int.matrix {lmDiallel}

Utilities for fitting diallel models.

Description

These functions are used internally by the package, but they can also called from the outside, to fit specific needs

Usage

int.matrix(Xa, Xb)
checkScheme(P1, P2)
emm.diallel(obj)

Arguments

Xa

Incidence matrix of genetic effects

Xb

Incidence matrix for an external factor

P1

A vector with parentals

P2

A vector with parentals

obj

A glht object

Details

The function 'int.matrix()' produces the incidence matrix for the interaction between two main effects; 'Xa' and 'Xb' are two incidence matrices for two main effects. The function 'checkScheme()' takes two vectors containing the codings for parentals (P1 and P2), retrieves the mating scheme and detects whether there are missing crosses. The function 'emm.diallel()' is used with multi-environment diallel experiments to obtain the expected marginal means for genetic effects across environments.

Value

The function 'int.matrix()' returns an incidence matrix. The function 'checkScheme()' returns a list, containing the main traits of the mating scheme. The function 'emm.diallel()' retrns a data.frame with the marginal means, standard errors and t-test statistics.

Note

No further notes

Author(s)

Andrea Onofri

References

Onofri, A., Terzaroli, N. & Russi, L. Linear models for diallel crosses: a review with R functions. Theor Appl Genet (2020). https://doi.org/10.1007/s00122-020-03716-8

Examples

data(griffing56)
head(griffing56)
checkScheme(griffing56$Par1, griffing56$Par2)