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  • Committer: Bazaar Package Importer
  • Author(s): Douglas Bates
  • Date: 2005-05-20 09:30:11 UTC
  • mfrom: (1.1.3 upstream)
  • Revision ID: james.westby@ubuntu.com-20050520093011-vp8clxugp8hbjejp
Tags: 0.95.8-1
http://bugs.debian.org/307497
* New upstream release
* Upstream release no longer requires r-cran-latticeextra. Closes: Bug#307497 

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R/AllClass.R
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.onLoad <- function(lib, pkg)
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{
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    if ("package:nlme" %in% search()) {
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        stop(paste("Package lme4 conflicts with package nlme.\n",
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                   "To attach lme4 you must restart R without package nlme."))
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    }
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}
 
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## Class definitions for the package
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setOldClass("data.frame")
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setOldClass("family")
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setOldClass("logLik")
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setOldClass("terms")
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setClass("lme", representation(call = "call",
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                               facs = "list",
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                               x = "list",
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                               model = "data.frame",
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                               REML = "logical",
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                               rep = "ssclme",
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                               fitted = "numeric",
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                               residuals = "numeric",
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                               terms = "terms",
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                               assign = "integer"))
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setClass("GLMM", representation(family = "family",
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                                logLik = "numeric",
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                                fixef = "numeric",
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                                Hessian = "matrix",
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                                method = "character"),
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         contains = "lme")
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setClass("lmList",
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         representation(call = "call",
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                        pool = "logical"),
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                        useScale="logical"),
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         prototype = list(scale = 1.0, useScale = TRUE))
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setClass("summary.ssclme",
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         representation(coefficients="matrix",
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                        scale="numeric",
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                        denomDF="integer",
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                        REML="logical",
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                        ngrps="integer",
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                        nobs="integer",
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                        corFixed="corrmatrix",
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                        VarCorr="VarCorr",
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                        useScale="logical",
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                        showCorrelation="logical"
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                        ))
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setClass("summary.lme",
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         representation(call = "call",
 
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## mixed effects representation
 
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setClass("mer",
 
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         representation(
 
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                        flist = "list", # list of grouping factors
 
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                        perm = "list",  # list of permutations of levels (0-based)
 
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                        Parent = "list",# list of Parent arrays for ZZpO
 
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                        D = "list",     # list of diagonal factors (upper triangle)
 
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                        bVar = "list",  # list of conditional variance factors (upper triangle)
 
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                        L = "list",     # list of blocks of L
 
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                        ZZpO = "list",  # list of diagonal blocks of Z'Z+Omega
 
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                        Omega = "list", # list of relative precision matrices
 
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                        REML = "logical", 
 
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                        RXX = "matrix", # Augmented RXX component or its inverse
 
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                        RZX = "matrix", # Augmented RZX component or its inverse
 
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                        XtX = "matrix", # Original X'X matrix
 
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                        ZtZ = "list",   # list of blocks of Z'Z
 
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                        ZtX = "matrix", # Original Z'X matrix
 
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                        cnames = "list",# column names of model matrices
 
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                        devComp = "numeric", # Components of deviance
 
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                        deviance = "numeric", # Current deviance (ML and REML)
 
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                        nc = "integer", # number of columns in (augmented)
 
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                                        # model matrices and number of observations
 
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                        Gp = "integer", # Pointers to groups of rows in RZX
 
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                        status = "logical"
 
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                        ),
 
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         validity = function(object) {
 
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             .Call("lmer_validate", object, PACKAGE = "Matrix")
 
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         })
 
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## Representation of a linear mixed effects model
 
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setClass("lmer",
 
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         representation(call = "call", terms = "terms",
 
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                        assign = "integer", fitted = "numeric",
 
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                        residuals = "numeric", frame = "data.frame"),
 
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         contains = "mer")
 
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## Representation of a generalized linear mixed effects model
 
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setClass("glmer",
 
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         representation(family = "family", glmmll = "numeric",
 
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                        method = "character", fixed = "numeric"),
 
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         contains = "lmer")
 
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setClass("summary.lmer",
 
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         representation(useScale="logical",
 
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                        showCorrelation="logical",
 
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                        method = "character",
 
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                        family = "family",
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                        logLik = "logLik",
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                        re = "summary.ssclme",
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                        residuals = "numeric"))
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setClass("summary.GLMM", representation(family = "family"),
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         contains = "summary.lme")
 
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                        fixed = "numeric"),
 
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         contains = "lmer")
 
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setClass("lmList.confint", contains = "array")
 
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setClass("lmer.ranef",
 
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         representation(varFac = "list", stdErr = "numeric"),
 
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         contains = "list")
 
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setClass("lmer.ranef.confint", contains = "list")
 
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setClass("lmer.coef",
 
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         representation(varFac = "list", stdErr = "numeric"),
 
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         contains = "list")
 
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