Single Environment REML Analysis Further Output

Use this to select further output following a preliminary single environment REML analysis.

Model for further output

The preliminary single environment analysis runs a REML analysis twice. In the first analysis the genotypes are used as a random term and in the second analysis they are fitted as a fixed term. This option lets you select further output for either of these REML models.

Display

This specifies which items of output are to be produced by the analysis.

Model	Description of the model fitted by the analysis
Variance components	Estimates of variance parameters
Estimated effects	Estimates of regression coefficients
Stratum variances	Estimates of approximate stratum variances
Covariance model	Estimated covariance models in matrix format
Heritability	For the model where the genotype factor is fitted as a random term this displays the measure of heritability
Variance-covariance matrix	Variance-covariance matrix for the variance parameters
Deviance	The residual deviance
Wald tests	Wald Tests for fixed model terms and accompanying F-statistics
Missing value estimates	Estimates of missing values
Monitoring	Monitoring information at each iteration
Akaike information coefficient (AIC)	Akaike information coefficient to assess the random model
Schwarz information coefficient (SIC)	Schwarz information coefficient to assess the random model

Standard Errors

Tables of effects are accompanied by estimates of standard errors. You can choose whether Genstat computes standard errors or standard errors of differences (SEDs) for the tables.

Method for calculating F-statistics

This controls whether Wald tests for fixed effects are accompanied with approximate F statistics and corresponding numbers of residual degrees of freedom. The computations, using the method devised by Kenward & Roger (1997), can be time consuming with large or complicated models. So, the default setting automatic, can be used to allow Genstat to assess the model itself and decide automatically whether to do the computations and which method to use. The other settings allow you to control what to do yourself:

none	No F statistics are produced
algebraic	F statistics are calculated using algebraic derivatives (which may involve large matrix calculations)
numerical	F statistics are calculated using numerical derivatives (which require an extra evaluation of the mixed model equations for every variance parameter).

Graphics

The residual plots button can be used to generate plots of residuals. For the spatial models use the Display variogram button to display the residuals in a variogram.

Action Icons

	Pin	Controls whether to keep the dialog open when you click Run. When the pin is up the dialog will remain open, otherwise when the pin is down the dialog will close.
	Clear	Clear all fields and list boxes.
	Help	Open the Help topic for this dialog.