[Lme4-commits] r1432 - pkg/lme4Eigen/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Nov 2 21:13:04 CET 2011
Author: dmbates
Date: 2011-11-02 21:13:03 +0100 (Wed, 02 Nov 2011)
New Revision: 1432
Added:
pkg/lme4Eigen/man/merPredD-class.Rd
Removed:
pkg/lme4Eigen/man/lmerMod-class.Rd
Modified:
pkg/lme4Eigen/man/merMod-class.Rd
Log:
incorporate documentation for [gn]lmerMod-class in the merMod-class docs; document merPredD-class
Deleted: pkg/lme4Eigen/man/lmerMod-class.Rd
===================================================================
--- pkg/lme4Eigen/man/lmerMod-class.Rd 2011-11-02 18:18:14 UTC (rev 1431)
+++ pkg/lme4Eigen/man/lmerMod-class.Rd 2011-11-02 20:13:03 UTC (rev 1432)
@@ -1,41 +0,0 @@
-\name{lmerMod-class}
-\Rdversion{1.1}
-\docType{class}
-\alias{lmerMod-class}
-
-\title{Class \code{"lmerMod"} of Fitted Linear Mixed-Effect Models}
-
-\description{
- A fitted linear mixed-effects model contains specific response module
- plus the parts, i.e., \code{\link{slot}}s of a general mixed-effects
- model, from class \code{\linkS4class{merMod}}, notably with it
- prediction module.
-}
-\section{Objects from the Class}{
- Objects can in priniciple be created by calls of the form
- \code{new("lmerMod", ...)}, but practically from \code{\link{lmer}()}.
-}
-\section{Slots}{
- \describe{
- \item{\code{resp}:}{a response module object of class
- \code{"\linkS4class{lmerResp}"}, see there.}
-
- \item{\code{call}, \code{frame}, ..., \code{pp}:}{all other slots
- are inherited from the super class \code{"\linkS4class{merMod}"}.}
- }
-}
-\section{Extends}{
- Class \code{"\linkS4class{merMod}"}, directly.
-}
-\section{Methods}{
- No methods defined with class "lmerMod" in the signature.
-}
-% \references{
-% }
-\seealso{
- \code{\link{lmer}()}; class \code{\linkS4class{merMod}}.
-}
-\examples{
-showClass("lmerMod")
-}
-\keyword{classes}
Modified: pkg/lme4Eigen/man/merMod-class.Rd
===================================================================
--- pkg/lme4Eigen/man/merMod-class.Rd 2011-11-02 18:18:14 UTC (rev 1431)
+++ pkg/lme4Eigen/man/merMod-class.Rd 2011-11-02 20:13:03 UTC (rev 1432)
@@ -3,6 +3,9 @@
\Rdversion{1.1}
\docType{class}
\alias{merMod-class}
+\alias{lmerMod-class}
+\alias{glmerMod-class}
+\alias{nlmerMod-class}
%% FIXME --- currently only sigma() and show() ...
\alias{anova,merMod-method}
\alias{coef,merMod-method}
@@ -32,10 +35,12 @@
\alias{vcov,summary.mer-method}
%
\description{
- A mixed-effects model represented as a \code{\linkS4class{reModule}}
- for the random effects, an \code{\linkS4class{feModule}} for the
- fixed-effects parameters and an \code{\linkS4class{respModule}} module
- for the response.
+ A mixed-effects model represented as a \code{\linkS4class{merPredD}} object
+ and a response module of a class that inherits from class
+ \code{\linkS4class{lmResp}}. A model with a
+ \code{\linkS4class{lmerResp}} response has class \code{lmerMod};
+ a \code{\linkS4class{glmResp}} response has class \code{glmerMod};
+ and a \code{\linkS4class{nlsResp}} response has class \code{nlmerMod}.
}
\section{Objects from the Class}{
Objects are created by calls to \code{\link{lmer}},
@@ -57,22 +62,18 @@
\item{\code{devcomp}:}{Object of class \code{"list"} ~~ }
\item{\code{pp}:}{A prediction module object of class
\code{"\linkS4class{merPredD}"}.}
- % \item{\code{devcomp}:}{A list with two components:
- % \dQuote{\code{cmp}}, a numeric vector of components used to
- % evaluate the deviance, and \dQuote{\code{dims}}, an integer vector
- % of dimensions and flags.}
- % \item{\code{re}:}{An \code{\linkS4class{reModule}} object
- % representing the random effects values and various matrices
- % associated with them.}
- % \item{\code{fe}:}{An \code{\linkS4class{feModule}} object
- % representing the fixed-effects parameters and various matrices
- % associated with them.}
- % \item{\code{resp}:}{An \code{\linkS4class{respModule}} object containing
- % information on the response, the fitted values, the residuals
- % and various forms of weights. According to the class of this
- % object the model is a linear mixed model (\code{\link{lmer}}), a
- % generalized linear mixed model (\code{\link{glmer}}) or a
- % nonlinear mixed model (\code{\link{nlmer}}).}
+ \item{\code{devcomp}:}{A list with two components:
+ \dQuote{\code{cmp}}, a numeric vector of components used to
+ evaluate the deviance, and \dQuote{\code{dims}}, an integer vector
+ of dimensions and flags.}
+ \item{\code{re}:}{An \code{\linkS4class{lmerResp}},
+ \code{\linkS4class{glmResp}} or \code{\linkS4class{nlsResp}}
+ object containing information on the response, the fitted values,
+ the residuals and various forms of weights. According to the
+ class of this object the model is a linear mixed model
+ (\code{\link{lmer}}), a generalized linear mixed model
+ (\code{\link{glmer}}) or a nonlinear mixed model
+ (\code{\link{nlmer}}).}
}
}
\section{Methods}{
@@ -105,9 +106,8 @@
%%\author{}
\seealso{\code{\link{lmer}}, \code{\link{glmer}}, \code{\link{nlmer}},
- % \code{\linkS4class{reModule}}, \code{\linkS4class{feModule}},
- % \code{\linkS4class{respModule}}
- \code{\linkS4class{merPredD}}
+ \code{\linkS4class{merPredD}}, \code{\linkS4class{lmerResp}},
+ \code{\linkS4class{glmResp}}, \code{\linkS4class{nlsResp}}
}
\examples{
showClass("merMod")
Added: pkg/lme4Eigen/man/merPredD-class.Rd
===================================================================
--- pkg/lme4Eigen/man/merPredD-class.Rd (rev 0)
+++ pkg/lme4Eigen/man/merPredD-class.Rd 2011-11-02 20:13:03 UTC (rev 1432)
@@ -0,0 +1,150 @@
+\name{merPredD-class}
+\alias{merPredD-class}
+\alias{merPredD}
+\title{Class \code{"merPredD"} - a dense predictor reference class}
+\usage{
+ merPredD$new(X=X, Zt=Zt, Lambdat=Lambdat, Lind=Lind, theta=theta)
+}
+\arguments{
+ \item{X}{dense model matrix for the fixed-effects parameters, to be
+ stored in the \code{X} field.}
+ \item{Zt}{transpose of the sparse model matrix for the random
+ effects. It is stored in the \code{Zt} field.}
+ \item{Lambdat}{transpose of the sparse lower triangular relative
+ variance factor (stored in the \code{Lambdat} field).}
+ \item{Lind}{integer vector of the same length as the \code{"x"} slot
+ in the \code{Lambdat} field. Its elements should be in the range 1
+ to the length of the \code{theta} field.}
+ \item{theta}{numeric vector of variance component parameters (stored
+ in the \code{theta} field).}
+}
+\description{
+ A reference class for a mixed-effects model predictor module with a
+ dense model matrix for the fixed-effects parameters. The reference
+ class is associated with a C++ class of the same name. As is
+ customary, the generator object for the class has the same name as the
+ class.
+}
+\section{Extends}{
+ All reference classes extend and inherit methods from
+ \code{"\linkS4class{envRefClass}"}.
+}
+%\references{}
+%\author{}
+\note{
+ Objects from this reference class correspond to objects in a C++ class.
+ Methods are invoked on the C++ class object using the external pointer in
+ the \code{ptr} field.
+ % When saving such an object the external pointer
+ % is converted to a null pointer, which is why there are redundant
+ % fields containing enough information as R objects to be able to
+ % regenerate the C++ object. The convention is that a field whose name begins
+ % with an upper-case letter is an R object and the corresponding field
+ % whose name begins with the lower-case letter is an active-binding
+ % function. The values should be accessed through the active-binding
+ % function, not directly as the R object field.
+}
+\seealso{
+ \code{\link{lmer}}, \code{\link{glmer}}, \code{\link{nlmer}}, \code{\linkS4class{merMod}}.
+}
+\examples{
+showClass("merPredD")
+str(lmer(Yield ~ 1|Batch, Dyestuff)@pp)
+}
+\keyword{classes}
+\section{Fields}{
+ For class \code{"lmResp"},
+ \describe{
+ \item{\code{X}:}{dense model matrix of class \code{\linkS4class{ddenseModelMatrix}}}
+ \item{\code{Zt}:}{transposed sparse model matrix of class \code{\linkS4class{dgCMatrix}}}
+ \item{\code{Lambdat}:}{transposed sparse relative covariance factor
+ of class \code{\linkS4class{dgCMatrix}}}
+ \item{\code{Lind}:}{integer vector of 1-based indices into the
+ \code{theta} field.}
+ \item{\code{theta}:}{numeric vector of variance component
+ parameters. Assignment of this field causes an update of values
+ in the C++ class.}
+ \item{\code{ptr}:}{\code{externalptr} to the instance of the C++ class}
+ % \item{\code{ptr}:}{\code{activeBindingFunction} that returns the
+ % external pointer, \code{Ptr}, regenerating it if necessary. All
+ % access to the external pointer should be through this field.}
+ \item{\code{beta0}:}{numeric vector of offsets for the fixed-effects
+ coefficients}
+ \item{\code{u0}:}{numeric vector of offsets for the orthogonal
+ random effects}
+ }
+}
+\section{Methods}{
+ \describe{
+ \item{\code{b()}:}{returns the conditional mode of the random
+ effects (numeric vector).}
+ \item{\code{beta()}:}{returns the fixed-effects parameters (numeric
+ vector).}
+ \item{\code{CcNumer()}:}{returns the numerator of the orthogonality
+ convergence criterion (numeric scalar).}
+ \item{\code{delb()}:}{returns the full increment for the
+ fixed-effects parameters (numeric vector).}
+ \item{\code{delu()}:}{returns the full increment for the
+ orthogonal random effects (numeric vector).}
+ \item{\code{getLambdat()}:}{returns the relative covariance factor
+ at the current value of \code{theta} (a
+ \code{\linkS4class{dgCMatrix}} object). The \code{Lambdat} field
+ is not updated with each change in the \code{theta} field but the
+ value returned by this method is.}
+ \item{\code{initialize()}:}{the standard \code{initialize} method is
+ overridden in this class.}
+ \item{\code{installPars(fac)}:}{updates the offset for the
+ fixed-effects parameters and the orthogonal random effects using
+ step factor \code{fac}.}
+ \item{\code{L()}:}{returns the sparse Cholesky factor for the random
+ effects (a \code{\linkS4class{dCHMsimpl}} object).}
+ \item{\code{LamtUt()}:}{returns the product of \code{Lambdat} and
+ \code{Ut}, a \code{linkS4class{dgCMatrix}} object.}
+ \item{\code{ldL2()}:}{returns the log of the square of the
+ determinant of the sparse Cholesky factor, \code{L} (numeric
+ scalar).}
+ \item{\code{ldRX2()}:}{returns the log of the square of the
+ determinant of the dense Cholesky factor, \code{RX} (numeric
+ scalar).}
+ \item{\code{linPred(fac)}:}{returns the linear predictor for step
+ factor \code{fac} (numeric vector).}
+ \item{\code{P()}:}{returns the 0-based permutation vector of the
+ sparse Cholesky factor (integer vector).}
+ \item{\code{RX()}:}{returns the upper-triangular dense Cholesky
+ factor for the random effects (numeric matrix).}
+ \item{\code{RXdiag()}:}{returns the diagonal of \code{RX} (numeric
+ vector)}
+ \item{\code{RZX()}:}{returns the off-diagonal block of full Cholesky
+ factor (numeric matrix).}
+ \item{\code{solve()}:}{updates both increments, \code{delu} and
+ \code{delb}, as the least squares solutions given the updated
+ residuals and X-weights.}
+ \item{\code{solveU()}:}{updates only the increment \code{delu}
+ the least squares solutions given the updated residuals and
+ X-weights.}
+ \item{\code{u()}:}{returns the conditional mode of the orthogonal
+ random effects (numeric vector).}
+ \item{\code{unsc()}:}{returns the unscaled variance-covariance
+ matrix of the fixed-effects parameters (numeric matrix).}
+ \item{\code{updateDecomp()}:}{causes an update of \code{L},
+ \code{RZX} and \code{RX}, the parts of the full Cholesky
+ decomposition in the C++ object. Also updates \code{ldL2} and
+ \code{ldRX2} (returns NULL).}
+ \item{\code{updateRes(wtres)}:}{updates the C++ object for the
+ numeric vector of weighted residuals, \code{wtres} (returns
+ NULL).}
+ \item{\code{updateXwts(wts)}:}{updates the C++ object for the
+ numeric matrix of square roots of the X weights \code{wts}
+ (returns NULL).}
+ \item{\code{Ut()}:}{the transposed, weighted random effects model
+ matrix, a \code{\linkS4class{dgCMatrix}} object.}
+ \item{\code{Utr()}:}{the product of \code{Ut} and the weighted
+ residuals (numeric vector).}
+ \item{\code{V()}:}{the weighted fixed effects model matrix (numeric
+ matrix).}
+ \item{\code{Vtr()}:}{the cross-product of \code{V} and the weighted
+ residuals (numeric vector).}
+ \item{\code{VtV()}:}{the cross-product of \code{V} (numeric
+ matrix).}
+ }
+}
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