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selection.index

Stop wasting days manually assembling complex variance-covariance matrices and resolving selection weights. selection.index is the definitive, production-ready R package built specifically for agricultural statisticians and quantitative geneticists to instantly calculate optimal multi-trait selection indices. Whether you are running classical phenotypic field trials or building advanced genomic evaluations, this package provides a fully integrated mathematical engine that directly maximizes genetic advance and substantially accelerates your breeding pipeline.

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Install

install.packages('selection.index')

Monthly Downloads

633

Version

2.0.0

License

GPL (>= 3)

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Repository

https://github.com/zankrut20/selection.index

Homepage

https://zankrut20.github.io/selection.index/

Maintainer

Zankrut Goyani

Last Published

March 1st, 2026

Functions in selection.index (2.0.0)

Synthetic Maize Genomic Data

Synthetic Maize Phenotypic Data

Multistage Linear Genomic Selection Index (MLGSI)

Multistage Restricted Linear Genomic Selection Index (MRLGSI)

Multistage Linear Phenotypic Selection Index (MLPSI)

Multistage Restricted Linear Phenotypic Selection Index (MRLPSI)

Predetermined Proportional Gain Eigen Selection Index (PPG-ESIM)

multistage_genomic_indices

Multistage Linear Genomic Selection Indices (Chapter 9)

haldane_mapping

Haldane's Mapping Function

mean_performance

Mean performance of phenotypic data

Linear Genomic Eigen Selection Index Method (GESIM)

Genome-Wide Linear Eigen Selection Index Method (GW-ESIM)

Genome-Wide Linear Marker Selection Index (GW-LMSI)

Predetermined Proportional Gain Genomic Eigen Selection Index (PPG-GESIM)

Genomic Variance-Covariance Matrix (\(\Gamma\))

Linear Marker Selection Index (LMSI)

multistage_phenotypic_indices

Multistage Linear Phenotypic Selection Indices (Chapter 9)

Linear Marker and Genome-Wide Selection Indices (Chapter 4)

Multistage Predetermined Proportional Gain Linear Genomic Selection Index (MPPG-LGSI)

Multistage Predetermined Proportional Gain Linear Phenotypic Selection Index (MPPG-LPSI)

Combinatorial Linear Phenotypic Selection Index

phenotypic_indices

Phenotypic Selection Indices (Chapter 2)

phenomic_genomic_varcov

Phenomic-Genomic Variance-Covariance Matrix (\(\Phi\))

Phenotypic Variance-Covariance Analysis

Print method for GESIM

plot.selection_simulation

Plot Method for Selection Simulation Results

Print method for GW-ESIM

Print method for MESIM

Print method for Desired Gains Index

Print method for ESIM

print.smith_hazel

Print method for Smith-Hazel Index

Predetermined Proportional Gains Linear Genomic Selection Index (PPG-LGSI)

Restricted Linear Phenotypic Eigen Selection Index (RESIM)

Missing Value Imputation for Experimental Designs

Linear Genomic Selection Index (LGSI)

inverse_haldane_mapping

Inverse Haldane Mapping Function

Molecular Eigen Selection Index Method (MESIM)

print.ppg_gesim

Print method for PPG-GESIM

Selection Index DataSet

Summary method for GESIM

Print method for RESIM

Summary method for ESIM

Restricted Linear Phenotypic Selection Index (RLPSI)

summary.selection_simulation

Summary Method for Selection Simulation Results

Print method for PPG-ESIM

Predetermined Proportional Gains (PPG-LPSI)

Print method for RGESIM

print.selection_simulation

Print Method for Selection Simulation Results

summary.gw_esim

Summary method for GW-ESIM

predict_selection_score

Predict selection index scores

print.base_index

Print method for Base Index

Restricted Linear Genomic Eigen Selection Index Method (RGESIM)

Summary method for MESIM

summary.dg_lpsi

Summary method for Desired Gains Index

summary.base_index

Summary method for Base Index

simulate_selection_cycles

Simulate Multi-Cycle Selection Using Different Indices

selection.index-package

selection.index: Analysis of Selection Index in Plant Breeding

summary.ppg_gesim

Summary method for PPG-GESIM

summary.ppg_esim

Summary method for PPG-ESIM

summary.smith_hazel

Summary method for Smith-Hazel Index

Summary method for RGESIM

Summary method for RESIM

Smith-Hazel Linear Phenotypic Selection Index

stochastic_simulation

Stochastic Simulation of Selection Indices (Chapter 10)

Convert dataframe to matrix

Restricted Linear Genomic Selection Index (RLGSI)

cpp_math_primitives

Generic C++ Math Primitives for Experimental Design Statistics

constrained_genomic_indices

Constrained Genomic Selection Indices

Base Index (Williams, 1962)

Combined Restricted Linear Genomic Selection Index (CRLGSI)

Desired Gains Index (DG-LPSI)

Combined Linear Genomic Selection Index (CLGSI)

constrained_indices

Constrained Phenotypic Selection Indices (Chapter 3)

Combined Predetermined Proportional Gains Linear Genomic Selection Index (CPPG-LGSI)

C++ Function Wrappers with Uniform Validation

Package Constants

genomic_indices

Genomic Selection Indices

genetic_genomic_varcov

Genetic-Genomic Variance-Covariance Matrix (A)

Genotypic Variance-Covariance Analysis

Linear Phenotypic Eigen Selection Index Methods (Chapter 7)

estimate_missing_values

Estimate Missing Values in Experimental Data

Linear Phenotypic Eigen Selection Index (ESIM)

Genetic Advance for PRE

genomic_eigen_indices

Linear Molecular and Genomic Eigen Selection Index Methods (Chapter 8)

Genomic Variance-Covariance Functions