# Analysis of Selection Index in Plant Breeding

## Documentation for package ‘selection.index’ version 2.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

base_index | Base Index (Williams, 1962)
clgsi | Combined Linear Genomic Selection Index (CLGSI)
cppg_lgsi | Combined Predetermined Proportional Gains Linear Genomic Selection Index (CPPG-LGSI)
cpp_math_primitives | Generic C++ Math Primitives for Experimental Design Statistics
crlgsi | Combined Restricted Linear Genomic Selection Index (CRLGSI)
dg_lpsi | Desired Gains Index (DG-LPSI)
esim | Linear Phenotypic Eigen Selection Index (ESIM)
estimate_missing_values | Estimate Missing Values in Experimental Data
genetic_genomic_varcov | Genetic-Genomic Variance-Covariance Matrix (A)
genomic_varcov | Genomic Variance-Covariance Matrix (Gamma)
gen_advance | Genetic Advance for PRE
gen_varcov | Genotypic Variance-Covariance Analysis
gesim | Linear Genomic Eigen Selection Index Method (GESIM)
gw_esim | Genome-Wide Linear Eigen Selection Index Method (GW-ESIM)
gw_lmsi | Genome-Wide Linear Marker Selection Index (GW-LMSI)
haldane_mapping | Haldane's Mapping Function
inverse_haldane_mapping | Inverse Haldane Mapping Function
lgsi | Linear Genomic Selection Index (LGSI)
lmsi | Linear Marker Selection Index (LMSI)
lpsi | Combinatorial Linear Phenotypic Selection Index
maize_geno | Synthetic Maize Genomic Data
maize_pheno | Synthetic Maize Phenotypic Data
mean_performance | Mean performance of phenotypic data
mesim | Molecular Eigen Selection Index Method (MESIM)
missing-value | Missing Value Imputation for Experimental Designs
mlgsi | Multistage Linear Genomic Selection Index (MLGSI)
mlpsi | Multistage Linear Phenotypic Selection Index (MLPSI)
mppg_lgsi | Multistage Predetermined Proportional Gain Linear Genomic Selection Index (MPPG-LGSI)
mppg_lpsi | Multistage Predetermined Proportional Gain Linear Phenotypic Selection Index (MPPG-LPSI)
mrlgsi | Multistage Restricted Linear Genomic Selection Index (MRLGSI)
mrlpsi | Multistage Restricted Linear Phenotypic Selection Index (MRLPSI)
phenomic_genomic_varcov | Phenomic-Genomic Variance-Covariance Matrix (Phi)
phen_varcov | Phenotypic Variance-Covariance Analysis
plot.selection_simulation | Plot Method for Selection Simulation Results
ppg_esim | Predetermined Proportional Gain Eigen Selection Index (PPG-ESIM)
ppg_gesim | Predetermined Proportional Gain Genomic Eigen Selection Index (PPG-GESIM)
ppg_lgsi | Predetermined Proportional Gains Linear Genomic Selection Index (PPG-LGSI)
ppg_lpsi | Predetermined Proportional Gains (PPG-LPSI)
predict_selection_score | Predict selection index scores
print.base_index | Print method for Base Index
print.dg_lpsi | Print method for Desired Gains Index
print.esim | Print method for ESIM
print.gesim | Print method for GESIM
print.gw_esim | Print method for GW-ESIM
print.mesim | Print method for MESIM
print.ppg_esim | Print method for PPG-ESIM
print.ppg_gesim | Print method for PPG-GESIM
print.resim | Print method for RESIM
print.rgesim | Print method for RGESIM
print.selection_simulation | Print Method for Selection Simulation Results
print.smith_hazel | Print method for Smith-Hazel Index
resim | Restricted Linear Phenotypic Eigen Selection Index (RESIM)
rgesim | Restricted Linear Genomic Eigen Selection Index Method (RGESIM)
rlgsi | Restricted Linear Genomic Selection Index (RLGSI)
rlpsi | Restricted Linear Phenotypic Selection Index (RLPSI)
seldata | Selection Index DataSet
simulate_selection_cycles | Simulate Multi-Cycle Selection Using Different Indices
smith_hazel | Smith-Hazel Linear Phenotypic Selection Index
summary.base_index | Summary method for Base Index
summary.dg_lpsi | Summary method for Desired Gains Index
summary.esim | Summary method for ESIM
summary.gesim | Summary method for GESIM
summary.gw_esim | Summary method for GW-ESIM
summary.mesim | Summary method for MESIM
summary.ppg_esim | Summary method for PPG-ESIM
summary.ppg_gesim | Summary method for PPG-GESIM
summary.resim | Summary method for RESIM
summary.rgesim | Summary method for RGESIM
summary.selection_simulation | Summary Method for Selection Simulation Results
summary.smith_hazel | Summary method for Smith-Hazel Index
weight | Weight dataset
weight_mat | Convert dataframe to matrix