1. Home
  2. VALINEBYTESTER procedure

VALINEBYTESTER procedure

Provides combinabilities and deviances for a line-by-tester trial analysed by VABLOCKDESIGN or VAROWCOLUMNDESIGN (R.W. Payne).

Options

PRINT = string tokens Controls what summary output is produced about the models (combinability, tests); default comb, test
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
PCOMBINABILITYTERMS = formula Terms whose combinability effects are to be printed (LINES and/or LINES.TESTERS; default is to print both of them
MVINCLUDE = string tokens When the SAVE parameter is not set, this specifies 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
VCONSTRAINTS = string token Whether to constrain variance components to be positive (none, positive); default none

Parameters

Y = variates Response variates
MODELSTRUCTURE = pointers Model-definition structure used for the analysis of each y-variate
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 and LINES.TESTERS
SAVE = REML save structures Save structure from the analysis of each y-variate

Description

VALINEBYTESTER provides further output for a line-by-tester trial, already analysed using VABLOCKDESIGN or VAROWCOLUMNDESIGN. 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 factor used to define the lines must be specified by the LINES option. Similarly, the testers factor must be specified by the TESTERS option. If there are any control genotypes, their factor must be specified by the CONTROLS option; this should have a different level for each control genotype, and a single level for all the line-by-tester genotypes.

The PRINT option specifies the output to be produced, with settings:

    combinability to print the BLUPs for LINES (i.e. SCA) and/or LINES.TESTERS (i.e. GCA), within CONTROLS if specified, and
    tests to print deviances for LINES, LINES.TESTERS.

You can set the PCOMBINABILITYTERMS option to a model formula specifying exactly which of the combinability terms you want; by default, both are printed.

You can define the analysis with either the MODELSTRUCTURE or the SAVE parameter or, preferably, both. The SAVE parameter specifies the REML save structure from the analysis. This used to obtain the combinability effects. The MODELSTRUCTURE parameter specifies the model-definition structure for the analysis. This is needed to calculate the deviances, and also allows a save structure to be formed if SAVE is not set. If both MODELSTRUCTURE and SAVE are specified, VALINEBYTESTER aims to check that the save structure genuinely corresponds to the supplied model structure, in case of mistakes. However, the checks are not foolproof, so you do need to be careful. When the SAVE parameter is unset, MVINCLUDE specifies whether to include units with missing values in the explanatory factors and variates and/or the y-variates in the analyses. (When SAVE is set, the units to include can be determined from the save structure.)

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.

Options: PRINT, LINES, TESTERS, CONTROLS, PCOMBINABILITYTERMS, MVINCLUDE, VCONSTRAINTS.

Parameters: Y, MODELSTRUCTURE, COMBINABILITY, SECOMBINABILITY, DEVIANCES, SAVE.

See also

Directives: REML, VCOMPONENTS, VSTRUCTURE.

Procedures: VABLOCKDESIGN, VAROWCOLUMNDESIGN, VLINEBYTESTER.

Commands for: REML analysis of linear mixed models.

Example

CAPTION        'VALINEBYTESTER 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'
VABLOCKDESIGN  [PRINT=best,description,deviance,aic,bic,dfrandom;\
               FIXED=Controls/Testers; RANDOM=Controls.Lines/Testers;\
               REPLICATES=Replicates; BLOCKS=Blocks; RSTRATEGY=optimal]\
               Yield; BESTMODEL=bestmodel; SAVE=save
VALINEBYTESTER [LINES=Lines; TESTERS=Testers; CONTROLS=Controls]\
               Yield; MODEL=bestmodel; SAVE=save
Updated on June 17, 2019

Was this article helpful?