Prepares pedigree information to generate an inverse relationship matrix for use when fitting animal or plant breeding models by `REML`

(S.A. Gezan & R.W. Payne).

### Options

`FREPRESENTATION` = string token |
Whether to match factor values by their levels or their labels (`levels` , `labels` ); default `leve` |
---|---|

SEX = string token |
Possible sex categories of parents (`fixed` , `either` ); default `fixe` |

`UNKNOWN` = scalar or string |
Value to be treated as unknown in the pedigree factors |

INVMETHOD = string token |
How to represent the `INVERSE` (`full` , `sparse` ); default `spar` |

### Parameters

`INDIVIDUALS` = factors |
Individuals on which data have been measured |
---|---|

`MALEPARENTS` = factors |
Male parents (or sires) of the progeny |

`FEMALEPARENTS` = factors |
Female parents (of dams) of the progeny |

`NEWINDIVIDUALS` = factors |
New individuals factor, with levels standardized for use in `VPEDIGREE` |

`NEWMALEPARENTS` = factors |
New males factor, with levels standardized to match those in the `NEWINDIVIDUALS` factor |

`NEWFEMALEPARENTS` = factors |
New females factor, with levels standardized to match those in the `NEWINDIVIDUALS` factor |

`OTHERFACTORS` = pointers |
Pointer containing additional factors, that may be used in the `REML` models, whose levels must also be standardized to match those in the `NEWINDIVIDUALS` factor |

`NEWOTHERFACTORS` = pointers |
Pointer containing new additional factors, with standardized levels |

`INVERSE` = pointer |
Inverse relationship matrix in sparse matrix form |

`POPULATION` = variates |
Full list of identifiers generated from the individuals and parents |

### Description

In the analysis of animal and plant breeding experiments it may be interesting to take account of the parentage of the animals or genotypes. This *pedigree* information is specified by three factors, one that identifies the individuals for which data are available, and two others that indicate their male parents and their female parents (if available). This information can be used to generate a sparse inverse relationship matrix that can be used by `VSTRUCTURE`

to define a correlation model of the individual (or animal) effects for use in a `REML`

analysis. The matrix is formed using the `VPEDIGREE`

directive. First, however, `VPEDIGREE`

needs to standardize the factors so that the levels and labels of the individual male and female factors match, and that the levels are in ascending order, with the parents defined in the individuals factor before their offspring. Otherwise `VPEDIGREE`

will fail. If you are confident that your factors are already standardized, you can call `VPEDIGREE`

direct (and use VFPEDIGREE instead if that fails).

The factors defining the individuals, the male parents (or sires) and, optionally, the female parents (or dams) in the pedigree data set.are specified by the `INDIVIDUALS`

, `MALEPARENTS`

and `FEMALEPARENTS`

parameters respectively. The `OTHERFACTORS`

parameter can specify a pointer containing additional factors, involving the individuals in the pedigree, that may also be needed in the `REML`

models. You can use the `NEWINDIVIDUALS`

, `NEWMALEPARENTS`

, `NEWFEMALEPARENTS`

and the `NEWOTHERFACTORS`

parameter parameters to save the new standardized factors. Otherwise, the original factors are redefined.

The `FREPRESENTATION`

option indicates whether the factor values are to be matched by their levels (the default) or their labels. If the `INDIVIDUALS`

, `MALEPARENTS`

and `FEMALEPARENTS`

factors are being matched by levels, and the number corresponding to each level needs to be redefined, the factors will be given labels to help identify the original values. If `INDIVIDUALS`

has labels, these will be used. Otherwise the labels will be textual forms of the original levels.

The `POPULATION`

option can save the levels of the standardized factors when `FREPRESENTATION=levels`

, or their labels when `FREPRESENTATION=labels`

.

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 code to represent unknown individuals. This should be a scalar (e.g. 0 or -1) when `FREPRESENTATION=levels`

, or a single-valued text (e.g. `'*'`

or `'0'`

) when `FREPRESENTATION=labels`

.

The inverse relationship matrix can be saved by the `INVERSE`

parameter. By default, this 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 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. Alternatively, you can set option `INVMETHOD=full`

to store the full matrix as a symmetric matrix (which can also be used by `VSTRUCTURE`

). However, this is not recommended for large pedigrees.

Options: `FREPRESENTATION`

, `SEX`

, `UNKNOWN`

, `INVMETHOD`

.

Parameters: `INDIVIDUALS`

, `MALEPARENTS`

, `FEMALEPARENTS`

, `NEWINDIVIDUALS`

, `NEWMALEPARENTS`

, `NEWFEMALEPARENTS`

, `OTHERFACTORS`

, `NEWOTHERFACTORS`

, `INVERSE`

, `POPULATION`

.

### Action with `RESTRICT`

`VFPEDIGREE`

ignores any restrictions on the factors.

### See also

Directives: `REML`

, `VCOMPONENTS`

, `VPEDIGREE`

, `VSTRUCTURE`

, `VRESIDUAL`

, `VSTATUS`

.

Commands for: REML analysis of linear mixed models.

### Example

CAPTION 'VFPEDIGREE example'; STYLE=meta " Basic example of animal model" " Read the data: pedigree and response (in the same file)" " with levels all Individuals" FACTOR [NVALUES=5; LEVELS=!(3,4,5,6,7)] Indiv & [LEVELS=!(0,1,3,5)] Sire & [LEVELS=!(0,2,4,6)] Dam VARIATE [NVALUES=5] Size READ Indiv,Sire,Dam,Size; 3 1 0 12.8 4 1 2 14.5 5 3 4 11.2 6 1 4 12.6 7 5 6 9.9 : VFPEDIGREE [FREPRESENTATION=levels; UNKNOWN=0] Indiv; NEWIndivIDUALS=ID_Indiv;\ MALEPARENTS=Sire; NEWMALEPARENTS=ID_Sire;\ FEMALEPARENTS=Dam; NEWFEMALEPARENTS=ID_Dam;\ OTHERFACTORS=!p(Indiv); NEWOTHERFACTORS=!p(f_Indiv) VPEDIGREE [SEX=fixed] ID_Indiv; MALEPARENTS=ID_Sire; INVERSE=AINV;\ FEMALEPARENTS=ID_Dam VCOMPONENTS RANDOM=f_Indiv; CONSTRAINTS=pos VSTRUCTURE [TERMS=f_Indiv] MODEL=fixed; INVERSE=AINV REML [PRINT=model,components,means; PARAM=sigmas] Size