The R Project SVN R-packages

## -------------------- lmer-related Classes --------------------------------

setOldClass("data.frame")

setOldClass("family")

setOldClass("logLik")

setOldClass("terms")

setClass("VarCorr",

         representation(scale="numeric",

                        reSumry="list",

                        useScale="logical"),

         prototype = list(scale = 1.0, useScale = TRUE))

## mixed effects representation

setClass("mer",

         representation(

                        flist = "list", # list of grouping factors

                        perm = "list",  # list of permutations of levels (0-based)

                        Parent = "list",# list of Parent arrays for ZZpO

                        D = "list",     # list of diagonal factors (upper triangle)

                        bVar = "list",  # list of conditional variance factors (upper triangle)

                        L = "list",     # list of blocks of L

                        ZZpO = "list",  # list of diagonal blocks of Z'Z+Omega

                        Omega = "list", # list of relative precision matrices

                        method = "character", # parameter estimation method

                        RXX = "matrix", # Augmented RXX component or its inverse

                        RZX = "matrix", # Augmented RZX component or its inverse

                        XtX = "matrix", # Original X'X matrix

                        ZtZ = "list",   # list of blocks of Z'Z

                        ZtX = "matrix", # Original Z'X matrix

                        cnames = "list",# column names of model matrices

                        devComp = "numeric", # Components of deviance

                        deviance = "numeric", # Current deviance (ML and REML)

                        nc = "integer", # number of columns in (augmented)

                                        # model matrices and number of observations

                        Gp = "integer", # Pointers to groups of rows in RZX

                        status = "logical"

                        ),

         validity = function(object) {

             .Call("lmer_validate", object, PACKAGE = "Matrix")

         })

## Representation of a linear or generalized linear mixed effects model

setClass("lmer",

         representation(assign = "integer", call = "call",

                        family = "family", fitted = "numeric",

                        fixed = "numeric", frame = "data.frame",

                        logLik = "logLik", residuals = "numeric",

                        terms = "terms"),

         contains = "mer")

## Representation of a generalized linear mixed effects model

##setClass("glmer",

##         representation(family = "family", glmmll = "numeric", fixed = "numeric"),

##         contains = "lmer")

setClass("summary.lmer",

         representation(useScale="logical",

                        showCorrelation="logical"),

         contains = "lmer")

setClass("lmer.ranef",

         representation(varFac = "list", stdErr = "numeric"),

         contains = "list")

setClass("lmer.ranef.confint", contains = "list")

setClass("lmer.coef",

         representation(varFac = "list", stdErr = "numeric"),

         contains = "list")