Analyses a line-by-tester trial by `REML`

(R.W. Payne).

### Options

`PRINT` = string tokens |
Specifies the output to be produced (`model` , `components` , `effects` , `means` , `monitoring` , `vcovariance` , `deviance` , `Waldtests` , `missingvalues` , `covariancemodels` , `aic` , `sic` , `bic` , `combinability` , `tests` ); default `mode` , `comp` , `wald` , `comb` , `test` |
---|---|

`PRECOVERY` = string tokens |
Controls what summary output is produced about the models that are tried during recovery (`deviance` , `aic` , `bic` , `sic` , `dffixed` , `dfrandom` , `change` , `exit` , `best` ); default `devi` , `aic` , `sic` , `dfra` , `best` |

`LINES` = factor |
Specifies the line (usually female parent); no default (must be specified) |

`TESTERS` = factor |
Specifies the tester (usually male parent); no default (must be specified) |

`CONTROLS` = factor |
Distinguishes between control and test (line × tester) genotypes; default is that there are no controls |

`FIXED` = formula |
Fixed model terms, in addition to the `TESTERS` main effect and any control comparisons; default `*` i.e. none |

`RANDOM` = formula |
Random model terms, in addition to the terms involving `LINES` , `TESTERS` and `EXPERIMENTS` that are included automatically; default `*` i.e. none |

`CONSTANT` = string token |
How to treat the constant term (`estimate` , `omit` ); default `esti` |

`FACTORIAL` = scalar |
Limit on the number of factors or covariates in each fixed term; default 3 |

`EXPERIMENTS` = factor |
Specifies the different experiments for a `REML` meta analysis; default is that the data are all from a single experiment |

`PCOMBINABILITYTERMS` = formula |
Terms whose combinability effects are to be printed, selected from `LINES` , `LINES.TESTERS` and their interactions with `EXPERIMENTS` ; default is to print all of them |

`PTERMS` = formula |
Terms (fixed or random) for which effects or means are to be printed; default `*` implies all the fixed terms |

`PSE` = string token |
Standard errors to be printed with tables of effects and means (`differences` , `estimates` , `alldifferences` , `allestimates` , `none` ); default `diff` |

`MVINCLUDE` = string tokens |
Whether to include units with missing values in the explanatory factors and variates and/or the y-variates (`explanatory` , `yvariate` ); default `*` i.e. omit units with missing values in either explanatory factors or variates or y-variates |

`RECOVER` = string token |
Whether to try to recover with a simpler random model if `REML` cannot fit the model (`yes` , `no` ); default `no` |

`METHOD` = string token |
How to choose the best model during recovery (`aic` , `sic` , `bic` ); default `sic` |

### Parameters

`Y` = variates |
Response variates |
---|---|

`COMBINABILITY` = pointers |
Pointer to tables of combinability effects for each y-variate |

`SECOMBINABILITY` = pointers |
Pointer to tables of standard errors of combinability effects for each y-variate |

`DEVIANCES` = variates |
Saves deviances for `LINES` , `LINES.TESTERS` and their interactions with `EXPERIMENTS` |

`EXIT` = scalars |
Exit status for each y-variate (zero to indicate that the analysis was successful) |

`SAVE` = REML save structures |
Save structure from the analysis of each y-variate |

### Description

`VLINEBYTESTER`

does a mixed-model analysis of data from a line-by-tester trial, using `REML`

. These are trials in which several “lines” (usually female parents) are all mated with a smaller number of testers (usually male parents). Generally, all combinations of parent will be present in the trial, but incomplete arrangements, such as diallels, are also possible. Control, or check, genotypes may also be present.

The lines must be specified (in a factor) by the `LINES`

option. Similarly, the testers must be specified (again in a factor) by the `TESTERS`

option. If there are any control genotypes, these are specified by using the `CONTROLS`

option to supply a factor with a different level for each control genotype, and a single level for all the line-by-tester genotypes.

You can use the `FIXED`

and `RANDOM`

options to specify fixed and random terms to be fitted in the analysis. The `FACTORIAL`

option sets a limit on the number of factors and variates allowed in each fixed term (default), and the `CONSTANT`

option can be set to omit the constant.

By default, the testers main effect is treated as fixed, so it will be added to any fixed model that you specify. However, you can put `TESTERS`

into the random model (specified by `RANDOM`

), if you would prefer it to be treated as random. Likewise, the main effect of the `CONTROLS`

factor (comparisons amongst control genotypes, and between controls and the mean of the tests) is treated as fixed, but can be put into the random model if you prefer. The model terms `LINES`

and `LINES.TESTERS`

are treated as random, and so will be added automatically to any random model that is specified by `RANDOM`

. If an `EXPERIMENTS`

factor is specified, its main effect and its interactions with `LINES`

and `TESTERS`

are also added to the random model.

The `PRINT`

option specifies the output to be produced. Its settings are mainly the same as those of the `PRINT`

option of the `REML`

directive. There are extra settings `aic`

and `sic`

(with a synonym `bic`

) to print the Akaike and Schwarz (Bayesian) information coefficients, respectively. There is a setting `combinability`

to print the BLUPs for `LINES`

, `LINES.TESTERS`

and any interations with `EXPERIMENTS`

(within `CONTROLS`

, if specified). By default, with this setting, BLUPs are printed for all these terms. However, you can set the `PCOMBINABILITYTERMS`

option to a model formula specifying exactly which ones you want. Finally, there is an extra setting `tests`

to print deviances for `LINES`

, `LINES.TESTERS`

and their interations with `EXPERIMENTS`

, so that you can assess whether their effects are genuinely present.

The `PTERMS`

option operates as in `REML`

, to specify the terms whose means and effects are printed; the default is all the fixed terms. Likewise, the `PSE`

option controls the type of standard error that is displayed with the means and effects; the default is to give a summary of the standard errors of differences.

The `MVINCLUDE`

option controls whether units with missing values in the explanatory factors and variates and/or the y-variate are included in the analysis, as in the `REML`

directive.

`REML`

may be unable to achieve a successful fit if the model contains more random terms than are actually needed to explain the random variation.(The `REML`

likelihood may be too flat for any clear optimum to be found.) You can guard against having specified an over-complicated random model using the `RANDOM`

option, by setting option `RECOVER=yes`

. `VLINEBYTESTER`

then tries models removing first one term from `RANDOM`

, then two and so on, until successful. Note: it regards a model as successful, if the `REML`

directive returns an exit status of zero (i.e. successful fitting) and there are no bound or aliased variance parameters.

The `METHOD`

option specifies how to choose the random (and spatial) model if there is more than one possible model with the same number of random terms removed:

`aic` |
uses their Akaike information coefficients, |
---|---|

`sic` or `bic` |
uses their Schwarz (Bayesian) information coefficients (default). |

The `PRECOVERY`

option specifies the summary output to be produced about the models that are fitted during recovery. The settings are mainly the same as those of the `VRACCUMULATE`

procedure (which is used to store and then print details of the analyses). There is an extra setting, `best`

, to print the description of the best model. The default is to print the best description, together with the deviance, the Akaike and Schwarz (Bayesian) information coefficients and the number of degrees, for all the models.

The `Y`

parameter specifies the response variate. The `COMBINABILITY`

parameter can save a pointer to tables containing the combinability BLUPs, requested by the `PCOMBINABILITYTERMS`

option. Similarly, the `SECOMBINABILITY`

parameter can save a pointer to tables containing the standard errors of the BLUPs. The `DEVIANCES`

parameter can save the deviances printed by the `test`

setting of `PRINT`

, in a variate. The `EXIT`

parameter allows you to save a code from `REML`

, giving the “exit status” of the fit (zero if successful). Finally, you can save the `REML`

save structure from the analysis with the best model, using the `SAVE`

parameter.

Options: `PRINT`

, `PRECOVERY`

, `LINES`

, `TESTERS`

, `CONTROLS`

, `FIXED`

, `RANDOM`

, `CONSTANT`

, `FACTORIAL`

, `EXPERIMENTS`

, `PCOMBINABILITYTERMS`

, `PTERMS`

, `PSE`

, `MVINCLUDE`

, `RECOVER`

, `METHOD`

.

Parameters: `Y`

, `COMBINABILITY`

, `SECOMBINABILITY`

, `DEVIANCES`

, `EXIT`

, `SAVE`

.

### See also

Directives: `REML`

, `VCOMPONENTS`

, `VSTRUCTURE`

.

Procedure: `VALINEBYTESTER`

, `VARECOVER`

.

Commands for: REML analysis of linear mixed models.

### Example

CAPTION 'VLINEBYTESTER example',!t(\ '33 lines x 2 testers and a check genotype,',\ 'in a resolvable incomplete block design'); STYLE=meta,plain SPLOAD [PRINT=*] '%gendir%/examples/VLIN-1.gsh' VLINEBYTESTER [LINES=Lines; TESTERS=Testers; CONTROLS=Controls;\ RANDOM=Replicates/Blocks] Yield