Defines options for the fitting of models by VARANDOM and associated procedures (R.W. Payne).
Options
MAXCYCLE = scalar |
Limit on the number of iterations in REML analyses; default 100 |
|---|---|
WORKSPACE = scalar |
Number of blocks of internal memory to be set up for use by the REML algorithm |
MINSPATIALCOORDINATES = scalar |
Minimum number of different coordinates in a direction for a spatial model to be fitted by VAROWCOLUMNDESIGN; default 4 |
LIMPRTREND = scalar |
Critical value for the probability of a row or column trend in the initial basic REML analysis (with replicates but no other random terms) for this to be included in the later analyses) by VAROWCOLUMNDESIGN; default 0.01 |
REPORTFAILURES = string token |
Whether the accumulated summary should include models that fail to fit or that have bound variance parameters (yes, no) ; default no |
No parameters
Description
There are several procedures, with the prefix VA, that investigate potential models for a REML analysis. For example, VABLOCKDESIGN does this for data from an incomplete-block design, and VAROWCOLUMNDESIGN does it for data from a field trial arranged in rows and columns. These two procedures both use a general procedure VARANDOM, which allows you to try several alternative random models for a REML analysis, and then select the best one according to either their Akaike or Schwarz (Bayesian) information coefficients.
VABLOCKDESIGN and VAROWCOLUMNDESIGN are designed to be used by non-expert users, and so various decisions are made there (and in VARANDOM) about how the analysis is to be done and how the models are to be selected. This procedure, VAOPTIONS, is provided to allow more experienced users to modify some of the options that control the process.
The MAXCYCLE and WORKSPACE options are relevant to all the procedures, and define the settings for the MAXCYCLE and WORKSPACE options of the REML directive, when this is used in any of the procedures.
Other options are relevant to specific procedures. The MINSPATIALCOORDINATES and LIMPRTREND options control aspects of the analyses in VAROWCOLUMNDESIGN. MINSPATIALCOORDINATES sets a limit on the number of different row or column coordinates for a spatial model to be fitted in that direction (default 4). LIMPRTREND defines the critical value for the probability of a row or column trend in an initial basic REML analysis, that is performed with replicates but no other random terms, to decide whether this is be included in the later analyses (default 0.01). The REPORTFAILURES option controls whether the accumulated summary, printed from VARANDOM, should include models that fail to fit or that have bound variance parameters.
Options: MAXCYCLE, WORKSPACE, MINSPATIALCOORDINATES, LIMPRTREND, REPORTFAILURES.
Parameters: none.
See also
Directive: REML.
Procedures: VABLOCKDESIGN, VAROWCOLUMNDESIGN, VARANDOM.
Commands for: REML analysis of linear mixed models.
Example
CAPTION 'VAOPTIONS example',\
'Slate Hall Farm data (Guide to REML in Genstat, Section 1.8).';\
STYLE=meta,plain
SPLOAD '%gendir%/data/slatehall.gsh'
" define model for analysis as a randomized-blocks design "
VFMODEL [MODELSTRUCTURE=RCBD; DESCRIPTION='Randomized blocks';\
FIXED=variety] replicates
" define model for analysis as a Lattice square design "
VFMODEL [MODELSTRUCTURE=Latticesq; DESCRIPTION='Lattice square';\
FIXED=variety] replicates/(rows*columns)
" define model for analysis with an Ar1 (x) Ar1 model "
VFMODEL [MODELSTRUCTURE=AR1xAR1; DESCRIPTION='Ar1 (x) AR1';\
FIXED=variety] fieldrow.fieldcolumn
VFSTRUCTURE [MODELSTRUCTURE=AR1xAR1; TERMS=fieldrow.fieldcolumn]\
2('AR'); ORDER=1; FACTOR=fieldrow,fieldcolumn
" define model for analysis with an Ar1 (x) Ar1 model + measurement error "
VFMODEL [MODELSTRUCTURE=AR1xAR1p; DESCRIPTION='Ar1 (x) AR1 + plots';\
FIXED=variety] fieldrow.fieldcolumn+plotnumber
VFSTRUCTURE [MODELSTRUCTURE=AR1xAR1p; TERMS=fieldrow.fieldcolumn]\
2('AR'); ORDER=1; FACTOR=fieldrow,fieldcolumn
" find the best random model "
VARANDOM [PTRY=monitor; MODELSTRUCTURES=RCBD,Latticesq,AR1xAR1,AR1xAR1p]\
yield; SAVE=savebest
" set MAXCYCLE=8 in future REMLs (the spatial analyses will now fail) "
VAOPTIONS [MAXCYCLE=8]
VARANDOM [PTRY=monitor; MODELSTRUCTURES=RCBD,Latticesq,AR1xAR1,AR1xAR1p]\
yield; SAVE=savebest
" restore MAXCYCLE to the default 100 "
VAOPTIONS [MAXCYCLE=100]