heritability-package {heritability} | R Documentation |
Marker-Based Estimation of Heritability Using Individual Plant or Plot Data.
Description
The package implements marker-based estimation
of heritability when observations on genetically identical replicates are available.
These can be either observations on individual plants (e.g. in a growth chamber) or plot-level data in a field trial.
The function marker_h2
estimates heritability using a mixed model for the
individual plant or plot data, as proposed in Kruijer et al.
For comparison, also mixed-model based estimation using genotypic means (marker_h2_means
)
and estimation of repeatability with ANOVA (repeatability
) are implemented.
For illustration the package contains several datasets for the model species Arabidopsis thaliana.
Author(s)
Willem Kruijer Maintainer: Willem Kruijer <willlem.kruijer@wur.nl>
References
Kruijer, W. et al. (2015) Marker-based estimation of heritability in immortal populations. Genetics, Vol. 199(2), p. 1-20.
Examples
# A) marker-based estimation of heritability, given individual plant-data
# and a marker-based relatedness matrix:
data(LDV)
data(K_atwell)
# This may take up to 30 sec.
#out1 <- marker_h2(data.vector=LDV$LDV,geno.vector=LDV$genotype,
# covariates=LDV[,4:8],K=K_atwell)
#
# B) marker-based estimation of heritability, given genotypic means
# and a marker-based relatedness matrix:
data(means_LDV)
data(R_matrix_LDV)
data(K_atwell)
out2 <- marker_h2_means(data.vector=means_LDV$LDV,geno.vector=means_LDV$genotype,
K=K_atwell,Dm=R_matrix_LDV)
#
# C) estimation of repeatability using ANOVA:
data(LDV)
out3 <- repeatability(data.vector=LDV$LDV,geno.vector= LDV$genotype,
covariates.frame=as.data.frame(LDV[,3]))