asremlPlus (version 2.0-2)

choose.model.asrtests: Determines the set of significant terms taking into account the hierarchy or marginality relations.

Description

Performs a series of hypothesis tests taking into account the marginality of terms. In particular, a term will not be tested if it is marginal to (or nested in) one that is significant. For example, if A:B is significant, then neither A nor B will be tested. For a random term, the term is removed from the model fit, any boundary terms are removed using rmboundary.asrtests and a REML likelihood ratio test is performed using reml.lrt.asreml. If it is not significant and drop.ran.ns is TRUE, the term is permanently removed from the model. Note that if boundary terms are removed, the reduced model may not be nested in the full model in which case the test is not valid. For fixed terms, the Wald tests are performed and the p-value for the term obtained. If it is not significant and drop.fix.ns is TRUE, the term is permanently removed from the model. A row is added to test.summary for each term that is tested.

Usage

choose.model.asrtests(terms.marginality=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

terms.marginality

a square matrix of ones and zeros with row and column names being the names of the terms. The diagonal elements should be one, indicating that a term is marginal to itself. Elements should be one if the row term is marginal to the column term.

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 nonsignificant random terms from the model.

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 TRUEthen update.asreml is called in testing models. In doing this the arguments R.param and G.param are set to those in the asreml object stored in a

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 wald.asreml via testranfix.asrtests.

Value

• A list containing:
  1. asrtests.obj: anasrtestsobject, containing theasremlobject correspondiing to the final fit, awald.tabdata.frame, and atest.summarydata.framethat contains a record of the testing of the terms (seeasrtestsfor more details);
  2. sig.tests: acharacter vectorwhose elements are the the significant terms amongst those tested.

See Also

asrtests, testranfix.asrtests, testrcov.asrtests, reml.lrt.asreml, rmboundary.asrtests, newfit.asreml, addrm.terms.asrtests, sig.devn.reparam.asrtests

Examples

terms.treat <- c("Sources", "Type", "Species", 
                 "Sources:Type", "Sources:Species")
terms <- sapply(terms.treat, 
                FUN=function(term){paste("spl(xDay):",term,sep="")}, 
                simplify=TRUE)
terms <- c("spl(xDay)",terms)
marginality <-  matrix(c(1,0,0,0,0,0, 1,1,0,0,0,0,  1,0,1,0,0,0, 
                         1,0,1,1,0,0, 1,1,1,1,1,0, 1,1,1,1,1,1), nrow=6)
rownames(marginality) <-terms
colnames(marginality) <-terms
choose <- choose.model.asrtests(marginality, current.asrt, 
                                       pos=TRUE)
         current.asrt <- choose$asrtests.obj