[Lme4-commits] r1633 - pkg/lme4Eigen/man

[noreply at r-forge.r-project.org]

Author: mmaechler
Date: 2012-02-29 22:28:48 +0100 (Wed, 29 Feb 2012)
New Revision: 1633

Removed:
   pkg/lme4Eigen/man/bootMer2.Rd
Log:
2nd part of r1631

Deleted: pkg/lme4Eigen/man/bootMer2.Rd
===================================================================
--- pkg/lme4Eigen/man/bootMer2.Rd	2012-02-29 14:28:07 UTC (rev 1632)
+++ pkg/lme4Eigen/man/bootMer2.Rd	2012-02-29 21:28:48 UTC (rev 1633)
@@ -1,115 +0,0 @@
-\name{bootMer2}
-\alias{bootMer2}
-\title{Model-based (Semi-)Parametric Bootstrap for Mixed Models}
-\usage{
-  bootMer2(x, FUN, nsim = 1, seed = NULL, use.u = FALSE,
-    type = c("parametric", "semiparametric"),
-    verbose = FALSE, control = list(), .progress = "none",
-    PBargs = list())
-}
-\arguments{
-  \item{x}{fitted \code{*lmer()} model, see
-  \code{\link{lmer}}, \code{\link{glmer}}, etc.}
-
-  \item{FUN}{a \code{\link{function}(x)}, computating the
-  \emph{statistic} of interest, which must be a numeric
-  vector, possibly named.}
-
-  \item{nsim}{number of simulations, positive integer; the
-  bootstrap \eqn{B} (or \eqn{R}).}
-
-  \item{seed}{optional argument to \code{\link{set.seed}}.}
-
-  \item{use.u}{logical, indicating, if the spherized random
-  effects should be simulated / bootstrapped as well.  If
-  \code{FALSE}, they are not changed, and all inference is
-  conditional on these.}
-
-  \item{type}{character string specifying the type of
-  bootstrap, \code{"parametric"} or
-  \code{"semiparametric"}.  Default is \code{"parametric"}.
-  Partial matching is allowed.}
-
-  \item{verbose}{logical indicating if progress should
-  print output}
-
-  \item{control}{an optional \code{\link{list}}, to be
-  passed to the minimizer (of the log-likelihood, or RE
-  likelihood).}
-
-  \item{.progress}{character string - type of progress bar
-  to display.  Default is \code{"none"}.}
-
-  \item{PBargs}{a list of additional arguments to the
-  progress bar function.}
-}
-\value{
-  an object of S3 \code{\link{class}} \code{"boot"},
-  compatible with \pkg{boot} package's \code{boot()}
-  result.
-}
-\description{
-  Perform model-based (Semi-)parametric bootstrap for mixed
-  models.
-}
-\details{
-  The semi-parametric variant is not yet implemented, and
-  we only provide a method for \code{\link{lmer}} and
-  \code{\link{glmer}} results.
-
-  The working name for bootMer() was
-  \dQuote{simulestimate()}, as it is an extension of
-  \code{\link{simulate}}, but we rather want to emphasize
-  its potential for valid inference.
-
-  In each of the \code{nsim} simulations --- that is what
-  the \emph{parametric} bootstrap does, both
-  \dQuote{\emph{spherized}} random effects \eqn{u} and the
-  i.i.d errors \eqn{\epsilon} are generated, using
-  \code{\link{rnorm}()} with parameters corresponding to
-  the fitted model \code{x}.
-}
-\examples{
-fm01ML <- lmer(Yield ~ 1|Batch, Dyestuff, REML = FALSE)
-## see ?"profile-methods"
-mySumm <- function(.) { s <- sigma(.)
-    c(beta =getME(., "beta"), sigma = s, sig01 = s * getME(., "theta")) }
-(t0 <- mySumm(fm01ML)) # just three parameters
-
-\dontrun{\%\%--- fails for now --- FIXME
-
-## 3.8s (on a 5600 MIPS 64bit fast(year 2009) desktop "AMD Phenom(tm) II X4 925"):
-system.time( boo01 <- bootMer(fm01ML, mySumm, nsim = 100) )
-
-## to "look" at it
-if(need.boot <- is.na(match("package:boot", search())))
-  require("boot")## is a recommended package, i.e. *must* be there
-boo01 # look at estimated bias for sig01 (-9.1, also when nsim = 1000)
-
-## ------ Bootstrap-based confidence intervals ------------
-
-(bCI.1 <- boot.ci(boo01, index=1, type=c("norm", "basic", "perc")))# beta
-
-## Sigma - original scale, and interval calculation on log-scale:
-(bCI.2  <- boot.ci(boo01, index=2, type=c("norm", "basic", "perc")))
-(bCI.2l <- boot.ci(boo01, index=2, type=c("norm", "basic", "perc"),
-                   h = log, hdot = function(.) 1/., hinv = exp))
-
-(bCI.3 <- boot.ci(boo01, index=3, type=c("norm", "basic", "perc")))# sig01
-}
-}
-\references{
-  Davison, A.C. and Hinkley, D.V. (1997) \emph{Bootstrap
-  Methods and Their Application}.  Cambridge University
-  Press.
-}
-\seealso{
-  For inference, including confidence intervals,
-  \code{\link{profile-methods}}.
-
-  \code{\link[boot]{boot}()}, and then
-  \code{\link[boot]{boot.ci}} from package \pkg{boot}.
-}
-\keyword{htest}
-\keyword{models}
-