as.asrtests: Forms an asrtests object that stores (i) a fitted asreml...

In asremlPlus: Augments 'ASReml-R' in Fitting Mixed Models and Packages Generally in Exploring Prediction Differences

Forms an asrtests object that stores (i) a fitted asreml object, (ii) a pseudo-anova table for the fixed terms and (iii) a history of changes and hypothesis testing used in obtaining the model.

Description

An asrtests.object that is a list consisting of the components asreml.obj, wald.tab and test.summary.

A call to as.asrtests with test.summary = NULL re-initializes the test.summary
data.frame.

If there is no wald.tab, wald.asreml is called. In all cases, recalcWaldTab is called and any changes made as specified by the recalcWaldTab arguments supplied via ....

The label argument can be used to include an entry in test.summary for the starting model. If a label is included, (i) the information criteria calculated using the asreml.obj will be added to the test.summary, if IClikelihood is not set to none and (ii) the number of variance parameters is included in the denDF column, if IClikelihood is set to none.

Usage

as.asrtests(asreml.obj, wald.tab = NULL, test.summary = NULL, 
            denDF = "numeric", label = NULL, 
            IClikelihood = "none", bound.exclusions = c("F","B","S","C"), ...)

Arguments

asreml.obj	an asreml object for a fitted model.
wald.tab	A data.frame containing a pseudo-anova table for the fixed terms produced by wald.asreml; it should have 4 or 6 columns. Sometimes wald.asreml returns a data.frame and at other times a list. For example, it may return a list when denDF is used. In this case, the Wald component of the list is to be extracted and stored. It is noted that, as of asreml version 4, wald.asreml has a kenadj argument.
test.summary	A data.frame with columns term, DF, denDF, p and action containing the results of previous hypothesis tests.
denDF	Specifies the method to use in computing approximate denominator degrees of freedom when wald.asreml is called. Can be none to suppress the computations, numeric for numerical methods, algebraic for algebraic methods or default, the default, to automatically choose numeric or algebraic computations depending on problem size. The denominator degrees of freedom are calculated according to Kenward and Roger (1997) for fixed terms in the dense part of the model.
label	A character to use as an entry in the terms column in test.summary to indicate as far as is possible the nature of the model that has been fitted. The action column in test.summary will be Starting model.
IClikelihood	A character that controls both the occurrence and the type of likelihood for information criterion in the test.summary of the new asrtests.object. If none, none are included. Otherwise, if REML, then the AIC and BIC based on the Restricted Maximum Likelihood are included; if full, then the AIC and BIC based on the full likelihood, evaluated using REML estimates, are included. (See also infoCriteria.asreml.)
bound.exclusions	A character specifying the bound (constraint) codes that will result in a variance parameter being excluded from the count of estimated variance parameters in calculating information criteria. If set to NULL then none will be excluded.
...	further arguments passed to wald.asreml and recalcWaldTab.

Value

An object of S3-class asrtests.

Author(s)

Chris Brien

References

Kenward, M. G., & Roger, J. H. (1997). Small sample inference for fixed effects from restricted maximum likelihood. Biometrics, 53, 983-997.

See Also

asremlPlus-package, is.alldiffs, as.alldiffs, recalcWaldTab,
testranfix.asrtests, chooseModel.asrtests, rmboundary.asrtests,
reparamSigDevn.asrtests

Examples

## Not run: 
data(Wheat.dat)

# Fit initial model
current.asr <- asreml(yield ~ Rep + WithinColPairs + Variety, 
                      random = ~ Row + Column + units,
                      residual = ~ ar1(Row):ar1(Column), 
                      data=Wheat.dat)

# Load current fit into an asrtests object
current.asrt <- as.asrtests(current.asr, NULL, NULL)

# Check for and remove any boundary terms
current.asrt <- rmboundary(current.asrt)

## End(Not run)

asremlPlus documentation built on Oct. 27, 2024, 5:06 p.m.