heritability: Marker-Based Estimation of Heritability Using Individual Plant or Plot Data

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Implements marker-based estimation of heritability when observations on genetically identical replicates are available. These can be either observations on individual plants or plot-level data in a field trial. Heritability can then be estimated using a mixed model for the individual plant or plot data. For comparison, also mixed-model based estimation using genotypic means and estimation of repeatability with ANOVA are implemented. For illustration the package contains several datasets for the model species Arabidopsis thaliana.

Author
Willem Kruijer, with a contribution from Ian White (the internal function pin). Contains data collected by Padraic Flood and Rik Kooke.
Date of publication
2015-02-10 19:49:03
Maintainer
Willem Kruijer <willem.kruijer@wur.nl>
License
GPL-3
Version
1.1
URLs

View on CRAN

Man pages

BT_LW_H
Bolting time and leaf width for the Arabidopsis hapmap...
floweringTime
Flowering time data taken from Atwell _et al._ (2010).
heritability-package
Marker-Based Estimation of Heritability Using Individual...
K_arabidopsis
Marker-based relatedness matrices for 3 populations of...
leafArea
_Arabidopsis_ leaf area data for the hapmap and Swedish...
marker_h2
Compute a marker-based estimate of heritability, given...
marker_h2_means
Compute a marker-based estimate of heritability, given...
means_floweringTime
Flowering time from Atwell _et al._ (2010): accession means.
repeatability
ANOVA-based estimates of repeatability
R_matrix
Covariance matrix of the accession means for flowering time.

Files in this package

heritability
heritability/NAMESPACE
heritability/data
heritability/data/K_hapmap.rda
heritability/data/BT_LW_H.rda
heritability/data/R_matrix_LDV.rda
heritability/data/LA_S.rda
heritability/data/LDV.rda
heritability/data/R_matrix_LD.rda
heritability/data/means_LD.rda
heritability/data/LD.rda
heritability/data/K_atwell.rda
heritability/data/datalist
heritability/data/K_swedish.rda
heritability/data/LA_H.rda
heritability/data/means_LDV.rda
heritability/R
heritability/R/repeatability.R
heritability/R/GINV.R
heritability/R/pin.R
heritability/R/marker_h2_means.r
heritability/R/AI_algorithm_weights.r
heritability/R/KinshipTransform.R
heritability/R/marker_h2.R
heritability/R/AI_algorithm.R
heritability/MD5
heritability/DESCRIPTION
heritability/man
heritability/man/BT_LW_H.Rd
heritability/man/repeatability.Rd
heritability/man/marker_h2_means.Rd
heritability/man/K_arabidopsis.Rd
heritability/man/means_floweringTime.Rd
heritability/man/heritability-package.Rd
heritability/man/leafArea.Rd
heritability/man/R_matrix.Rd
heritability/man/marker_h2.Rd
heritability/man/floweringTime.Rd