, and reliability estimates.

Quick Start

Request free access from Listo Agriculture:

# Mandala is distributed directly by Listo Agriculture.
# 1. Request free access at https://listoagriculture.com/products
# 2. You will receive an email with installation instructions
# 3. Follow the emailed instructions to install from the Listo repository

Analyze a field trial in just a few lines:

library(mandala)

# Fit a Randomized Complete Block Design
model <- mandala(
  fixed  = yield ~ genotype,
  random = ~ block,
  data   = field_data
)

# View variance components
summary(model)$varcomp

# Get heritability estimates
h2 <- h2_estimates(random_mod = model_random, 
                   fixed_mod  = model, 
                   genotype   = "genotype")

# Extract BLUEs for selection
blues <- model$BLUEs

Supported Experimental Designs

RCBD

Randomized Complete Block Design with genotypes as fixed effects and blocks as random.

Alpha-Lattice

Incomplete block designs with nested blocking structure for large germplasm sets.

Row-Column

Resolvable designs accounting for both row and column effects in field layouts.

Multi-Environment

Analyze G×E with diagonal, FA, or heterogeneous variance structures across locations.

Spatial Models

AR1×AR1 correlation and P-spline (pspline2D) smoothing with variogram diagnostics.

Genomic Selection

GBLUP with relationship matrices, cross-validation, and two-stage genomic workflows.

Package Comparison

Wondering which package to use? Here’s how Mandala compares:

Feature	Mandala	Sommer	lme4	SpATS
Field trial focus	✓✓✓	✓✓	✓	✓✓✓
Spatial models	✓✓✓	✓✓✓	○	✓✓✓
P-spline spatial	✓✓✓	✓✓	○	✓✓✓
Genomic selection	✓✓✓	✓✓✓	○	○
Built-in two-stage workflow	✓✓✓	✓	○	○
Factor-analytic G×E	✓✓✓	✓✓	○	○
General purpose	✓	✓✓	✓✓✓	✓
Ease of use	✓✓✓	✓✓	✓✓	✓✓✓
Multi-trait (multivariate)	○	✓✓✓	○	○
Speed (typical trials)	✓✓✓	✓✓	✓✓✓	✓✓

✓✓✓ = Excellent | ✓✓ = Good | ✓ = Basic | ○ = Limited

Use Mandala when:

Analyzing standard field trial designs
Spatial modeling (AR1 or P-spline)
Genomic prediction (GBLUP) workflows
Factor-analytic G×E analysis
Multi-environment trial analysis
Two-stage workflow with uncertainty propagation

Consider alternatives when:

Multi-trait analysis (→ sommer)
General mixed models outside agriculture (→ lme4)
Need maximum flexibility (→ lme4/sommer)
Already invested in SpATS workflows (→ SpATS)

Learn More

Introduction to Mandala

Installation, key features, and your first analysis

Working with Example Datasets

RCBD, alpha-lattice, and multi-environment trial examples

Comparison with Sommer

Side-by-side analysis for quantitative genetics applications

Comparison with lme4

When to use Mandala vs general-purpose mixed models

Comparison with SpATS

P-spline spatial analysis and variogram diagnostics

About

Mandala is developed by Listo Agriculture, a software company specializing in tools for plant and animal breeding programs.

Mandala is free to use for any lawful purpose, including commercial use, with no restrictions on outputs. See the full Mandala License for details.

Citation

If you use Mandala in your research, please cite:

Bhoja R. Basnet (2025). mandala: Mixed Models with Modular G/R Structures.
R package version 1.0.1. https://listoagriculture.com/products