asremlPlus (version 4.2-32)

changeModelOnIC.asrtests: Uses information criteria to decide whether to change an already fitted model.

Description

Uses information criteria to decide whether to change the fitted model stored in the supplied asrtests.object according to the specified modifications. The function changeTerms is used to change the model. Thus, the model can be modified using a combination of adding and removing sets of terms from one or both of the fixed or random models and replacing the residual model.

A row is added to the test.summary data.frame of the asrtests.object using the supplied label and stating whether or not the new model has been swpped for the supplied model. 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 exhibit the differences between the suupplied and new model.

To obtain a list of the information criteria for a set of models use changeTerms.asrtests with IClikelihood set to REML or full, or use infoCriteria.asreml.

Usage

# S3 method for asrtests
changeModelOnIC(asrtests.obj, 
                dropFixed = NULL, addFixed = NULL, 
                dropRandom = NULL,  addRandom = NULL, 
                newResidual = NULL, label = "Changed terms", 
                allow.unconverged = TRUE, checkboundaryonly = FALSE, 
                trace = FALSE, update = TRUE, denDF = "numeric", 
                set.terms = NULL, ignore.suffices = TRUE, 
                bounds = "P", initial.values = NA, 
                which.IC = "AIC", IClikelihood = "REML", 
                fixedDF = NULL, varDF = NULL, 
                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.object.

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.

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 names must match those in the vparameters component of the asreml.obj component in the asrtests.object.

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 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.

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 then update.asreml is called to fit the model to be tested. In doing this the arguments R.param and G.param are set to those in the asreml object stored in asrtests.obj so that the values from the previous model are used as starting values. If FALSE then a call is made to asreml in which the only changes from the previous call are that (i) models are modifed as specified and (ii) modifications specified via … are made.

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.

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 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.

which.IC

A character specifying the information criterion to be used in selecting the best model. Possible values are AIC and BIC. The values of the criterion for supplied model must exceed that for changed model for the changed model to be returned.

IClikelihood

A character specifying whether Restricted Maximum Likelihood (REML) or the full likelihood (full) are to be used in calculating the information criteria.

fixedDF

A numeric giving the number of estimated fixed parameters. If NULL then this is determined from the information in asreml.obj.

varDF

A numeric giving the number of estimated variance parameters. If NULL then this is determined from the information in asreml.obj. It replaces the varDF argument.

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.

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. The values of the degrees of freedom and the information criteria are differences between those of the changed model and those of the model supplied to changeModelOnIC.

See Also

as.asrtests, rmboundary.asrtests, testranfix.asrtests, testresidual.asrtests, newfit.asreml, reparamSigDevn.asrtests, chooseModel.asrtests, changeTerms.asrtests, infoCriteria.asreml

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, 
                            label = "Maximal model")
current.asrt <- rmboundary(current.asrt)

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

# }