New/Changed job control qualifiers

Introduction

These changes are associated with Chapter 5 in the User guide. The following qualifiers have been added or modified.

General Job Control Qualifiers

!DEFINE s t p     Formerly !CONTRAST, it provides a convenient way to define how particular effects, 'contrasts' among treatment levels, are defined in the linear model. !DEFINE lines occur as separate lines between the datafile line and the model line. For example
!DEFINE LinN Nitrogen 3 1 -1 -3
defines LinN as a 'contrast' based on the 4 (implied by the length of the list) levels of factor Nitrogen. Missing values in the factor become missing values in the 'contrast'. Zero values in the factor (no level assigned) become zeros in the 'contrast'.

!NOZEROVC     suppresses the (new) default action of fixing simple variance components exactly at 0.0 rather than fixing them at a small value. This is equivalent to dropping the term from the model. The default action applies to simple components, elements in a diag() structure and Ψ values in the extended factor analytic models.

!S2LIMIT     limits the size of the residual variance in a multi-environment spatial analysis to a tenth of the average spatial residual variance across all environments, fixing it at that small but not unreasonable value if the updated value is smaller. The motivation is that occasionally in unreplicated trials with a nugget variance also fitted, the spatial variance is poorly estimated and will otherwise go to almost zero, which may cause ASReml to fail.

Job Saving the Coefficient Matrix and Related Matrices

ASReml 4.3 has a few qualifiers to generate and save the coefficient matrix C and its inverse. All forms are typically sparse, and only the known non-zero cells are written.
!CINV [t]     writes the known cells in the sparse portion of the C inverse, pertaining to model term t, to basename.cii. The known cells are primarily those that were not zero before inversion. The .cii file is ASCII sparse stored with row column value for each known cell, lower triangle row-wise.

!CMAT, !CPMAT, !CAMAT, !CIPMAT, !CIMAT, !DOUBLE     output matrices to facilitate research into effcient processing of the C matrix of the mixed model equations. They write five forms of C as follows
  • !CMAT writes basename_Cmat.bin, C in model order,
  • !CPMAT writes basename_CPmat.bin, C permuted to analysis order,
  • !CAMAT writes basename_CAmat.bin, C absorbed in analysis order,
  • !CIPMAT writes basename_CIPmat.bin, the sparse C-1 in analysis order,
  • !CIMAT writes basename_CImat.bin, the sparse C-1 in model order,
  • !DOUBLE stores the column numbers and matrix values in double precision. with file extension .dbin.

    The ASReml User Guide discusses the format of these files and how to read them.

    Deprecated and Superseded Functions Qualifiers

    The following qualifiers are now deprecated and superseded.

    !CONTRAST     has been renamed !DEFINE because the variate inserted in the model is not necessarily a formal treatment (sum to zero) contrast, and the fitted effect is not necessarily the contrast that may be expected.

    !VCC n Its functionality has been replaced with the directive used for linking variance parameters.
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