rmboundary.asrtests: Removes any boundary or singular variance components from the fit stored in `asrtests.obj` and records their removal in an `asrtests.object`.

Description

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.

Usage

# 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, ...)

Value

An asrtests.object containing the components (i) asreml.obj, (ii) wald.tab, and (iii) test.summary.

Arguments

asrtests.obj: an asrtests.object containing the components (i) asreml.obj, (ii) wald.tab, and (iii) test.summary.
checkboundaryonly: If TRUE then boundary and singular terms are not removed by rmboundary.asrtests; a warning is issued instead.
IClikelihood: A character that controls both the occurrence and the type of likelihood for information criterion in the test.summary of the new 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, evaluated using REML estimates, are included. (See also infoCriteria.asreml.)
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, and set.terms is NULL, then newfit.asreml is called to fit the model with any boundary terms removed and using the values of the variance parameters stored in the asreml.object, that is stored in asrtests.obj, as starting values. If FALSE or set.terms is not NULL, then newfit.asreml will not use the stored variance parameter values as starting values when fitting the model without the boundary terms.
set.terms: 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.
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, including asreml arguments, passed to newfit.asreml.

Author

Chris Brien

Examples

Run this code

if (FALSE) {
current.asrt <- rmboundary(current.asrt)
}