Generates an inverse relationship matrix for use when fitting animal or plant breeding models by REML.
Options
SEX = string token |
Possible sex categories of parents (fixed, either); default fixe |
|---|---|
UNKNOWN = scalar |
Value to be treated as unknown |
Parameters
INDIVIDUALS = factors |
Individuals on which data has been measured |
|---|---|
MALEPARENTS = factors |
Male parents of the progeny |
FEMALEPARENTS = factors |
Female parents of the progeny |
INVERSE = pointer |
Inverse relationship matrix in sparse matrix form |
POPULATION = variates |
Full list of identifiers generated from the individuals and parents |
Description
VPEDIGREE is used to generate a sparse inverse relationship matrix for use when fitting animal (or plant) breeding models by REML. The algorithm requires three parallel factors as input. The numerical levels of these factors must give identifiers for the individuals from which data are available (INDIVIDUALS) and the identifiers for the male and female parents for each individual (MALEPARENTS and FEMALEPARENTS). Note that an individual may appear as both progeny and a parent (for example, when data has been taken from several generations) and conversely, that if an identifier appears in more than one list then it is assumed to refer to a single individual. Also, the algorithm does not take account of labels, so where textual labels are used the labels vectors of the three factors should be identical in order to generate matching levels vectors and thus avoid errors. A complete list of all individuals in the three factors is compiled and can be saved using the POPULATION option, and on output, the three factors will be redefined with this list as their levels vector.
The inverse relationship matrix that is generated is held in a special sparse matrix form (that is, only non-zero values are stored), using a pointer. This is usable in the VSTRUCTURE directive but not, currently, elsewhere in Genstat. The second element of the pointer is a variate storing the non-zero values of the inverse matrix in lower-triangular order. The first element of the pointer is an integer index vector. This vector is not a standard Genstat data structure, and so cannot be used except by VSTRUCTURE.
By default, it is assumed that an individual can act as either a male or female parent but not both. Option SEX=either can be used to specify that individuals can act as both male and female parents. This may be useful, for example, in plant breeding analyses.
Missing values in any of the factors will be treated as coding for unknown individuals. Option UNKNOWN allows you to specify an additional scalar value used to represent unknown individuals.
Options: SEX, UNKNOWN.
Parameters: INDIVIDUALS, MALEPARENTS, FEMALEPARENTS, INVERSE, POPULATION.
Action with RESTRICT
VPEDIGREE ignores any restrictions on the factors.
See also
Directives: REML, VCOMPONENTS, VSTRUCTURE, VRESIDUAL, VSTATUS.
Procedure: VFPEDIGREE.
Commands for: REML analysis of linear mixed models.
Example
" Example REML-6: genetic analysis example
(Harvey, W.R. (1977). Users' guide to LSML76)."
SPLOAD '%GENDIR%/Examples/harvey.gsh'
VPEDIGREE [UNKNOWN=0] INDIVIDUALS=Calf; MALEPARENTS=Sire; FEMALEPARENTS=Dam;\
INVERSE=inv; POPULATION=pop
VCOMPONENTS [FIXED=Line] RANDOM=Calf
VSTRUCTURE [TERMS=Calf] MODEL=fixed; INVERSE=inv
REML [PRINT=model,components,effects,means,vcovariance,Waldtests]\
Y=Y3; SAVE=harvey
" Calculate heritability "
VKEEP [VESTIMATE=vestim]
CALCULATE h2 = vestim$[1]/(1+vestim$[1])
PRINT 22; HEADING='Heritability'