asremlPlus (version 2.0-2)

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

Description

Tests for a single term, using a REML LRT 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 REML likelihood ratio test is performed using reml.lrt.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

testranfix.asrtests(term=NULL, asrtests.obj, alpha = 0.05, 
                    drop.ran.ns = TRUE, positive.zero = FALSE, 
                    drop.fix.ns = FALSE, denDF="default", dDF.na = "none", 
                    dDF.values = NULL, trace = FALSE, update = TRUE,
                    set.terms = NULL, ignore.suffices = TRUE, 
                    constraints = "P", initial.values = NA, ...)

Arguments

term

a single model term that is valid in asreml, stored as a character.

asrtests.obj

an asrtests object for a fitted model that is a list containing an asreml object, a wald.tab data.frame with 4 columns, and a

alpha

the significance level for the test.

drop.ran.ns

a logical indicating whether to drop a random term from the model when it is nonsignificant .

positive.zero

a logical indicating whether the hypothesized values for the varaince components being tested are on the boundary of the parameter space. For example, this is be true for positively-c

drop.fix.ns

a logical indicating whether to drop a fixed term from the model when it is nonsignificant

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,

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

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 nu

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

set.terms

a character vector specifying the terms that are to have constraints 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 igno

constraints

a character vector specifying the constraints to be applied to the terms specified in terms. This vector must be of length one or the same length as terms. If it i

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 leng

...

further arguments passed to asreml and to wald.asreml.

Value

• An asrtests object, which is a list containing:
  1. asreml.obj: anasremlobject containing the fit after thetermhas been tested; it will be a new model if thetermis nonsignificant and the appropriate argument out ofdrop.ran.nsanddrop.fix.nsisTRUE;
  2. wald.tab: a 4-columndata.framecontaining a pseudo-anova table for the fixed terms produced bywald.asreml;
  3. test.summary: adata.framewith columnsterm,DF,denDF,pandaction. A row is added to it for each term that is tested, the row containing the name of the term, the degrees of freedom (numerator DF for a Wald test and the number of extra paramters for a REML ratio tests), the p-value and a for the action taken. Possible codes are:Dropped,Retained,Significant,Nonsignificant,Absent,Added,RemovedandBoundary. If the changed model did not converge,Unconvergedwill be added to the code. Note that the logicalasreml.obj$convergealso reflects whether there is convergence.
  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.

See Also

asremlPlus-package, asrtests, choose.model.asrtests, reml.lrt.asreml, rmboundary.asrtests, newfit.asreml, sig.devn.reparam.asrtests, addrm.terms.asrtests

Examples

data(Wheat.dat)
current.asr <- asreml(yield ~ Rep + WithinColPairs + Variety, 
                      random = ~ Row + Column + units,
                      rcov = ~ ar1(Row):ar1(Column), 
                      data=Wheat.dat)
current.asrt <- asrtests(current.asr, NULL, NULL)
current.asrt <- rmboundary.asrtests(current.asrt)
# Test nugget term
current.asrt <- testranfix.asrtests("units", current.asrt, positive=TRUE)