newfit.asreml {asremlPlus}R Documentation

Refits an asreml model with modified model formula using either a call to update.asreml or a direct call to asreml.

Description

Extracts the call from the asreml.obj and evaluates that call, replacing any arguments with changed values. If update is TRUE and set.terms is not set, the call is evaluated using update.asreml; otherwise, it is evaluated using a direct call to asreml. The principal difference is that the latter does not enforce the use of previous values of the variance parameters as initial values; it sets G.param and R.param to NULL or to values as specified for set.terms. The ... argument can be used to pass G.param and/or R.param, provided update is FALSE and set.terms is not set.

Usage

## S3 method for class 'asreml'
newfit(asreml.obj, fixed., random., sparse., 
       residual., rcov., update = TRUE, trace = FALSE, 
       allow.unconverged = TRUE, keep.order = TRUE, 
       set.terms = NULL, ignore.suffices = TRUE, bounds = "P", 
       initial.values = NA, ...)

Arguments

asreml.obj

A valid asreml object with with a component named call (from a previous call to either asreml or update.asreml).

fixed.

A character or formula specifying changes to the fixed formula. This is a two-sided formula where "." is substituted for existing components in the fixed component of asreml.obj$call.

random.

A character or formula specifying changes to the random formula. This is a one-sided formula where "." is substituted for existing components in the random component of asreml.obj$call.

sparse.

A character or formula specifying changes to the sparse formula. This is a one-sided formula where "." is substituted for existing components in the sparse component of asreml.obj$call.

residual.

A character or formula specifying changes to the error formula, used when version 4 or later of ASReml-R is loaded. This is a one-sided formula where "." is substituted for existing components in the residual component of asreml.obj$call.

rcov.

A character or formula specifying changes to the error formula, used when version 3 of ASReml-R is loaded. This is a one-sided formula where "." is substituted for existing components in the residual component of asreml.obj$call.

update

A logical indicated whether to use update.asreml or asreml to evaluate the modified call. If TRUE, use update.asreml to evaluate the modified call. In doing this the arguments R.param and G.param are set to those in the asreml.obj so that the values from the previous model are used as starting values. If FALSE then a call is made to asreml itself, in which the only changes from the previous call are those specified in the arguments to newfit.asreml.

trace

A logical that control output from ASReml-R. If TRUE then partial iteration details are displayed when ASReml-R functions are invoked; if FALSE then no output is displayed.

allow.unconverged

A logical indicating whether to accept a new model even when it does not converge. If FALSE and the fit does not converge, the supplied asreml object is returned.

keep.order

A logical value indicating whether the terms should keep their positions. If FALSE the terms are reordered so that main effects come first, followed by the interactions, all second-order, all third-order and so on. Effects of a given order are kept in the order specified.

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.

...

additional arguments to the call, or arguments with changed values.

Value

An asreml object.

Author(s)

Chris Brien

References

Butler, D. G., Cullis, B. R., Gilmour, A. R., Gogel, B. J. and Thompson, R. (2018). ASReml-R Reference Manual Version 4. VSN International Ltd, https://asreml.kb.vsni.co.uk/.

See Also

update.asreml, setvarianceterms.call

Examples

## Not run: 
    m2.asreml <- newfit(m1.asreml, random. = "~ . - Blocks:Plots", maxiter=75)

## End(Not run)

[Package asremlPlus version 4.2-32 Index]