testresidual.asrtests: Fits a new residual formula, tests whether the change is...

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

Fits a new residual formula, tests whether the change is significant and records the result in an asrtests.object.

Description

Fits a new residual formula using asreml-R4 (replaces the rcov formula of asreml-R3) and tests whether the change is significant. If simpler = FALSE the model to be fitted must be more complex than the one whose fit has been stored in asrtests.obj. That is, the new model must have more parameters. However, if simpler = TRUE the model to be fitted must be simpler than the one whose fit has been stored in asrtests.obj in that it must have fewer parameters. Any boundary terms are removed using rmboundary.asrtests, which may mean that the models are not nested. The test is a REML likelihood ratio test that is performed using REMLRT.asreml, which is only valid if the models are nested. It compares the newly fitted model with the fit of the model in asrtest.obj. If the two models have the same number of variance parameters, then no change is made to the residual. A row is added to the test.summary data.frame using the supplied label.

Usage

## S3 method for class 'asrtests'
testresidual(asrtests.obj, terms=NULL, label = "R model", 
             simpler = FALSE, alpha = 0.05, 
             allow.unconverged = TRUE, allow.fixedcorrelation = TRUE, 
             checkboundaryonly = FALSE, positive.zero = FALSE, 
             bound.test.parameters = "none", 
             bound.exclusions = c("F","B","S","C"), REMLDF = NULL, 
             denDF="numeric", IClikelihood = "none", 
             update = TRUE, trace = FALSE,
             set.terms = NULL, ignore.suffices = TRUE, 
             bounds = "P", initial.values = NA, ...)

Arguments

asrtests.obj	an asrtests.object for a fitted model that is a list containing the componets (i) asreml.obj, (ii) wald.tab (iii) test.summary.
terms	A model for the residual argument in asreml-R4 (the rcov formula in older versions of asreml), stored as a character. To remove the model, enter "-(.)".
label	A character string to use as the label in test.summary and which indicates what is being tested.
simpler	A logical indicating whether the new model to be fitted is simpler than the already fitted model whose fit is stored in asrtests.obj.
alpha	The significance level for the test.
allow.unconverged	A logical indicating whether to accept a new model even when it does not converge. If FALSE and the fit of the new model does not converge, the supplied asreml object is returned. Also, if FALSE and the fit of the new model has converged, but that of the old model has not, the new model will be accepted.
allow.fixedcorrelation	A logical indicating whether to accept a new model even when it contains correlations in the model whose values have been designated as fixed, bound or singular. If FALSE and the new model contains correlations whose values have not been able to be estimated, the supplied asrtests.obj is returned. The fit in the asreml.obj component of the supplied asrtests.obj will also be tested and a warning issued if both fixed correlations are found in it and allow.fixedcorrelation is FALSE.
checkboundaryonly	If TRUE then boundary and singular terms are not removed by rmboundary.asrtests; a warning is issued instead.
positive.zero	Indicates whether the hypothesized values for the variance components being tested are on the boundary of the parameter space. For example, this is true for positively-constrained variance components that, under the reduced model, are zero. This argument does not need to be set if bound.test.parameters is set.
bound.test.parameters	Indicates whether for the variance components being tested, at least some of the hypothesized values are on the boundary of the parameter space. The possibilities are "none", "onlybound" and "one-and-one". The default is "none", although if it is set to "none" and positive.zero is TRUE then bound.test.parameters is taken to be "onlybound". When bound.test.parameters is set to "one-and-one", it signifies that there are two parameters being tested, one of which is bound and the other is not. For example, the latter is true for testing a covariance and a positively-constrained variance component that, under the reduced model, are zero.
bound.exclusions	A character specifying one or more bound (constraint) codes that will result in a variance parameter being excluded from the count of estimated variance parameters in using REMLRT.asreml. If set to NULL then none will be excluded.
REMLDF	A numeric giving the difference in the number of variance parameters whose estimates are not of the type specified in bound.exclusions for two models being compared in a REML ratio test using REMLRT.asreml. If NULL then this is determined from the information in the asreml object for the two models.
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.
IClikelihood	A character that controls both the occurence 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.)
update	If TRUE, and set.terms is NULL, then newfit.asreml is called to fit the model to be tested, using the values of the variance parameters stored in the asreml.object, that is stored in asrtests.obj, as starting values. If FALSE or set.terms is not NULL, then newfit.asreml will not use the stored variance parameter values as starting values when fitting the new model, the only modifications being (i) the residual (rcov) model is that specified in terms (ii) those specified via ....
trace	If TRUE then partial iteration details are displayed when ASReml-R functions are invoked; if FALSE then no output is displayed.
set.terms	A character vector specifying the terms that are to have bounds and/or initial values set prior to fitting. The names must match those in the vparameters component of the asreml.obj component in the new asrtests.object.
ignore.suffices	A logical vector specifying whether the suffices of the asreml-assigned names of the variance terms (i.e. the information to the right of an "!", other than "R!") is to be ignored in matching elements of terms. If TRUE for an element of terms, the suffices are stripped from the asreml-assigned names. If FALSE for an element of terms, the element must exactly match an asreml-assigned name for a variance term. This vector must be of length one or the same length as terms. If it is of length one then the same action is applied to the asreml-assigned suffices for all the terms in terms.
bounds	A character vector specifying the bounds to be applied to the terms specified in set.terms. This vector must be of length one or the same length as set.terms. If it is of length one then the same constraint is applied to all the terms in set.terms. If any of the bounds are equal to NA then they are left unchanged for those terms.
initial.values	A character vector specifying the initial values for the terms specified in terms. This vector must be of length one or the same length as terms. If it is of length one then the same initial value is applied to all the terms in terms. If any of the initial.values are equal to NA then they are left unchanged for those terms.
...	Further arguments passed to asreml, wald.asreml and as.asrtests.

Value

An asrtests.object containing the components (i) asreml.obj, (ii) wald.tab, and (iii) test.summary. If the term is not in the model, then the supplied asreml.obj will be returned. Also, reml.test will have the likelihood ratio and the p-value set to NA and the degrees of freedom to zero. Similarly, the row of test.summary for the term will have its name, a p-value set to NA, and action set to Absent.

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, as.asrtests, changeTerms.asrtests,
chooseModel.asrtests, REMLRT.asreml, rmboundary.asrtests,
newfit.asreml, testswapran.asrtests, changeModelOnIC.asrtests,
changeTerms.asrtests, reparamSigDevn.asrtests

Examples

## Not run: 
data(Wheat.dat)
current.asr <- asreml(yield ~ Rep + WithinColPairs + Variety, 
                      random = ~ Row + Column + units,
                      residual = ~ ar1(Row):ar1(Column), 
                      data=Wheat.dat)
current.asrt <- as.asrtests(current.asr, NULL, NULL)
current.asrt <- rmboundary(current.asrt)
# Test Row autocorrelation
current.asrt <- testresidual(current.asrt, "~ Row:ar1(Column)", 
                             label="Row autocorrelation", simpler=TRUE)
print(current.asrt)

## End(Not run)

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