Analyses a line-by-tester trial by
REML (R.W. Payne).
|Specifies the output to be produced (
||Controls what summary output is produced about the models that are tried during recovery (
||Specifies the line (usually female parent); no default (must be specified)|
||Specifies the tester (usually male parent); no default (must be specified)|
||Distinguishes between control and test (line × tester) genotypes; default is that there are no controls|
||Fixed model terms, in addition to the
||Random model terms, in addition to the terms involving
||How to treat the constant term (
||Limit on the number of factors or covariates in each fixed term; default 3|
||Specifies the different experiments for a
||Terms whose combinability effects are to be printed, selected from
||Terms (fixed or random) for which effects or means are to be printed; default
||Standard errors to be printed with tables of effects and means (
||Whether to include units with missing values in the explanatory factors and variates and/or the y-variates (
||Whether to try to recover with a simpler random model if
||How to choose the best model during recovery (
||Pointer to tables of combinability effects for each y-variate|
||Pointer to tables of standard errors of combinability effects for each y-variate|
||Saves deviances for
||Exit status for each y-variate (zero to indicate that the analysis was successful)|
||Save structure from the analysis of each y-variate|
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
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.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
TESTERS are also added to the random model.
REML directive. There are extra settings
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.TESTERS and any interations with
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.TESTERS and their interations with
EXPERIMENTS, so that you can assess whether their effects are genuinely present.
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.
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 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
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.
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:
||uses their Akaike information coefficients,|
||uses their Schwarz (Bayesian) information coefficients (default).|
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.
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
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
Commands for: REML analysis of linear mixed models.
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