Smith_Hazel {metan} | R Documentation |
Smith-Hazel index
Description
Computes the Smith (1936) and Hazel (1943) index given economic weights and phenotypic and genotypic variance-covariance matrices. The Smith-Hazel index is computed as follows: \[\bf{b = P^{-1}Aw}\]
where \(\bf{P}\) and \(\bf{G}\) are phenotypic and genetic covariance matrices, respectively, and \(\bf{b}\) and \(\bf{w}\) are vectors of index coefficients and economic weightings, respectively.
The genetic worth \(I\) of an individual genotype based on traits x, y, ..., n, is calculated as:
\[I = b_xG_x + b_yG_y + ... + b_nG_n\]where b the index coefficient for the traits x, y, ..., n, respectively, and G is the individual genotype BLUPs for the traits x, y, ..., n, respectively.
Usage
Smith_Hazel(
.data,
use_data = "blup",
pcov = NULL,
gcov = NULL,
SI = 15,
weights = NULL
)
Arguments
.data |
The input data. It can be either a two-way table with genotypes
in rows and traits in columns, or an object fitted with the function
|
use_data |
Define which data to use If |
pcov , gcov |
The phenotypic and genotypic variance-covariance matrix,
respectively. Defaults to |
SI |
The selection intensity (percentage). Defaults to |
weights |
The vector of economic weights. Defaults to a vector of 1s with the same length of the number of traits. |
Details
When using the phenotypic means in .data
, be sure the genotype's code
are in rownames. If .data
is an object of class gamem
them the
BLUPs for each genotype are used to compute the index. In this case, the
genetic covariance components are estimated by mean cross products.
Value
An object of class hz
containing:
-
b: the vector of index coefficient.
-
index: The genetic worth.
-
sel_dif_trait: The selection differencial.
-
sel_gen: The selected genotypes.
-
gcov: The genotypic variance-covariance matrix
-
pcov: The phenotypic variance-covariance matrix
Author(s)
Tiago Olivoto tiagoolivoto@gmail.com
References
Smith, H.F. 1936. A discriminant function for plant selection. Ann. Eugen. 7:240-250. doi:10.1111/j.1469-1809.1936.tb02143.x
Hazel, L.N. 1943. The genetic basis for constructing selection indexes. Genetics 28:476-90. https://www.genetics.org/content/28/6/476.short
See Also
Examples
vcov <- covcor_design(data_g, GEN, REP, everything())
means <- as.matrix(vcov$means)
pcov <- vcov$phen_cov
gcov <- vcov$geno_cov
index <- Smith_Hazel(means, pcov = pcov, gcov = gcov, weights = rep(1, 15))