simulate.lme {nlme}  R Documentation 
The model object
is fit to the data. Using
the fitted values of the parameters, nsim
new data vectors from
this model are simulated. Both m1
and m2
are fit by
maximum likelihood (ML) and/or by restricted maximum likelihood (REML)
to each of the simulated data vectors.
simulate.lme(object, nsim, seed, m2, method, niterEM, useGen, ...)
object 
an object inheriting from class lme , representing a fitted
linear mixedeffects model, or a list containing an lme model
specification. If given as a list, it should contain
components fixed , data , and random
with values suitable for a call to lme . This argument
defines the null model.

m2 
an lme object, or a list, like m1 containing a second
lme model specification. This argument defines the alternative model.
If given as a list, only those parts of the specification that
change between model m1 and m2 need to be specified.

seed 
an optional integer that is passed to set.seed . Defaults to
a random integer.

method 
an optional character array. If it includes "REML" the models
are fit by maximizing the restricted loglikelihood. If it includes
"ML" the loglikelihood is maximized. Defaults to
c("REML", "ML") , in which case both methods are used.

nsim 
an optional positive integer specifying the number of simulations to perform. Defaults to 1. This has changed. Previously the default was 1000. 
niterEM 
an optional integer vector of length 2 giving the number of
iterations of the EM algorithm to apply when fitting the m1
and m2 to each simulated set of data. Defaults to
c(40,200) .

useGen 
an optional logical value. If TRUE , numerical derivatives are
used to obtain the gradient and the Hessian of the loglikelihood in
the optimization algorithm in the ms function. If
FALSE , the default algorithm in ms for functions that
do not incorporate gradient and Hessian attributes is used. Default
depends on the pdMat classes used in m1 and m2 :
if both are standard classes (see pdClasses ) then
defaults to TRUE , otherwise defaults to FALSE .

... 
optional additional arguments. None are used. 
an object of class simulate.lme
with components null
and
alt
. Each of these has components ML
and/or REML
which are matrices. An attribute called Random.seed
contains
the seed that was used for the random number generator.
Jose Pinheiro Jose.Pinheiro@pharma.novartis.com and Douglas Bates bates@stat.wisc.edu
## Not run: orthSim < simulate.lme(list(fixed = distance ~ age, data = Orthodont, random = ~ 1  Subject), nsim = 1000, m2 = list(random = ~ age  Subject)) ## End(Not run)