asremlPlus (version 4.1-26)

changeTerms.asrtests: Adds and drops the specified sets of terms from one or both of the fixed or random model and/or replaces the residual (rcov) model with a new model.

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. 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 using the supplied label and stating which models have been changed. 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.

Usage

# S3 method for asrtests
changeTerms(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, ...)

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.

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.

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 string to use as the label in test.summary and which indicates what is being tested.

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 asreml object is returned.

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 enthod 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.

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.

See Also

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

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")

# }