[Lme4-commits] r1648 - in pkg/lme4Eigen: . man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Mar 13 17:16:49 CET 2012
Author: dmbates
Date: 2012-03-13 17:16:49 +0100 (Tue, 13 Mar 2012)
New Revision: 1648
Added:
pkg/lme4Eigen/man/glmer.nb.Rd
Modified:
pkg/lme4Eigen/NAMESPACE
pkg/lme4Eigen/man/Nelder_Mead.Rd
pkg/lme4Eigen/man/bootMer.Rd
pkg/lme4Eigen/man/getME.Rd
pkg/lme4Eigen/man/glmer.Rd
pkg/lme4Eigen/man/lmer.Rd
pkg/lme4Eigen/man/mcmcsamp.Rd
pkg/lme4Eigen/man/mkdevfun.Rd
pkg/lme4Eigen/man/nlmer.Rd
pkg/lme4Eigen/man/ranef.Rd
Log:
Updated the .Rd and NAMESPACE files from a do-roxy run
Modified: pkg/lme4Eigen/NAMESPACE
===================================================================
--- pkg/lme4Eigen/NAMESPACE 2012-03-13 16:13:53 UTC (rev 1647)
+++ pkg/lme4Eigen/NAMESPACE 2012-03-13 16:16:49 UTC (rev 1648)
@@ -118,7 +118,6 @@
S3method(plot,coef.mer)
S3method(plot,lmList.confint)
S3method(plot,ranef.mer)
-S3method(plot,merMod)
S3method(predict,merMod)
S3method(print,merMod)
S3method(print,summary.mer)
Modified: pkg/lme4Eigen/man/Nelder_Mead.Rd
===================================================================
--- pkg/lme4Eigen/man/Nelder_Mead.Rd 2012-03-13 16:13:53 UTC (rev 1647)
+++ pkg/lme4Eigen/man/Nelder_Mead.Rd 2012-03-13 16:16:49 UTC (rev 1648)
@@ -7,31 +7,39 @@
}
\arguments{
\item{fn}{a function of one numeric vector argument
- returning a numeric scalar}
+ returning a numeric scalar}
+
\item{par}{numeric vector of starting values for the
parameters.}
+
\item{lower}{numeric vector of lower bounds - elements
may be \code{-Inf}.}
+
\item{upper}{numeric vector of upper bounds - elements
may be \code{Inf}.}
+
\item{control}{a named list of control settings.
- Possible settings are \describe{
- \item{verbose}{FIXME (Roxygen sync?)}
- \item{iprint}{numeric
- scalar - frequency of printing evaluation information.
- Defaults to 0 indicating no printing.}
- \item{maxfun}{numeric scalar - maximum number of function
- evaluations allowed.} \item{FtolAbs}{numeric scalar -
- absolute tolerance on change in function values}
- \item{FtolRel}{numeric scalar - relative tolerance on
- change in function values} \item{XtolRel}{numeric scalar
- - relative tolerance on change in parameter values}
- \item{MinfMax}{numeric scalar - maximum value of the
- minimum}
- \item{xst}{numeric vector of initial step sizes to
- establish the simplex - all elements must be non-zero.}
- \item{xt}{numeric vector of tolerances on the
- parameters.}
+ Possible settings are \describe{ \item{iprint}{numeric
+ scalar - frequency of printing evaluation information.
+ Defaults to 0 indicating no printing.}
+ \item{maxfun}{numeric scalar - maximum number of function
+ evaluations allowed (default:10000).}
+ \item{FtolAbs}{numeric scalar - absolute tolerance on
+ change in function values (default: 1e-5)}
+ \item{FtolRel}{numeric scalar - relative tolerance on
+ change in function values (default:1e-15)}
+ \item{XtolRel}{numeric scalar - relative tolerance on
+ change in parameter values (default: 1e-7)}
+ \item{MinfMax}{numeric scalar - maximum value of the
+ minimum (default: .Machine$double.xmin)}
+ \item{xst}{numeric vector of initial step sizes to
+ establish the simplex - all elements must be non-zero
+ (default: rep(0.02,length(par)))} \item{xt}{numeric
+ vector of tolerances on the parameters (default:
+ xst*5e-4)} \item{verbose}{numeric value: 0=no printing,
+ 1=print every 20 evaluations, 2=print every 10
+ evalutions, 3=print every evaluation. Sets
+ \sQuote{iprint}, if specified, but does not override it.}
}}
}
\value{
Modified: pkg/lme4Eigen/man/bootMer.Rd
===================================================================
--- pkg/lme4Eigen/man/bootMer.Rd 2012-03-13 16:13:53 UTC (rev 1647)
+++ pkg/lme4Eigen/man/bootMer.Rd 2012-03-13 16:16:49 UTC (rev 1648)
@@ -11,7 +11,7 @@
\item{x}{fitted \code{*lmer()} model, see
\code{\link{lmer}}, \code{\link{glmer}}, etc.}
- \item{FUN}{a \code{\link{function}(x)}, computing the
+ \item{FUN}{a \code{\link{function}(x)}, computating the
\emph{statistic} of interest, which must be a numeric
vector, possibly named.}
@@ -73,7 +73,7 @@
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")) }
+ c(beta =getME(., "beta"), sigma = s, sig01 = unname(s * getME(., "theta"))) }
(t0 <- mySumm(fm01ML)) # just three parameters
## 3.8s (on a 5600 MIPS 64bit fast(year 2009) desktop "AMD Phenom(tm) II X4 925"):
@@ -94,7 +94,6 @@
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
@@ -110,3 +109,4 @@
}
\keyword{htest}
\keyword{models}
+
Modified: pkg/lme4Eigen/man/getME.Rd
===================================================================
--- pkg/lme4Eigen/man/getME.Rd 2012-03-13 16:13:53 UTC (rev 1647)
+++ pkg/lme4Eigen/man/getME.Rd 2012-03-13 16:16:49 UTC (rev 1648)
@@ -4,10 +4,8 @@
\alias{getME}
\title{Extract or Get Generalize Components from a Fitted Mixed Effects Model}
\usage{
-getME(object,
- name = c("X", "Z", "Zt", "u", "Gp", "L", "Lambda", "Lambdat",
- "Lind", "RX", "RZX", "beta", "theta", "REML", "n_rtrms",
- "is_REML", "devcomp", "offset", "lower"))
+ getME(object,
+ name = c("X", "Z", "Zt", "u", "Gp", "L", "Lambda", "Lambdat", "Lind", "RX", "RZX", "beta", "theta", "REML", "n_rtrms", "is_REML", "devcomp", "offset", "lower"))
}
\arguments{
\item{object}{a fitted mixed-effects model of class
@@ -34,14 +32,15 @@
fixed-effects parameters} \item{RZX}{cross-term in the
full Cholesky factor} \item{beta}{fixed-effects parameter
estimates (same as the result of \code{\link{fixef}})}
- \item{n_rtrms}{number of random-effects terms}
- \item{is_REML}{same as the result of
- \code{\link{isREML}}} \item{devcomp}{a list consisting of
- a named numeric vector, \dQuote{cmp}, and a named integer
- vector, \dQuote{dims}, describing the fitted model}
-\item{offset}{model offset}
-\item{lower}{lower bounds on model parameters}
-}}
+ \item{theta}{random-effects parameter estimates: these
+ are parameterized as the relative Cholesky factors of
+ each random effect term} \item{n_rtrms}{number of
+ random-effects terms} \item{is_REML}{same as the result
+ of \code{\link{isREML}}} \item{devcomp}{a list consisting
+ of a named numeric vector, \dQuote{cmp}, and a named
+ integer vector, \dQuote{dims}, describing the fitted
+ model} \item{offset}{model offset} \item{lower}{lower
+ bounds on model parameters} ## FIXME: theta only? }}
}
\value{
Unspecified, as very much depending on the
@@ -60,11 +59,6 @@
\code{\link{fixef}}, \code{\link{ranef}},
\code{\link{vcov}}, etc.
}
-\seealso{
- \code{\link{getCall}()}, More standard methods for mer
- objects, such as \code{\link{ranef}},
- \code{\link{fixef}}, \code{\link{vcov}}, etc.
-}
\examples{
## shows many methods you should consider *before* getME():
methods(class = "merMod")
@@ -79,5 +73,11 @@
## All that can be accessed [potentially ..]:
(nmME <- eval(formals(getME)$name))
}
+\seealso{
+ \code{\link{getCall}()}, More standard methods for mer
+ objects, such as \code{\link{ranef}},
+ \code{\link{fixef}}, \code{\link{vcov}}, etc.: see
+ \code{methods(class="merMod")}
+}
\keyword{utilities}
Modified: pkg/lme4Eigen/man/glmer.Rd
===================================================================
--- pkg/lme4Eigen/man/glmer.Rd 2012-03-13 16:13:53 UTC (rev 1647)
+++ pkg/lme4Eigen/man/glmer.Rd 2012-03-13 16:16:49 UTC (rev 1648)
@@ -7,7 +7,7 @@
nAGQ = 1L, compDev = TRUE, subset, weights, na.action,
offset, contrasts = NULL, mustart, etastart,
devFunOnly = FALSE, tolPwrss = 1e-10,
- optimizer = c("bobyqa","Nelder_Mead"), ...)
+ optimizer = c("bobyqa", "Nelder_Mead"), ...)
}
\arguments{
\item{family}{a GLM family, see \code{\link[stats]{glm}}
@@ -36,12 +36,37 @@
\code{start} argument of the appropriate length is used
as the starting value of \code{theta}.}
- \item{optimizer}{which optimizer to use in the second
- phase of optimization. The default is
- \code{\link{NelderMead}} and the alternative is
- \code{\link{bobyqa}}. For difficult model fits we have
- found \code{\link{NelderMead}} to be more reliable but
- occasionally slower than \code{\link{bobyqa}}.}
+ \item{optimizer}{which optimizer(s) to use for each phase
+ of optimization. A character vector or list of
+ functions. If \code{length(optimizer)==2}, the first
+ element will be used for the preliminary (random effects
+ parameters only) optimization, while the second will be
+ used for the final (random effects plus fixed effect
+ parameters) phase. The built-in optimizers are
+ \code{\link{Nelder_Mead}} and \code{\link{bobyqa}} (from
+ the \code{minqa} package; the default is to use
+ \code{\link{bobyqa}} for the first and
+ \code{\link{Nelder_Mead}} for the final phase. (FIXME:
+ simplify if possible!). For difficult model fits we have
+ found \code{\link{Nelder_Mead}} to be more reliable but
+ occasionally slower than \code{\link{bobyqa}}. Any
+ minimizing function that allows box constraints can be
+ used provided that it (1) takes input parameters
+ \code{fn} (function to be optimized), \code{par}
+ (starting parameter values), \code{lower} (lower bounds)
+ and \code{control} (control parameters, passed through
+ from the \code{control} argument) and (2) returns a list
+ with (at least) elements \code{par} (best-fit
+ parameters), \code{fval} (best-fit function value),
+ \code{conv} (convergence code) and (optionally)
+ \code{message} (informational message, or explanation of
+ convergence failure). Special provisions are made for
+ \code{\link{bobyqa}}, \code{\link{Nelder_Mead}}, and
+ optimizers wrapped in the \code{optimx} package; to use
+ \code{optimx} optimizers (including \code{L-BFGS-B} from
+ base \code{optim} and \code{nlminb}), pass the
+ \code{method} argument to \code{optim} in the
+ \code{control} argument.}
\item{mustart}{optional starting values on the scale of
the conditional mean, as in \code{\link[stats]{glm}}; see
@@ -173,6 +198,8 @@
}
\examples{
## generalized linear mixed model
+library(lattice)
+xyplot(incidence/size ~ period, group=herd, type="a", data=cbpp)
(gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd),
data = cbpp, family = binomial))
## using nAGQ=0L only gets close to the optimum
Added: pkg/lme4Eigen/man/glmer.nb.Rd
===================================================================
--- pkg/lme4Eigen/man/glmer.nb.Rd (rev 0)
+++ pkg/lme4Eigen/man/glmer.nb.Rd 2012-03-13 16:16:49 UTC (rev 1648)
@@ -0,0 +1,21 @@
+\name{glmer.nb}
+\alias{glmer.nb}
+\title{glmer() for Negative Binomial}
+\usage{
+ glmer.nb(..., interval = log(th) + c(-3, 3),
+ verbose = FALSE)
+}
+\arguments{
+ \item{...}{formula, data, etc: the arguments for
+ \code{\link{glmer}(..)} (apart from \code{family}!).}
+
+ \item{interval}{interval in which to start the
+ optimization}
+
+ \item{verbose}{logical indicating how much progress
+ information should be printed.}
+}
+\description{
+ glmer() for Negative Binomial
+}
+
Modified: pkg/lme4Eigen/man/lmer.Rd
===================================================================
--- pkg/lme4Eigen/man/lmer.Rd 2012-03-13 16:13:53 UTC (rev 1647)
+++ pkg/lme4Eigen/man/lmer.Rd 2012-03-13 16:16:49 UTC (rev 1648)
@@ -5,7 +5,7 @@
lmer(formula, data, REML = TRUE, sparseX = FALSE,
control = list(), start = NULL, verbose = 0L, subset,
weights, na.action, offset, contrasts = NULL,
- devFunOnly = FALSE, optimizer="Nelder_Mead", ...)
+ devFunOnly = FALSE, optimizer = "Nelder_Mead", ...)
}
\arguments{
\item{formula}{a two-sided linear formula object
@@ -86,9 +86,10 @@
\code{contrasts.arg} of \code{model.matrix.default}.}
\item{devFunOnly}{logical - return only the deviance
- evaluation function.}
- \item{optimizer}{optimizer to use}
+ evaluation function.}
+ \item{optimizer}{character - name of optimizing function}
+
\item{\dots}{other potential arguments. A \code{method}
argument was used in earlier versions of the package. Its
functionality has been replaced by the \code{REML}
Modified: pkg/lme4Eigen/man/mcmcsamp.Rd
===================================================================
--- pkg/lme4Eigen/man/mcmcsamp.Rd 2012-03-13 16:13:53 UTC (rev 1647)
+++ pkg/lme4Eigen/man/mcmcsamp.Rd 2012-03-13 16:16:49 UTC (rev 1648)
@@ -12,7 +12,7 @@
\item{verbose}{should verbose output be given?}
- \item{...}{unused currently}
+ \item{...}{}
}
\value{
a Markov chain Monte Carlo sample as a matrix
Modified: pkg/lme4Eigen/man/mkdevfun.Rd
===================================================================
--- pkg/lme4Eigen/man/mkdevfun.Rd 2012-03-13 16:13:53 UTC (rev 1647)
+++ pkg/lme4Eigen/man/mkdevfun.Rd 2012-03-13 16:16:49 UTC (rev 1648)
@@ -35,8 +35,6 @@
\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)}.
-
- FIXME: out of date! See example.
}
\examples{
(dd <- lmer(Yield ~ 1|Batch, Dyestuff, devFunOnly=TRUE))
Modified: pkg/lme4Eigen/man/nlmer.Rd
===================================================================
--- pkg/lme4Eigen/man/nlmer.Rd 2012-03-13 16:13:53 UTC (rev 1647)
+++ pkg/lme4Eigen/man/nlmer.Rd 2012-03-13 16:16:49 UTC (rev 1648)
@@ -5,8 +5,7 @@
nlmer(formula, data, control = list(), start = NULL,
verbose = 0L, nAGQ = 1L, subset, weights, na.action,
offset, contrasts = NULL, devFunOnly = 0L,
- tolPwrss = 1e-10,
- optimizer = "Nelder_Mead", ...)
+ tolPwrss = 1e-10, optimizer = "Nelder_Mead", ...)
}
\arguments{
\item{formula}{a nonlinear mixed model formula (see
@@ -101,12 +100,37 @@
weighted residual sum-of-squares step. Defaults to
1e-10.}
- \item{optimizer}{which optimizer to use in the second
- phase of optimization. The default is
- \code{\link{NelderMead}} and the alternative is
- \code{\link{bobyqa}}. For difficult model fits we have
- found \code{\link{NelderMead}} to be more reliable but
- occasionally slower than \code{\link{bobyqa}}.}
+ \item{optimizer}{which optimizer(s) to use for each phase
+ of optimization. A character vector or list of
+ functions. If \code{length(optimizer)==2}, the first
+ element will be used for the preliminary (random effects
+ parameters only) optimization, while the second will be
+ used for the final (random effects plus fixed effect
+ parameters) phase. The built-in optimizers are
+ \code{\link{Nelder_Mead}} and \code{\link{bobyqa}} (from
+ the \code{minqa} package; the default is to use
+ \code{\link{bobyqa}} for the first and
+ \code{\link{Nelder_Mead}} for the final phase. (FIXME:
+ simplify if possible!). For difficult model fits we have
+ found \code{\link{Nelder_Mead}} to be more reliable but
+ occasionally slower than \code{\link{bobyqa}}. Any
+ minimizing function that allows box constraints can be
+ used provided that it (1) takes input parameters
+ \code{fn} (function to be optimized), \code{par}
+ (starting parameter values), \code{lower} (lower bounds)
+ and \code{control} (control parameters, passed through
+ from the \code{control} argument) and (2) returns a list
+ with (at least) elements \code{par} (best-fit
+ parameters), \code{fval} (best-fit function value),
+ \code{conv} (convergence code) and (optionally)
+ \code{message} (informational message, or explanation of
+ convergence failure). Special provisions are made for
+ \code{\link{bobyqa}}, \code{\link{Nelder_Mead}}, and
+ optimizers wrapped in the \code{optimx} package; to use
+ \code{optimx} optimizers (including \code{L-BFGS-B} from
+ base \code{optim} and \code{nlminb}), pass the
+ \code{method} argument to \code{optim} in the
+ \code{control} argument.}
}
\description{
Fit a nonlinear mixed-effects model
Modified: pkg/lme4Eigen/man/ranef.Rd
===================================================================
--- pkg/lme4Eigen/man/ranef.Rd 2012-03-13 16:13:53 UTC (rev 1647)
+++ pkg/lme4Eigen/man/ranef.Rd 2012-03-13 16:16:49 UTC (rev 1648)
@@ -79,9 +79,9 @@
fm2 <- lmer(Reaction ~ Days + (1|Subject) + (0+Days|Subject), sleepstudy)
fm3 <- lmer(diameter ~ (1|plate) + (1|sample), Penicillin)
ranef(fm1)
-if(FALSE) { ##-- postVar=TRUE is not yet implemented -- FIXME
str(rr1 <- ranef(fm1, postVar = TRUE))
dotplot(rr1,scales = list(x = list(relation = 'free')))[["Subject"]]
+if(FALSE) { ##-- postVar=TRUE is not yet implemented for multiple terms -- FIXME
str(ranef(fm2, postVar = TRUE))
}
op <- options(digits = 4)
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