update.asreml or a direct call to asreml.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.
# S3 method for 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, ...)A valid asreml object with with
a component named call (from a previous
call to either asreml or update.asreml).
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$call.
A character or formula specifying changes to the random
formula. This is a one-sided formula
where "." is substituted for existing components in the
random component of asreml.obj$call.
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$call.
A character or formula specifying changes to the error
formula, used when version 4 or later of ASReml-R is loaded.
This is a one-sided formula
where "." is substituted for existing components in the
residual component of asreml.obj$call.
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.
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.
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.
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.
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.
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.
additional arguments to the call, or arguments with changed values.
An asreml object.
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.org/.
update.asreml, setvarianceterms.call
# NOT RUN {
m2.asreml <- newfit(m1.asreml, random. = "~ . - Blocks:Plots", maxiter=75)
# }
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