# 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, !HOLD, !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,

Refining GLMM model fitting:
!GLMM,

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.
!HOLD ` list`
allows the user to temporarily fix the parameters listed.
Parameter numbers have been added to the reporting of input values
to facilitate use of this and other parameter number dependent
qualifiers. The list should be in increasing order using
colon to indicate a sequence. For example

!HOLD 1:20 30:40.

The
!VCC
qualifier indicates how many **V**ariance **C**omponent **C**onstraint
lines are supplied.
## Own F tests

!FOWN `terms to test` ; `background terms`
allows the user to specify the exact F tests required.
## 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 tests of fixed effects.

!EXTRA
requests ASReml do more iterations after the usual convergence
criterion have been satisfied.
## Adjusting sum of squares and/or 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 in 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.
## Refining GLMM model fitting

!GLMM `n`
sets the number of inner iterations performed when a iteratively weighted least squares
analysis is performed. Inner iterations are iterations to estimate the
effects in the linear model for the current set of variance parameters.
Outer iterations are the AI updates to the variance parameters. The
default is to perform 4 inner iterations in the first round and
2 in subsequent rounds of the outer iteration. Set `n` to 2 or more
to increase the number of inner iterations.
## Alternative Outlier Model

!OUTLIER
invokes a more formal calculation of the relative size of
random effects and the residual, and reports values
exceeding 3 standard deviations to the
.res
file.
More?
## 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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