recalcWaldTab.asrtests {asremlPlus}R Documentation

Recalculates the denDF, F.inc and P values for a table of Wald test statistics obtained using wald.asreml

Description

If some or all denDF are not available, either because they are NA or because F.inc values were not calculated, this function allows the user to specify how approximate denDF values are to be obtained. This is done through the dDF.na and dDF.values arguments. Note that if denDF values are available in the Wald table then only those that are NA will be replaced. The P values are recalculated using F.con, if present in the wald.tab, otherwise F.inc is used. It is noted that, as of asreml version 4, wald.asreml has a kenadj argument.

Usage

## S3 method for class 'asrtests'
recalcWaldTab(asrtests.obj, recalc.wald = FALSE,
              denDF="numeric", dDF.na = "none", 
              dDF.values = NULL, trace = FALSE, ...)

Arguments

asrtests.obj

an asrtests.object containing the components (i) asreml.obj, (ii) wald.tab, and (iii) test.summary.

recalc.wald

A logical indicating whether to call wald.asreml to recalculate the pseudoanova table for the model fit stored in the asreml object contained in asrtests.obj.

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 autommatically 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.

dDF.na

The method to use to obtain substitute denominator degrees of freedom. when the numeric or algebraic methods produce an NA. If dDF.na = "none", no subtitute denominator degrees of freedom are employed; if dDF.na = "residual", the residual degrees of freedom from asreml.obj$nedf are used; if dDF.na = "maximum", the maximum of those denDF that are available, excluding that for the Intercept, is used; if all denDF are NA, asreml.obj$nedf is used. If dDF.na = "supplied", a vector of values for the denominator degrees of freedom is to be supplied in dDF.values. Any other setting is ignored and a warning message produced. Generally, substituting these degrees of freedom is anticonservative in that it is likely that the degrees of freedom used will be too large.

dDF.values

A vector of values to be used when dDF.na = "supplied". Its values will be used when denDF in a test for a fixed effect is NA. This vector must be the same length as the number of fixed terms, including (Intercept) whose value could be NA.

trace

If TRUE then partial iteration details are displayed when ASReml-R functions are invoked; if FALSE then no output is displayed.

...

further arguments passed to asreml and to wald.asreml.

Value

A wald.tab: a 4- or 6-column data.frame containing a pseudo-anova table for the fixed terms produced by wald.asreml.

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

as.asrtests, testranfix.asrtests

Examples

## Not run: 
  wald.tab <- recalcWaldTab(current.asrt, 
                            dDF.na = "supplied", 
                            dDF.values = c(NA,rep(c(330,346), c(4,3))))

## End(Not run)

[Package asremlPlus version 4.2-32 Index]