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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 1149, Thu Jan 12 03:40:07 2006 UTC revision 1150, Thu Jan 12 03:41:25 2006 UTC
# Line 360  Line 360 
360           function(object) .Call("lsRMatrix_validate", object, PACKAGE = "Matrix")           function(object) .Call("lsRMatrix_validate", object, PACKAGE = "Matrix")
361           )           )
362    
 ## Compressed sparse column matrix in blocks  
   
 setClass("dgBCMatrix",  
          representation(p = "integer", i = "integer", x = "array"))  
   
363  ## Factorization classes  ## Factorization classes
364    
365  setClass("Cholesky", contains = "dtrMatrix")  setClass("Cholesky", contains = "dtrMatrix")
366    
367    setClass("LDL", contains = "dtrMatrix")
368    
369    setClass("correlation", representation(sd = "numeric"), contains = "dpoMatrix")
370    
371  setClass("pCholesky", contains = "dtpMatrix")  setClass("pCholesky", contains = "dtpMatrix")
372    
373  setClass("BunchKaufman",  setClass("BunchKaufman",
# Line 399  Line 398 
398           function(object) .Call("lCholCMatrix_validate", object, PACKAGE = "Matrix")           function(object) .Call("lCholCMatrix_validate", object, PACKAGE = "Matrix")
399           )           )
400    
401    setClass("CHMfactor",            # cholmod_factor struct as S4 object
402             representation(perm = "integer", type = "integer", "VIRTUAL"),
403             validity =
404             function(object) .Call("CHMfactor_validate", object, PACKAGE = "Matrix")
405             )
406    
407    setClass("CHMsuper",                   # supernodal cholmod_factor
408             representation(super = "integer", pi = "integer", px = "integer",
409                            s = "integer", "VIRTUAL"),
410             contains = "CHMfactor",
411             validity =
412             function(object) .Call("CHMsuper_validate", object, PACKAGE = "Matrix"))
413    
414    setClass("CHMsimpl",                   # simplicial cholmod_factor
415             representation(colcount = "integer", p = "integer", i = "integer",
416                            nz = "integer", nxt = "integer", prv = "integer", "VIRTUAL"),
417             contains = "CHMfactor",
418             validity =
419             function(object) .Call("CHMsuper_validate", object, PACKAGE = "Matrix"))
420    
421    setClass("dCHMsuper", representation(x = "numeric"), contains = "CHMsuper")
422    
423    setClass("lCHMsuper", contains = "CHMsuper")
424    
425    setClass("dCHMsimpl", representation(x = "numeric"), contains = "CHMsimpl")
426    
427    setClass("lCHMsimpl", contains = "CHMsimpl")
428    
429    
430  ##-------------------- permutation ----------------------------------------  ##-------------------- permutation ----------------------------------------
431    
432  setClass("pMatrix", representation(perm = "integer"),  setClass("pMatrix", representation(perm = "integer"),
# Line 442  Line 470 
470           validity = function(object) .Call("LU_validate", object, PACKAGE = "Matrix")           validity = function(object) .Call("LU_validate", object, PACKAGE = "Matrix")
471           )           )
472    
 ## Deprecated:  
                        ## positive-definite symmetric matrices as matrices  
 setClass("pdmatrix", contains = "matrix")  
   
 ##                       # factors of positive-definite symmetric matrices  
 ## setClass("pdfactor", representation("matrix", logDet = "numeric"))  
   
                        ## correlation matrices and standard deviations  
 setClass("corrmatrix", representation("matrix", stdDev = "numeric"))  
   
473  ## -------------------- lmer-related Classes --------------------------------  ## -------------------- lmer-related Classes --------------------------------
474    
475  setOldClass("data.frame")  setOldClass("data.frame")
# Line 459  Line 477 
477  setOldClass("logLik")  setOldClass("logLik")
478  setOldClass("terms")  setOldClass("terms")
479    
 setClass("VarCorr",  
          representation(scale = "numeric",  
                         reSumry = "list",  
                         useScale = "logical"),  
          prototype = list(scale = 1.0, useScale = TRUE))  
   
480  ## mixed effects representation  ## mixed effects representation
481  setClass("mer",  setClass("mer",
482           representation(           representation(## original data
483                          flist = "list", # list of grouping factors                          flist = "list", # list of grouping factors
484                          perm = "list",  # list of permutations of levels (0-based)                          Zt = "dgCMatrix",  # sparse representation of Z'
485                          Parent = "list",# list of Parent arrays for ZZpO                          X = "matrix",      # X
486                          D = "list",     # list of diagonal factors (upper triangle)                          y = "numeric",     # y
                         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  
487                          method = "character", # parameter estimation method                          method = "character", # parameter estimation method
488                          RXX = "matrix", # Augmented RXX component or its inverse                          useScale = "logical", # should scale factor be included
489                          RZX = "matrix", # Augmented RZX component or its inverse                          family = "family", # glm family
490                          XtX = "matrix", # Original X'X matrix                          call = "call",     # call to model-fitting function
491                          ZtZ = "list",   # list of blocks of Z'Z                          ## invariants derived from data structure
                         ZtX = "matrix", # Original Z'X matrix  
492                          cnames = "list",# column names of model matrices                          cnames = "list",# column names of model matrices
493                          devComp = "numeric", # Components of deviance                          nc = "integer",    # dimensions of blocks in Omega
494                          deviance = "numeric", # Current deviance (ML and REML)                          Gp = "integer",    # Pointers to groups of rows in Zt
495                          nc = "integer", # number of columns in (augmented)                          ## quantities that vary when Z, X or y are updated
496                                          ## model matrices and number of observations                          XtX = "dpoMatrix", # X'X
497                          Gp = "integer", # Pointers to groups of rows in RZX                          ZtZ = "dsCMatrix", # Z'Z
498                          status = "logical"                          ZtX = "dgeMatrix", # Z'X
499                          ),                          Zty = "numeric",   # Z'y
500           validity = function(object) {                          Xty = "numeric",   # X'y
501               .Call("lmer_validate", object, PACKAGE = "Matrix")                          ## primary slots that vary during the optimization
502           })                          ## When Omega is updated, these are updated
503                            Omega = "list", # list of relative precision matrices
504  setClass("mer2",                          ## Cholesky factor of inflated [Z:X:y]'[Z:X:y]
505           representation(                          L = "dCHMsuper", # sparse Cholesky factor of Z'Z + Omega
506                          flist = "list", # list of grouping factors                          RZX = "dgeMatrix",
507                          L = "list",     # lower Cholesky factor of Z'Z + Omega                          RXX = "dtrMatrix",
                         RXX = "dtrMatrix", # RXX component  
                         RZX = "dgeMatrix", # RZX component  
                         XtX = "dpoMatrix", # Original X'X matrix  
                         ZtZ = "dsCMatrix", # Original Z'Z  
                         ZtX = "dgeMatrix", # Original Z'X matrix  
                         Zty = "numeric", # Original Z'y vector  
                         Xty = "numeric", # Original X'y vector  
508                          rZy = "numeric",                          rZy = "numeric",
509                          rXy = "numeric",                          rXy = "numeric",
                         Omega = "list", # list of relative precision matrices  
                         method = "character", # parameter estimation method  
                         cnames = "list",# column names of model matrices  
510                          devComp = "numeric", # Components of deviance                          devComp = "numeric", # Components of deviance
511                          deviance = "numeric", # Current deviance (ML and REML)                          deviance = "numeric", # Current deviance (ML and REML)
512                          nc = "integer", # number of columns in (augmented)                          ## Secondary slots only evaluated when requested.
513                                          # model matrices and number of observations                          fixef = "numeric",
514                          Gp = "integer", # Pointers to groups of columns in ZtZ                          ranef = "numeric",
515                            RZXinv = "dgeMatrix",
516                            bVar = "list",
517                            gradComp = "list",
518                            ## status indicator
519                          status = "logical"                          status = "logical"
520                          )                          )
521          )          )
522    
523  ## Representation of a linear or generalized linear mixed effects model  ## Representation of a linear or generalized linear mixed effects model
524  setClass("lmer",  setClass("lmer",
525           representation(assign = "integer", call = "call",           representation(assign = "integer", fitted = "numeric",
                         family = "family", fitted = "numeric",  
526                          fixed = "numeric", frame = "data.frame",                          fixed = "numeric", frame = "data.frame",
527                          logLik = "logLik", residuals = "numeric",                          logLik = "logLik", residuals = "numeric",
528                          terms = "terms"),                          terms = "terms"),
529           contains = "mer")           contains = "mer")
530    
531  ## Representation of a generalized linear mixed effects model  setClass("lmer,ranef", contains = "list")
532  ##setClass("glmer",  
 ##         representation(family = "family", glmmll = "numeric", fixed = "numeric"),  
 ##         contains = "lmer")  
   
 setClass("summary.lmer",  
          representation(useScale = "logical",  
                         showCorrelation = "logical"),  
          contains = "lmer")  
   
 ## These are currently *private* classes  
 ## Note that consequently, they print "ugly" w/o an explicit show() method  
 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")  
533    

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