changeTerms.asrtests: Adds and drops terms from one or both of the fixed or random...

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

Adds and drops terms from one or both of the fixed or random model, replaces the residual (rcov) model with a new model and changes bounds or initial values of terms.

Description

The specified terms are simply added or dropped, without testing, from either the fixed or random model and/or the residual (rcov) model replaced. Also, the bounds and/or initial values of some terms can be changed. No hypothesis testing is performed, but a check is made for boundary or singular terms.

A row is added to the test.summary data.frame of the asrtests.object using the supplied label and stating which models have been changed. Information criteria can be included in the row of the test.summary. Convergence in fitting the model is checked and a note included in the action if there was not. All components of the asrtests.object are updated.

To only change the terms based on a comparison of information criteria use changeModelOnIC.asrtests.

Usage

## S3 method for class 'asrtests'
changeTerms(asrtests.obj, 
            dropFixed = NULL, addFixed = NULL, 
            dropRandom = NULL,  addRandom = NULL, 
            newResidual = NULL, label = "Changed terms", 
            allow.unconverged = TRUE, allow.fixedcorrelation = TRUE, 
            checkboundaryonly = FALSE, 
            trace = FALSE, update = TRUE, denDF = "numeric", 
            set.terms = NULL, ignore.suffices = TRUE, 
            bounds = "P", initial.values = NA, 
            IClikelihood = "none", bound.exclusions = c("F","B","S","C"), 
            ...)

Arguments

asrtests.obj	An asrtests.object containing the components (i) asreml.obj, (ii) wald.tab, and (iii) test.summary.
dropFixed	A single character string in the form of a formula which, after addition of ". ~ . -" and after expansion, specifies the sum of a set of terms to be dropped from the fixed formula. The names must match those in the wald.tab component of the asrtests.obj. The fixed terms will be reordered so that single-variable terms come first, followed by two-variable terms and so on. 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.
addFixed	A single character string in the form of a formula which, after addition of ". ~ . +" and expansion, specifies the sum of a set of terms to be added to the fixed formula. The fixed terms will be reordered so that single-variable terms come first, followed by two-variable terms and so on.
dropRandom	A single character string in the form of a formula which, after addition of " ~ . -" and expansion, specifies the sum of a set of terms to be dropped from the random formula. The terms must match those in the vparameters component of the asreml.obj component in the asrtests.obj. 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.
addRandom	A single character string in the form of a formula which, after addition of " ~ . +"and expansion, specifies the sum of a set of terms to be added to the random formula.
newResidual	A single character string in the form of a formula which, after addition of " ~ ", specifies the residual (or rcov) model. To remove the model, enter "-(.)".
label	A character to use as an entry in the terms column in test.summary to indicate as far as is possible the terms that are being manipulated.
allow.unconverged	A logical indicating whether to accept a new model even when it does not converge. If FALSE and the fit does not converge, the supplied asrtests.obj is returned.
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.
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 specified by this function's arguments and (ii) those specified via ....
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.
set.terms	A character vector specifying the terms that are to have bounds and/or initial values set prior to fitting the new model. The names must match those in the vparameters component of the asreml.obj component in the new asrtests.object. The terms in the model do not need to change from those in the model in the supplied asrtests.obj.
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.
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 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.)
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 the information criteria. If set to NULL then none will be excluded.
...	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.

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, rmboundary.asrtests, testranfix.asrtests, testresidual.asrtests,
newfit.asreml, reparamSigDevn.asrtests, chooseModel.asrtests,
changeModelOnIC.asrtests, infoCriteria.asreml

Examples

## Not run: 
terms <- "(Date/(Sources * (Type + Species)))"
current.asrt <- changeTerms(current.asrt, addFixed = terms)

current.asrt <- changeTerms(current.asrt, dropFixed = "A + B", denDF = "algebraic")

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)
# Add and drop both fixed and random terms
current.asrt <- changeTerms(current.asrt, 
                            addFixed = "vRow", dropFixed = "WithinColPairs", 
                            addRandom = "spl(vRow)", dropRandom = "units", 
                            checkboundaryonly = TRUE)
# Replace residual with model without Row autocorrelation
current.asrt <- changeTerms(current.asrt, 
                            newResidual = "Row:ar1(Column)", 
                            label="Row autocorrelation")


## End(Not run)

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