Minor job qualifiers.

Context: Datafile line qualifiers

Introduction

Qualifiers are described in 4 sections based on frequency of use.

The major qualifiers are !CONTINUE, !CONTRAST, !DDF, !FCON, !MAXIT, !SUM and XYplots ( !X !Y !G !JOIN )

The qualifiers described here are less frequently required. They include
    (de)selecting multivariate mode: !ASMV, !ASUV
    Comma/TAB delimited data file !CSV
    Spatial arrangement in multienvironment trials: !COLFAC !ROWFAC !SECTION
     ANOVA qualifiers: !FAMILY !GROUP !MBF !SPLINE SUBSET
    graphics qualifiers: !DISPLAY, !BMP, !EPS, !WMF, NODISPLAY
    Missing values in design variables: !MVINCLUDE, !MVREMOVE,
    Setting predict points: !GKRIGE !PVAL

Rarely used qualifiers

(De)selecting multivariate mode (!ASUV !ASMV)

!ASUV indicates that while the data structure and linear model are specified in a multivariate form, the residual variance structure is not IDENTITY for units crossed with US for traits. When !ASUV is specified, it is often also necessary to include mv in the linear model and to specify !SIGMAPAR on or before the (leading) model line (original syntax: the !S2==1 qualifier on the R-structure lines).

!ASMV t indicates that while the data structure and linear model are specified in a univariate form, the data is actually arranged in a units by traits form (t nested within n units) and is to be analysed using the residual variance structure IDENTITY for units crossed with US for traits.

Comma/TAB separated data.

Comma and TAB delimited files may have empty cells which are treated as missing values. A line beginning with TAB/Comma implies a leading missing value. Consecutive Comma/TAB characters imply a missing value. Comma separated files are recognised either from the file suffix .csv or specification of !CSV. TAB delimited files are recognised if the !CSV qualifier is set.

Spatial analysis of a multi-environment trial

When !SECTION site !ROWFAC row !COLFAC column
was specified in ASReml 3, it generated the R-structure lines to fit an AR1 x AR1 variance structure for each site. But that residual structure is now easily specified with the new syntax:

 residual at(site).ar1(row).ar1(col)

In ASReml 4, these 3 qualifiers will cause ASReml to 'complete the grid' provided 'mv' is included in the model. That is, after the data has been read in, any missing site/row/column grid cells (combinations) are created as extra data records. The residual statement causes them to be sorted into the appropriate order corresponding to the R structure specification.
Read More.

Graphics qualifiers

Whether ASReml produces graphics and whether they are displayed on the screen is controlled by

was the Winteracter graphics library available for this platform,

have graphics been turned OFF on the control line,

are they only produced in hardcopy.

Some graphics are produced by default but others must be requested. The !DISPLAY i qualifier controls which of four spatial analysis graphics are displayed. !TWOWAY modifies the appearance of the variogram from a regular spatial grid of points. !VGSECTORS requests a variogram based on radial coordinates for irregular points.

If you run ASReml from ASReml-W, graphics are produced as .cgm files and may then be exported in several formats. Otherwise the default format is postscript.

The format of these hardcopy files may be changed on the commandline or by specifying one of the following on the datafile line:
     !BMP bitmap
     !EPS encapsulated postscript
     !WMF Windows Meta file
     !PS postscript
     !PNG png
     !HPGL HP graphics language
     !HPGL 2 HP graphics language II

Missing values in the Design

When missing values occur in design variables (as opposed to the response variable), the user must indicate whether to discard the records containing the missing values, or whether to treat the missing values as zeros.
Read More.

Setting predict points

When fitting polynomials or splines, it is sometimes desirable to predict the response surface at points other than those for which there is data. Use !PVAL to specify these points before the design matrix is formed so that the extra points have the appropriate covariables generated. For predicting a grid of points modelled with a correlation structure on a fac(X,Y) model term, use !GKRIGE to indicate how the cordinates are specified. Read More.

Setting spline knot points

ASReml has a model term spl(x[,k]) which, when fitted as a random term in conjunction with the covariate x fitted as a fixed term generates a cubic smoothing spline model. Several qualifiers modify the defaults with respect to choosing knot points for the spline. Read More.

My Basis function

The spline function used in ASReml is the common cubic smoothing spline and has a particular basis function. The !MBF qualifier provides a mechanism for a user to specify the spline covariables based on some other basis function. Read More.

Redefining factors for use in the model

!FAMILY is used to construct a new factor by merging levels of an existing factor, taking the new levels from a file.

 !FAMILY fam(Genotype) Family.txt

!GROUP is used to construct a new factor by merging the levels of an existing factor for subsequent inclusion in the model.

 !GROUP Year  SiteYear  1 2 3 1 2 2 3 4

!SUBSET is used to construct a new factor having a subset of the levels of an existing factor for subsequent inclusion in the model.

 !SUBSET Rsite  site  1 3 4 8

advantage of using these forms (including !CONTRAST and !MBF ) over forming new variables/factors using transformations is that in prediction, ASReml knows the relationship between the levels/values of the derived variable to the original variable. It does not retain that connection when variables are derived using transformations.

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