asrtests.obj and records their removal in an asrtests.object.Any terms specified in the random model that are
estimated on the boundary or are singular and can be removed are removed from the fit
stored in the asreml object stored in the asrtests.object.
Terms that specify multiple parameters in the random model cannot be removed
(e.g. terms specified using the at function with more than one level of the
factor) and terms in residual model are not removed. Terms that can be removed
are selected for removal in the following order based on whether they involve:
(i) a dev function, (ii) only factors, (iii) an spl function,
(iv) a pol function and (v) a lin function or a variable that
is an integer or a numeric. It should be noted that this order of removal
presumes that random deviation terms are specified via the dev function
rather than via a random factor. Once the earliest of the above classes
with a boundary term is identified, a term within this class is selected for
removal. For all classes, except for factor-only terms, the smallest term
with the largest number of variables/factors is removed.
Amongst factor-only terms, the smallest term with the smallest number of
variables/factors is removed. After each
variance component is removed, a row for it is added to the
test.summary data.frame and the model refitted. If there are further
boundary or singular terms, one is removed using the above strategy.
This process continues until there are no further boundary or singular
variance components that are removable. Other types of boundary or singular terms,
which cannot be removed, are reported in warning messages.
# S3 method for asrtests
rmboundary(asrtests.obj, checkboundaryonly = FALSE,
IClikelihood = "none", trace = FALSE, update = TRUE,
set.terms = NULL, ignore.suffices = TRUE,
bounds = "P", initial.values = NA, ...)an asrtests.object containing the components (i) asreml.obj,
(ii) wald.tab, and (iii) test.summary.
If TRUE then boundary and singular terms are not removed by
rmboundary.asrtests; a warning is issued instead.
A character that controls both the occurence and the type
of likelihood for information criterion in the test.summary
of the asrtests.object. If none, none are
included. Otherwise, if REML, then the AIC and BIC based
on the Restricted Maximum Likelihood are included; if full,
then the AIC and BIC based on the full likelihood are included.
(See also infoCriteria.asreml.)
If TRUE then partial iteration details are displayed when ASReml-R
functions are invoked; if FALSE then no output is displayed.
If TRUE then update.asreml is called to fit the model with
any boundary terms removed. 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) the terms for boundary variance components are removed
from the models and (ii) modifications specified via … are made.
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.
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.
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.
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.
An asrtests.object containing the components (i) asreml.obj,
(ii) wald.tab, and (iii) test.summary.
as.asrtests, changeTerms.asrtests,
testranfix.asrtests, testresidual.asrtests,
newfit.asreml, reparamSigDevn.asrtests,
chooseModel.asrtests
# NOT RUN {
current.asrt <- rmboundary(current.asrt)
# }
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