testranfix.asrtests: Tests for a single fixed or random term in model fitted using...

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

Tests for a single fixed or random term in model fitted using asreml and records the result in an asrtests.object.

Description

Tests for a single term, using a REML ratio test (REMLRT) for a random term or based on Wald statistics for a fixed term. The term must be in the fitted model. A random term is removed from the model fit and a REMLRT is performed using REMLRT.asreml. It compares the fit of the model in asreml.obj and the newly fitted model without the term. If the newly fitted model is retained, any boundary terms are then removed using rmboundary.asrtests. For a fixed term, the probability of the Wald statistics is extracted from the pseudo-anova table produced by wald.asreml. If this is available in the asrtests.object, it is used; otherwise wald.asreml is called to add it to the asrtests.object. Whether nonsignificant terms are dropped is controlled by drop.ran.ns for random terms and drop.fix.ns for fixed terms. A row is added to the test.summary data.frame for the term that is tested.

Usage

## S3 method for class 'asrtests'
testranfix(asrtests.obj, term=NULL, alpha = 0.05, 
           allow.unconverged = TRUE, allow.fixedcorrelation = TRUE, 
           checkboundaryonly = FALSE, 
           drop.ran.ns = TRUE, positive.zero = FALSE, 
           bound.test.parameters = "none", 
           bound.exclusions = c("F","B","S","C"), REMLDF = NULL, 
           drop.fix.ns = FALSE, denDF="numeric", dDF.na = "none", 
           dDF.values = NULL, IClikelihood = "none", 
           trace = FALSE, update = TRUE,
           set.terms = NULL, ignore.suffices = TRUE, 
           bounds = "P", initial.values = NA, ...)

Arguments

asrtests.obj	An asrtests.object containing the components (i) asreml.obj, (ii) wald.tab, and (iii) test.summary.
term	A single model term that is valid in asreml, stored as a character. The names of fixed terms must match those in the wald.tab component of the asrtests.obj, while the names of random terms must match those in the vparameters component of the asreml.obj component in the 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, it will be checked whether convergence can be achieved with the removal of any boundary random terms; random terms will be retested if terms are removed. 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.
drop.ran.ns	A logical indicating whether to drop a random term from the model when it is nonsignificant. Note that multiple terms specified using a single asreml::at function will only be dropped as a whole. If the term was specified using an asreml::at function with a single level, then it can be removed and either the level itself or its numeric position in the levels returned by the levels function can be specified in term.
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.
drop.fix.ns	A logical indicating whether to drop a fixed term from the model when it is nonsignificant. Note that multiple terms specified using a single asreml::at function can only be dropped as a whole. If the term was specified using an asreml::at function with a single level, then it can be removed and either the level itself or its numeric position in the levels returned by the levels function can be specified.
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.
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 and family is set to asr_guassian (the default), then the AIC and BIC based on the Restricted Maximum Likelihood are included; if full and family is set to asr_guassian, then the AIC and BIC based on the full likelihood, evaluated using REML estimates, are included. If family is asr_binomial or asr_poisson, with dispersion set to 1, the deviance is extracted from object and used to calculate the AIC and BIC. (See also infoCriteria.asreml.)
trace	If TRUE then partial iteration details are displayed when ASReml-R functions are invoked; if FALSE then no output is displayed.
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) those for the supplied terms and (ii) those specified via ....
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 object 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, DF set to NA, 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, chooseModel.asrtests, REMLRT.asreml,
rmboundary.asrtests, newfit.asreml, 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 nugget term
current.asrt <- testranfix(current.asrt, "units", positive=TRUE)

## End(Not run)

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