calculateH2: Compute the broad-sense heritability from a mixed model...

In digiYozhik/msc_thesis: Functions to support master thesis

Description

The broad-sense heritability (H^2) is computed from the variance components from a linear mixed model

list(list("V_G"))

the genetic variance components

list(list("V_E"))

the residual variance component

Usage

calculateH2(model, which = c("line-mean", "overall"),
  genetic.factor = "GERMPLASM", by.location = FALSE, data = NULL,
  checks = NULL)

Arguments

model	An asreml-object, see asreml.
which	A character string/vector specifying which heritability measure to compute, choose from "line-mean" and "overall". By default both measures are computed.
genetic.factor	(Optional) Character string specifying the name of the genetic factor in the model. Default = "GERMPLASM".
by.location	Logical indicating whether to compute the heritability on location-basis or across locations. Default = FALSE.
data	(Optional) The data frame used in the preceeding asreml-call.
checks	(Optional) The names of the check-lines in the genetic.factor-column in data.

Details

The two approaches for calculating H^2:

which =

H^2 = \frac{V_G}{V_G + V_E}

list("\"overall\"")

H^2 = \frac{V_G}{V_G + V_E}

which =

H^2 = \frac{V_G}{V_G + V_E/r}

list("\"overall\"")

H^2 = \frac{V_G}{V_G + V_E/r}

Value

A data frame with the estimated genetic-, GxE- and residual standard deviations and the computed heritability.

Author(s)

Ruud Derijcker, Katrien Baert

digiYozhik/msc_thesis documentation built on May 14, 2019, 5:16 p.m.