Rarely used specialist qualifiers

Introduction

Qualifiers are described in 4 sections based on frequency of use.
  • general syntax
  • The
    • major qualifiers are !CONTINUE, !CONTRAST, !FCON, !MAXIT, !SUBSET, !SUM and XYplots ( !X !Y !G !JOIN )
  • Minor qualifiers
  • The qualifiers described here are rarely required specialist.
    • They include
        Controlling AI updates: !AISINGULARITIES, !AILOADINGS, !EMFLAG, !STEP, !SLOW, !VCC,
         Exporting the data: !PRINT, !RESIDUALS, !SAVE
        Best Linear Unbiased Prediction: !BLUP
        Modifying model defaults: !DENSE, !EXTRA
         Adjusting residual variance/degrees of freedom: !ADJUST, !DF, !YSS
         Modifying output format: !BRIEF, !PVSFORM, !TABFORM, !TXTFORM, !SLNFORM, !YHTFORM
         Equation ordering: !EQORDER, !LAST,
         Identify MYOWNGDG program: !OWN,
         Variogram settings: !SPATIAL, !TWOWAY, !VGSECTORS,
         Regression Screen: !SCREEN

    Very rarely used qualifiers

    Controlling AI updates

    ASReml stops if the Average Information Matrix is singular unless !AISINGULARITIES is specified

    Occasionally there are problems with the AI updates for factor analysis loadings which may be modified using !AILOADINGS.

    When trying to estimate an unstructured US variance matrix, you may use !EMFLAG to request EM updates if the AI updates would make the matrix non positive definite.

    As an ad hoc procedure, ASReml does not usually take the full AI update for the first few iterations. This is controlled by the !STEPSIZE and !SLOW qualifiers.

    The !VCC qualifier indicates how many Variance Component Constraint lines are supplied.

    Exporting the data:

    !PRINT, controls exporting the (transformed) data to an ASCII file,
    !RESIDUALS requests the data and residuals be written to a binary output file,
    !SAVE requests the data be written to a binary output file.

    !BLUP:

    When the user only wants to perform a BLUP analysis and is not interested in estimating variance parameters (assuminng that they are known), the !BLUP qualifier controls how much of an iteration is performed before the BLUP effects are written to file.

    Modifying model defaults:

    !DENSE, modifiers how many (fixed) effects (and consequently model terms) can be included in the DENSE portion of the mixed model equations; the portion used to generate the Analysis of Variance table.
    !EXTRA requests ASReml do more iterations after the usual convergence criterion have been satisfied.

    Adjusting residual degrees of freedom:

    Sometimes, a weighted analysis is performed where the weights are actually just providing a concise method of data entry. Then the mixed model equations actually represent more records than were actually supplied in the data file. Consequently the residual degrees of freedom will be wrong unless adjusted using either !ADJUST or !DF qualifiers.

    When anaylsing summarised data, you may have an independent estimate of the variance. To include that variation to the analysis, use !YSS 100 !DF 20 say, to add the equivalent of 20 observations with a variance of 5.

    Modifying output format:

    The amount of detail written to the .pvs file can be modified using the !BRIEF qualifier.

    The format of the .pvs, .sln, .tab and .yht files can be changed to TAB, COMMA or Ampersand separated ( .tex form) using the !PVSFORM, !TABFORM, !TXTFORM, !SLNFORM, !YHTFORM qualifiers.

    Equation ordering:

    The processing efficiency of ASReml is very dependent on the order the equations are solved. Some user control is provided by the !EQORDER and !LAST qualifiers.

    Defining your own variance structure.

    If you want to fit a variance structure not already included in ASReml, write a separate program to create it and its derivatives. The program name is specified with !OWN program.

    Variogram settings:

    The variogram is a popular diagnostic plot for examining spatial dependence. By default ASReml will produce a variogram display for spatially dependent residuals or BLUPs. Some user control is possible with the !SPATIAL, !TWOWAY and !VGSECTORS qualifiers.

    Regression Screen:

    A regression screen involves comparing the fit of (a subset of) all possible models obtained by selecting from a set of model terms. This is requested in ASReml with the !SCREEN   [ !SMX ] qualifiers.

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