choose.model.asrtests {asreml3Plus} | R Documentation |
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.
choose.model.asrtests(terms.marginality=NULL, asrtests.obj, alpha = 0.05, allow.unconverged = TRUE, drop.ran.ns=TRUE, positive.zero = FALSE, bound.test.parameters = "none", 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, ...)
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. All other elements should be zero. |
asrtests.obj |
an |
alpha |
the significance level for the test. |
allow.unconverged |
A |
drop.ran.ns |
a logical indicating whether to drop nonsignificant random terms from the model. |
positive.zero |
Indicates whether the hypothesized values for the
variance components being tested are on the boundary
of the parameter space. For example, this is true
for positively-constrained variance components that,
under the reduced model, are zero. This argument does
not need to be set if |
bound.test.parameters |
Indicates whether for the variance components
being tested, at least some of the hypothesized values
are on the boundary of the parameter space. The default
is |
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 |
dDF.na |
the method to use to obtain substitute denominator degrees of freedom.
when the numeric or algebraic methods produce an |
dDF.values |
A |
trace |
if TRUE then partial iteration details are displayed when ASReml-R functions are invoked; if FALSE then no output is displayed. |
update |
if |
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
|
constraints |
a character vector specifying the constraints to be applied
to the terms specified in |
initial.values |
a character vector specifying the initial values for
the terms specified in |
... |
further arguments passed to |
A list containing:
asrtests.obj
: an asrtests
object, containing
the asreml
object correspondiing to the final fit,
a wald.tab
data.frame
, and a test.summary
data.frame
that contains a record of the testing of the terms
(see asrtests
for more details);
sig.tests
: a character vector
whose elements are the
the significant terms amongst those tested.
asrtests
, testranfix.asrtests
,
testrcov.asrtests
, reml.lrt.asreml
,
rmboundary.asrtests
,
newfit.asreml
, addrm.terms.asrtests
,
sig.devn.reparam.asrtests
## Not run: data(WaterRunoff.dat) current.asr <- asreml(log.Turbidity ~ Benches + (Sources * (Type + Species)) * Date, random = ~Benches:MainPlots:SubPlots:spl(xDay), data = WaterRunoff.dat, keep.order = TRUE) current.asrt <- asrtests(current.asr, NULL, NULL) terms.treat <- c("Sources", "Type", "Species", "Sources:Type", "Sources:Species") terms <- sapply(terms.treat, FUN=function(term){paste("Date:",term,sep="")}, simplify=TRUE) terms <- c("Date", terms) terms <- unname(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, 1,1,1,0,1,0, 1,1,1,1,1,1), nrow=6) rownames(marginality) <- terms colnames(marginality) <- terms choose <- choose.model.asrtests(marginality, current.asrt) current.asrt <- choose$asrtests.obj sig.terms <- choose$sig.terms ## End(Not run)