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[matrix] Diff of /pkg/R/AllClass.R
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Diff of /pkg/R/AllClass.R

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revision 768, Wed Jun 8 17:19:21 2005 UTC revision 769, Wed Jun 8 23:47:45 2005 UTC
# Line 308  Line 308 
308    
309                         # correlation matrices and standard deviations                         # correlation matrices and standard deviations
310  setClass("corrmatrix", representation("matrix", stdDev = "numeric"))  setClass("corrmatrix", representation("matrix", stdDev = "numeric"))
311    
312    ## -------------------- lmer-related Classes --------------------------------
313    
314    setOldClass("data.frame")
315    setOldClass("family")
316    setOldClass("logLik")
317    setOldClass("terms")
318    
319    setClass("VarCorr",
320             representation(scale="numeric",
321                            reSumry="list",
322                            useScale="logical"),
323             prototype = list(scale = 1.0, useScale = TRUE))
324    
325    ## mixed effects representation
326    setClass("mer",
327             representation(
328                            flist = "list", # list of grouping factors
329                            perm = "list",  # list of permutations of levels (0-based)
330                            Parent = "list",# list of Parent arrays for ZZpO
331                            D = "list",     # list of diagonal factors (upper triangle)
332                            bVar = "list",  # list of conditional variance factors (upper triangle)
333                            L = "list",     # list of blocks of L
334                            ZZpO = "list",  # list of diagonal blocks of Z'Z+Omega
335                            Omega = "list", # list of relative precision matrices
336                            method = "character", # parameter estimation method
337                            RXX = "matrix", # Augmented RXX component or its inverse
338                            RZX = "matrix", # Augmented RZX component or its inverse
339                            XtX = "matrix", # Original X'X matrix
340                            ZtZ = "list",   # list of blocks of Z'Z
341                            ZtX = "matrix", # Original Z'X matrix
342                            cnames = "list",# column names of model matrices
343                            devComp = "numeric", # Components of deviance
344                            deviance = "numeric", # Current deviance (ML and REML)
345                            nc = "integer", # number of columns in (augmented)
346                                            # model matrices and number of observations
347                            Gp = "integer", # Pointers to groups of rows in RZX
348                            status = "logical"
349                            ),
350             validity = function(object) {
351                 .Call("lmer_validate", object, PACKAGE = "Matrix")
352             })
353    
354    ## Representation of a linear or generalized linear mixed effects model
355    setClass("lmer",
356             representation(assign = "integer", call = "call",
357                            family = "family", fitted = "numeric",
358                            fixed = "numeric", frame = "data.frame",
359                            logLik = "logLik", residuals = "numeric",
360                            terms = "terms"),
361             contains = "mer")
362    
363    ## Representation of a generalized linear mixed effects model
364    ##setClass("glmer",
365    ##         representation(family = "family", glmmll = "numeric", fixed = "numeric"),
366    ##         contains = "lmer")
367    
368    setClass("summary.lmer",
369             representation(useScale="logical",
370                            showCorrelation="logical"),
371             contains = "lmer")
372    
373    setClass("lmer.ranef",
374             representation(varFac = "list", stdErr = "numeric"),
375             contains = "list")
376    
377    setClass("lmer.ranef.confint", contains = "list")
378    
379    setClass("lmer.coef",
380             representation(varFac = "list", stdErr = "numeric"),
381             contains = "list")

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