[Lme4-commits] r1430 - pkg/lme4Eigen/man

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

Author: dmbates
Date: 2011-10-18 22:34:01 +0200 (Tue, 18 Oct 2011)
New Revision: 1430

Modified:
   pkg/lme4Eigen/man/mkdevfun.Rd
Log:
Cleanup.


Modified: pkg/lme4Eigen/man/mkdevfun.Rd
===================================================================
--- pkg/lme4Eigen/man/mkdevfun.Rd	2011-10-18 20:33:28 UTC (rev 1429)
+++ pkg/lme4Eigen/man/mkdevfun.Rd	2011-10-18 20:34:01 UTC (rev 1430)
@@ -10,9 +10,6 @@
 }
 \usage{
 mkdevfun(pp, resp)
-% mkdevfun(mod, nAGQ = 1L, beta0 = numeric(length(mod at fe@coef)),
-%          u0 = numeric(length(mod at re@u)),
-%          verbose = 0L, compDev = TRUE)
 }
 \arguments{
   \item{pp}{a prediction module, typically of class
@@ -20,42 +17,17 @@
   }
   \item{resp}{a response module, e.g., of class
     \code{\linkS4class{lmerResp}}.}
-  % \item{nAGQ}{
-  %   number of points per axis for adaptive Gauss-Hermite quadrature. The
-  %   default, \code{1}, creates the Laplace approximation.  The special
-  %   value, \code{0L}, creates the PIRLSBeta Laplace approximation in
-  %   which the penalized iteratively reweighted least squares (PIRLS) algorithm
-  %   is used to optimize all the coefficients.
-  % }
-  % \item{beta0}{
-  %   Starting value to use for \code{beta} in the PIRLS or PIRLSBeta algorithm
-  % }
-  % \item{u0}{
-  %   Starting value to use for \code{u} in the PIRLS or PIRLSBeta algorithm
-  % }
-  % \item{verbose}{
-  %   integer value indicating level of verbosity in the output.  Values
-  %   greater than 1 cause iteration output during the PIRLS algorithm,
-  %   which can be very verbose.
-  % }
-  % \item{compDev}{
-  %   should the compiled
-  %   deviance evaluation be used?  A value of \code{FALSE} provides an
-  %   evaluation function using functions from the Matrix package only.
-  %   (Only available for \code{lmer} model objects).
 }
 \details{
-  The function returned by \code{mkdevfun} evaluates the deviance but
-  does not update any slots in \code{mod}, thus it can be used to fit
-  variations on a fitted model without modifying the original object.
+  The function returned by \code{mkdevfun} evaluates the deviance of the
+  model represented by the predictor module, \code{pp}, and the response
+  module, \code{resp}.
 
-%% FIXME -- this was "lme4a":
   For \code{\link{lmer}} model objects the argument of the resulting
   function is the variance component parameter, \code{theta}, with lower
-  bound \code{mod at re@lower}.  For \code{glmer} or
-  \code{nlmer} model objects with \code{nAGQ = 0} the
-  argument is also \code{theta}.  However, when {nAGQ > 0} the argument
-  is \code{c(theta, beta)}.
+  bound.  For \code{glmer} or \code{nlmer} model objects with
+  \code{nAGQ = 0} the argument is also \code{theta}.  However, when {nAGQ > 0} the
+  argument is \code{c(theta, beta)}.
 }
 \value{
   A function of one numeric argument.
@@ -66,14 +38,8 @@
 \seealso{\code{\link{lmer}}, \code{\link{glmer}} and \code{\link{nlmer}}
 }
 \examples{
-fm1 <- lmer(Yield ~ 1|Batch, Dyestuff, doFit = FALSE)
-(dd0 <- mkdevfun(fm1))
-dd0(0.8)
-bobyqa(1, dd0, 0)
-(dd1 <- mkdevfun(fm1, compDev = FALSE))
-\dontrun{
-dd1(0.8)
-bobyqa(1, dd1, 0)
+(dd <- lmer(Yield ~ 1|Batch, Dyestuff, devFunOnly=TRUE))
+dd(0.8)
+bobyqa(1, dd, 0)
 }
-}
 \keyword{models}