From noreply at r-forge.r-project.org  Thu Jun  6 15:28:14 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu,  6 Jun 2013 15:28:14 +0200 (CEST)
Subject: [Georob-commits] r6 - in pkg: . R man
Message-ID: <20130606132814.8DA80184B6F@r-forge.r-project.org>

Author: papritz
Date: 2013-06-06 15:28:13 +0200 (Thu, 06 Jun 2013)
New Revision: 6

Modified:
   pkg/ChangeLog
   pkg/NAMESPACE
   pkg/R/georob.S3methods.R
   pkg/R/georob.cv.R
   pkg/R/georob.exported.functions.R
   pkg/R/georob.predict.R
   pkg/R/georob.private.functions.R
   pkg/man/cv.georob.Rd
   pkg/man/georob.control.Rd
   pkg/man/georobObject.Rd
   pkg/man/internal.functions.Rd
   pkg/man/predict.georob.Rd
Log:
handling design matrices with rank < ncol(x)
changes for solving estimating equations for xi

M    pkg/R/georob.cv.R
M    pkg/R/georob.S3methods.R
M    pkg/R/georob.predict.R
M    pkg/R/georob.exported.functions.R
M    pkg/R/georob.private.functions.R
M    pkg/ChangeLog
M    pkg/man/internal.functions.Rd
M    pkg/man/cv.georob.Rd
M    pkg/man/georob.control.Rd
M    pkg/man/georobObject.Rd
M    pkg/man/predict.georob.Rd
M    pkg/NAMESPACE



Modified: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog	2013-05-23 15:41:57 UTC (rev 5)
+++ pkg/ChangeLog	2013-06-06 13:28:13 UTC (rev 6)
@@ -68,8 +68,25 @@
 * georob.exported.functions.R (georob): improved way to handle missing observations and to construct model.frame
 * georob.predict.R (predict.georob): correct handling of missing observations
 * georob.S3methods.R (georob.residuals): new argument "terms"
-* georob.S3methods.R (ranef.georob, rstandard.georob,deviance.georob): correct handling of missing observations
+* georob.S3methods.R (ranef.georob, residuals.georob, rstandard.georob, deviance.georob): correct handling of missing observations
 * variogram.R (plot.georob): correct handling of missing observations
 
 
+2013-05-24  Andreas Papritz  <papritz at env.ethz.ch>
 
+* georob.cv.R (cv.georob): separate initial variogram parameters for each cross-validation set
+
+
+2013-05-31  Andreas Papritz  <papritz at env.ethz.ch>
+
+* georob.S3methods.R (ranef.georob, residuals.georob,rstandard.georob,deviance.georob): correct handling of missing observations
+* georob.S3methods.R (deviance.georob, ranef.georob, rstandard.georob, summary.georob): revised expansion of covariance matrices
+
+
+2013-06-06  Andreas Papritz  <papritz at env.ethz.ch>
+
+* georob.exported.function.R (georob, georob.control): handling fixed effects model matrices with rank < ncol(x)
+* georob.private.function.R (prepare.likelihood.calculations, compute.estimating.equations, negative.restr.loglikelihood, negative.restr.loglikelihood, gradient.negative.restricted.loglikelihood, georob.fit) : solving estimating equations for xi
+* georob.S3methods.R ranef.georob, rstandard.georob) : solving estimating equations for xi
+* georob.private.function.R (compute.covariances, estimate.xihat, update.xihat, negative.restr.loglikelihood): solving estimating equations for xi
+

Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE	2013-05-23 15:41:57 UTC (rev 5)
+++ pkg/NAMESPACE	2013-06-06 13:28:13 UTC (rev 6)
@@ -76,16 +76,15 @@
 ##   compute.covariances,
 ##   compute.estimating.equations,
 ##   compute.semivariance,
-##   compute.U,
 ##   dcorr.dparam,
-##   estimate.betahat.bhat,
+##   estimate.xihat,
 ##   gcr,
 ##   georob.fit,
 ##   getCall.georob,
 ##   gradient.negative.restricted.loglikelihood,
 ##   negative.restr.loglikelihood,
 ##   prepare.likelihood.calculations,
-##   update.betahat.bhat
+##   update.xihat
 
 S3method( deviance, georob  )
 S3method( fixed.effects, georob  )

Modified: pkg/R/georob.S3methods.R
===================================================================
--- pkg/R/georob.S3methods.R	2013-05-23 15:41:57 UTC (rev 5)
+++ pkg/R/georob.S3methods.R	2013-06-06 13:28:13 UTC (rev 6)
@@ -169,21 +169,30 @@
   ## 2012-10-18 AP changes for new definition of eta
   ## 2012-11-26 AP method for random.effects
   ## 2013-04-23 AP new names for robustness weights
-  ## 2013-05-23 AP correct handling of missing observations
+  ## 2013-05-31 AP correct handling of missing observations
+  ## 2013-05-31 AP revised expansion of covariance matrices
+  ## 2013-05-06 AP changes for solving estimating equations for xi
   
-  object$Valpha.objects <- expand( object$Valpha.objects )
-  object$cov       <- expand( object$cov )
+  ## temporarily redefine na.action component of object
   
+  object.na <- object$na.action
+  if( identical( class( object$na.action ), "exclude" ) ){
+    class( object$na.action ) <- "omit"
+  }
+
+  Valpha.objects <- expand( object$Valpha.objects )
+  covmat         <- expand( object$cov )
+  
   bhat <- object$bhat   
   
   if( standard ){
     
-    if( is.null( object$cov$cov.bhat ) ){
+    if( is.null( covmat$cov.bhat ) ){
       
       ## compute standard errors of residuals
       
-      if( is.null( object$Valpha.objects$Valpha.inverse ) || 
-        is.null( object$Valpha.objects$Valpha.ilcf ) 
+      if( is.null( Valpha.objects$Valpha.inverse ) || 
+        is.null( Valpha.objects$Valpha.ilcf ) 
       ) stop( 
         "'Valpha.objects' incomplete or missing in georob object;\n", 
         "'Valpha.objects' must include components 'Valpha.inverse' and 'Valpha.ilcf'"
@@ -194,12 +203,12 @@
       )
       
       
-      if( is.null( object$Valpha.objects$Valpha.ucf ) ){
+      if( is.null( Valpha.objects$Valpha.ucf ) ){
         
         ## compute upper cholesky factor of correlation matrix Valpha
         ## which is needed to compute cov( bhat )
         
-        object$Valpha.objects$Valpha.ucf <- t( solve( object$Valpha.objects$Valpha.ilcf ) )
+        Valpha.objects$Valpha.ucf <- t( solve( Valpha.objects$Valpha.ilcf ) )
         
       }            
       
@@ -209,7 +218,9 @@
       )[!duplicated( object$Tmat ), , drop = FALSE]
       
       r.cov <- compute.covariances(
-        Valpha.objects = object$Valpha.objects,
+        Valpha.objects = Valpha.objects,
+        Aalpha = object[["Aalpha"]],
+        Palpha = expand( object[["Palpha"]] ),
         rweights = object$rweights,
         XX = X, TT = object$Tmat, names.yy = rownames( model.frame( object ) ),
         nugget = object$param["nugget"],
@@ -218,8 +229,8 @@
         cov.bhat = TRUE, full.cov.bhat = FALSE,
         cov.betahat = FALSE, 
         cov.bhat.betahat = FALSE,
-        cov.delta.bhat = FALSE, full.cov.delta.bhat = FALSE,
-        cov.delta.bhat.betahat = FALSE,
+        cov.deltabhat = FALSE, full.cov.deltabhat = FALSE,
+        cov.deltabhat.betahat = FALSE,
         cov.ehat = FALSE, full.cov.ehat = FALSE,
         cov.ehat.p.bhat = FALSE, full.cov.ehat.p.bhat = FALSE,
         aux.cov.pred.target = FALSE,
@@ -236,10 +247,10 @@
       
       ## extract standard errors of residuals from georob object
       
-      if( is.matrix( object$cov$cov.bhat ) ){
-        se <- sqrt( diag( object$cov$cov.bhat ) )
+      if( is.matrix( covmat$cov.bhat ) ){
+        se <- sqrt( diag( covmat$cov.bhat ) )
       } else {
-        se <- sqrt( object$cov$cov.bhat )
+        se <- sqrt( covmat$cov.bhat )
       }
       
     }
@@ -248,8 +259,7 @@
     
   }
   
-  bhat <- naresid( object$na.action, bhat )
-  return( bhat )
+  naresid( object.na, bhat )
   
 }
 
@@ -303,12 +313,19 @@
   
   ## 2011-10-13 A. Papritz    
   ## 2011-12-14 AP modified for replicated observations
-  ## 2013-05-23 AP modified for computing partial residuals for single terms
+  ## 2013-05-31 AP modified for computing partial residuals for single terms
   
   type <- match.arg( type )
   
   if( !level %in% 1:0 ) stop( "wrong level: must be either 1 or 0" )
   
+  ## temporarily redefine na.action component of object
+  
+  object.na <- object$na.action
+  if( identical( class( object$na.action ), "exclude" ) ){
+    class( object$na.action ) <- "omit"
+  }
+  
   r <- object$residuals
   res <- switch(
     type, 
@@ -319,7 +336,6 @@
     partial = r
   )
   
-  res <- naresid(object$na.action, res)
     
   if( level == 0 && any( type %in% c( "working", "response", "partial" ) ) ){
     res <- res + ranef( object, standard = FALSE )[object$Tmat]
@@ -328,6 +344,8 @@
   if( type == "partial" ) 
     res <- res + predict( object, type = "terms", terms = terms )$fit
   drop( res )
+  
+  naresid( object.na, res )
 }
 
 
@@ -352,53 +370,63 @@
   ## 2012-01-05 AP modified for compress storage of matrices
   ## 2012-10-18 AP changes for new definition of eta
   ## 2013-04-23 AP new names for robustness weights
-  ## 2013-05-23 AP correct handling of missing observations
+  ## 2013-05-31 AP correct handling of missing observations
+  ## 2013-05-31 AP revised expansion of covariance matrices
+  ## 2013-05-06 AP changes for solving estimating equations for xi
   
-  object <- model
-  object$Valpha.objects <- expand( object$Valpha.objects )
-  object$cov       <- expand( object$cov )
+  ## temporarily redefine na.action component of model
   
+  model.na <- model$na.action
+  if( identical( class( model$na.action ), "exclude" ) ){
+    class( model$na.action ) <- "omit"
+  }
+  
+  Valpha.objects <- expand( model$Valpha.objects )
+  covmat         <- expand( model$cov )
+  
   if( !level %in% 1:0 ) stop( "wrong level: must be either 1 or 0" )
   
   if( 
-    ( is.null( object$cov$cov.ehat ) & level == 1 ) ||
-    ( is.null( object$cov$cov.ehat.p.bhat ) & level == 0 ) 
+    ( is.null( covmat$cov.ehat ) & level == 1 ) ||
+    ( is.null( covmat$cov.ehat.p.bhat ) & level == 0 ) 
   ){
     
     ## compute standard errors of residuals
     
-    if( is.null( object$Valpha.objects$Valpha.inverse ) || 
-      is.null( object$Valpha.objects$Valpha.ilcf ) 
+    if( is.null( Valpha.objects$Valpha.inverse ) || 
+      is.null( Valpha.objects$Valpha.ilcf ) 
     ) stop( 
       "'Valpha.objects' incomplete or missing in georob object;\n", 
       "'Valpha.objects' must include components 'Valpha.inverse' and 'Valpha.ilcf'"
     )
-    if( is.null( object$expectations ) ) stop( 
+    if( is.null( model$expectations ) ) stop( 
       "'expectations' missing in georob object;\n",
       "use 'full.output = TRUE' when fitting the model"
     )
     
     X <- model.matrix( 
-      terms( object), 
-      model.frame( object ) 
-    )[!duplicated( object$Tmat ), , drop = FALSE]
+      terms( model), 
+      model.frame( model ) 
+    )[!duplicated( model$Tmat ), , drop = FALSE]
     
-    if( is.null( object$Valpha.objects$Valpha.ucf ) ){
-      object$Valpha.objects$Valpha.ucf <- t( solve( object$Valpha.objects$Valpha.ilcf ) )
+    if( is.null( Valpha.objects$Valpha.ucf ) ){
+      Valpha.objects$Valpha.ucf <- t( solve( Valpha.objects$Valpha.ilcf ) )
     }
     
     r.cov <- compute.covariances(
-      Valpha.objects = object$Valpha.objects,
-      rweights = object$rweights,
-      XX = X, TT = object$Tmat, names.yy = rownames( model.frame( object ) ),
-      nugget = object$param["nugget"],
-      eta = sum( object$param[c( "variance", "snugget")] ) / object$param["nugget"],
-      expectations = object$expectations,
+      Valpha.objects = Valpha.objects,
+      Aalpha = model[["Aalpha"]],
+      Palpha = expand( model[["Palpha"]] ),
+      rweights = model$rweights,
+      XX = X, TT = model$Tmat, names.yy = rownames( model.frame( model ) ),
+      nugget = model$param["nugget"],
+      eta = sum( model$param[c( "variance", "snugget")] ) / model$param["nugget"],
+      expectations = model$expectations,
       cov.bhat = FALSE, full.cov.bhat = FALSE,
       cov.betahat = FALSE, 
       cov.bhat.betahat = FALSE,
-      cov.delta.bhat = FALSE, full.cov.delta.bhat = FALSE,
-      cov.delta.bhat.betahat = FALSE,
+      cov.deltabhat = FALSE, full.cov.deltabhat = FALSE,
+      cov.deltabhat.betahat = FALSE,
       cov.ehat = level == 1, full.cov.ehat = FALSE,
       cov.ehat.p.bhat = level == 0, full.cov.ehat.p.bhat = FALSE,
       aux.cov.pred.target = FALSE,
@@ -410,9 +438,9 @@
     )
     
     if( level == 1 ){
-      object$cov$cov.ehat <-r.cov$cov.ehat 
+      covmat$cov.ehat <-r.cov$cov.ehat 
     } else {
-      object$cov$cov.ehat.p.bhat <-r.cov$cov.ehat.p.bhat 
+      covmat$cov.ehat.p.bhat <-r.cov$cov.ehat.p.bhat 
     }
     
   } 
@@ -420,9 +448,9 @@
   ## extract standard errors of residuals from georob object
   
   if( level == 1 ){
-    se <- object$cov$cov.ehat
+    se <- covmat$cov.ehat
   } else {
-    se <- object$cov$cov.ehat.p.bhat
+    se <- covmat$cov.ehat.p.bhat
   }
   if( is.matrix( se ) ){
     se <- sqrt( diag( se ) )
@@ -432,10 +460,8 @@
   
   ## compute standardized residuals
   
-  se <- naresid( model$na.action, se )
+  naresid( model.na, residuals( model, level = level ) / se )
   
-  residuals( model, level = level ) / se
-  
 }
 
 ## ##############################################################################
@@ -489,8 +515,9 @@
   ## 2012-11-04 AP handling compressed cov.betahat
   ## 2012-11-27 AP changes in parameter back-transformation
   ## 2013-04-23 AP new names for robustness weights
+  ## 2013-05-31 AP revised expansion of covariance matrices
   
-  object$cov       <- expand( object$cov )
+  covmat       <- expand( object$cov )
   
   ans <- object[c(
     "call", "residuals", "bhat", "rweights", "converged", "convergence.code", 
@@ -507,7 +534,7 @@
   ans$scale <- sqrt(object$param["nugget"])
   ans$control$method <- "TODO: PRINT GLSROB CONTROL PARAMETERS HERE"
   
-  se <- sqrt(diag(expand(object$cov$cov.betahat)))
+  se <- sqrt(diag(covmat$cov.betahat))
   est <- object$coefficients
   tval <- est/se
   
@@ -519,7 +546,7 @@
   )
   
   if( correlation ){
-    ans$correlation <- expand( object$cov$cov.betahat ) / outer(se, se)
+    ans$correlation <- covmat$cov.betahat / outer(se, se)
   }
   
   ans$param <- as.matrix( object$param, ncol = 1 )
@@ -619,12 +646,12 @@
     } 
   }
   
-  ans$se.residuals <- if( !is.null( object$cov$cov.ehat ) ){
+  ans$se.residuals <- if( !is.null( covmat$cov.ehat ) ){
     
-    if( is.matrix( object$cov$cov.ehat ) ){
-      sqrt( diag( object$cov$cov.ehat ) )
+    if( is.matrix( covmat$cov.ehat ) ){
+      sqrt( diag( covmat$cov.ehat ) )
     } else {
-      sqrt( object$cov$cov.ehat )
+      sqrt( covmat$cov.ehat )
     }
     
   } else NULL
@@ -876,6 +903,7 @@
   
   ## 2012-12-22 A. Papritz
   ## 2013-05-23 AP correct handling of missing observations
+  ## 2013-05-31 AP revised expansion of covariance matrices
   
   ## redefine na.action component of object
   
@@ -886,12 +914,11 @@
   if( object[["tuning.psi"]] < georob.control()[["tuning.psi.nr"]] ){
     result <- NA_real_
   } else {
-    object[["Valpha.objects"]] <- expand( object[["Valpha.objects"]] )
+    Valpha.objects <- expand( object[["Valpha.objects"]] )
     G <- sum( object[["param"]][c("variance", "snugget")] ) *
-      t(object[["Valpha.objects"]][["Valpha.ucf"]]) %*% object[["Valpha.objects"]][["Valpha.ucf"]]
+      t(Valpha.objects[["Valpha.ucf"]]) %*% Valpha.objects[["Valpha.ucf"]]
       
     diag( G ) <- diag( G ) + object[["param"]]["nugget"]
-    object[["Valpha.objects"]] <- compress( object[["Valpha.objects"]] )
     G <- G[object[["Tmat"]], object[["Tmat"]]]
     iucf <- try(
       backsolve( 

Modified: pkg/R/georob.cv.R
===================================================================
--- pkg/R/georob.cv.R	2013-05-23 15:41:57 UTC (rev 5)
+++ pkg/R/georob.cv.R	2013-06-06 13:28:13 UTC (rev 6)
@@ -71,6 +71,7 @@
   ## 2012-12-04 AP modifiction for changes in predict.georob
   ## 2013-04-24 AP changes for parallelization on windows os
   ## 2013-05-23 AP correct handling of missing observations
+  ## 2013-05-24 AP separate initial variogram parameters for each cross-validation set
     
   ## auxiliary function that fits the model and computes the predictions of
   ## a cross-validation set
@@ -96,6 +97,11 @@
     
     environment( formula ) <- environment()
     environment( object$terms ) <- environment()
+    
+    ## read-off initial values of variogram parameters
+    
+    if( ( is.matrix( param ) || is.data.frame( param ) ) )  param <- param[..i..,]
+    if( ( is.matrix( fit.param ) || is.data.frame( fit.param ) ) )  fit.param <- fit.param[..i..,]
 
     t.georob <- update( 
       object, 
@@ -212,6 +218,7 @@
 
   } else {
     
+    nset <- length( unique( sets ) )
     if( length( sets ) != NROW( data ) ) stop(
       "sets must be an integer vector with length equal to the number of observations"      
     )
@@ -230,6 +237,16 @@
     function( x ) x
   )
   
+  ## check dimension of param and fit.param
+  
+  if( ( is.matrix( param ) || is.data.frame( param ) ) && nrow( param )!= nset ) stop(
+    "param must have 'nset' rows if it is a matrix or data frame"  
+  )
+    
+  if( ( is.matrix( fit.param ) || is.data.frame( fit.param ) ) && nrow( param )!= nset ) stop(
+    "fit.param must have 'nset' rows if it is a matrix or data frame"  
+  )
+    
   ## loop over all cross-validation sets
   
   if( .Platform$OS.type == "windows" ){
@@ -320,9 +337,9 @@
   
   t.fit <- lapply( t.result, function( x ) return( x$fit ) )
   
-  if( re.estimate && !all( sapply( t.fit, function(x) x$converged ) ) )
-  warning(
-    "lack of covergence when fitting model to cross-validation sets"
+  if( re.estimate && !all( sapply( t.fit, function(x) x$converged ) ) ) warning(
+    "lack of covergence for  ", 
+    sum( !sapply( t.fit, function(x) x$converged ) ), " cross-validation sets"
   )
   
   result <- list( 

Modified: pkg/R/georob.exported.functions.R
===================================================================
--- pkg/R/georob.exported.functions.R	2013-05-23 15:41:57 UTC (rev 5)
+++ pkg/R/georob.exported.functions.R	2013-06-06 13:28:13 UTC (rev 6)
@@ -76,6 +76,7 @@
   ## 2012-05-28 AP handle missing names of coefficients after calling update
   ## 2013-04-23 AP new names for robustness weights
   ## 2013-05-23 AP correct handling of missing observations and to construct model.frame
+  ## 2013-06-03 AP handling design matrices with rank < ncol(x)
   
   ## check whether input is complete
   
@@ -177,12 +178,22 @@
   min.max.sv <- range( svd( crossprod( x ) )$d )
   condnum <- min.max.sv[1] / min.max.sv[2] 
   
+  if( condnum <= control$min.condnum ){
+    if( initial.param || tuning.psi >= control$tuning.psi.nr ) stop(
+      "singular fixed effects design matrices cannot be handled if 'initial.param = TRUE'",
+      "or for Gaussian REML estimation"
+    )
+    cat( 
+      "design matrix has not full column rank (condition number of X^T X: ", 
+      signif( condnum, 2 ), ")\ninitial values of regression coefficients are computed by 'lm\n\n'"
+    )
+    control$initial.method <- "lm"
+    warning( 
+      "design matrix has not full column rank (condition number of X^T X: ", 
+      signif( condnum, 2 ), ")\ninitial values of regression coefficients are computed by 'lm'"
+    )
+  }
   
-  if( condnum <= control$min.condnum ) stop( 
-    "design matrix has not full column rank (condition number of X^T X: ", 
-    signif( condnum, 2 ), ")"
-  )
-  
   ## subtract offset
   
   yy <- y
@@ -224,7 +235,7 @@
       fit$formula <- formula
       fit$terms <- mt
       fit$xlevels <- .getXlevels(mt, mf)
-      fit$call <- call
+      fit$call <- cl
       fit$tau <- tau
       fit$weights <- w
       fit$residuals <- drop( fit$residuals )
@@ -250,6 +261,27 @@
       if( !is.null( offset ) ) fit$fitted.values + offset
       fit
       
+    },
+    lm = {
+      
+      fit <- if( is.null(w) ){
+        lm.fit(x, y, offset = offset, singular.ok = TRUE, ...)
+      } else {
+        lm.wfit(x, y, w, offset = offset, singular.ok = TRUE, ...)
+      }
+      class(fit) <- c(if (is.matrix(y)) "mlm", "lm")
+      fit$na.action <- attr(mf, "na.action")
+      fit$offset <- offset
+      fit$contrasts <- attr(x, "contrasts")
+      fit$xlevels <- .getXlevels(mt, mf)
+      fit$call <- cl
+      fit$terms <- mt
+      if (model) fit$model <- mf
+      if (ret.x) fit$x <- x
+      if (ret.y) fit$y <- y
+      fit$qr <- NULL
+      fit
+      
     }
   )
   
@@ -336,12 +368,13 @@
       cov.bhat = control$cov.bhat, full.cov.bhat = control$full.cov.bhat,
       cov.betahat = control$cov.betahat, 
       cov.bhat.betahat = control$cov.bhat.betahat,
-      cov.delta.bhat = control$cov.delta.bhat,
-      full.cov.delta.bhat = control$full.cov.delta.bhat,
-      cov.delta.bhat.betahat = control$cov.delta.bhat.betahat,
+      cov.deltabhat = control$cov.deltabhat,
+      full.cov.deltabhat = control$full.cov.deltabhat,
+      cov.deltabhat.betahat = control$cov.deltabhat.betahat,
       cov.ehat = control$cov.ehat, full.cov.ehat = control$full.cov.ehat,
       cov.ehat.p.bhat = control$cov.ehat.p.bhat, full.cov.ehat.p.bhat = control$full.cov.ehat.p.bhat,
       aux.cov.pred.target = control$aux.cov.pred.target,
+      min.condnum = control$min.condnum,
       psi.func = control$psi.func,
       tuning.psi.nr = control$tuning.psi.nr,
       irwls.initial = control$irwls.initial,
@@ -400,12 +433,13 @@
     cov.bhat = control$cov.bhat, full.cov.bhat = control$full.cov.bhat,
     cov.betahat = control$cov.betahat, 
     cov.bhat.betahat = control$cov.bhat.betahat,
-    cov.delta.bhat = control$cov.delta.bhat,
-    full.cov.delta.bhat = control$full.cov.delta.bhat,
-    cov.delta.bhat.betahat = control$cov.delta.bhat.betahat,
+    cov.deltabhat = control$cov.deltabhat,
+    full.cov.deltabhat = control$full.cov.deltabhat,
+    cov.deltabhat.betahat = control$cov.deltabhat.betahat,
     cov.ehat = control$cov.ehat, full.cov.ehat = control$full.cov.ehat,
     cov.ehat.p.bhat = control$cov.ehat.p.bhat, full.cov.ehat.p.bhat = control$full.cov.ehat.p.bhat,
     aux.cov.pred.target = control$aux.cov.pred.target,
+    min.condnum = control$min.condnum,
     psi.func = control$psi.func,
     tuning.psi.nr = control$tuning.psi.nr,
     irwls.initial = control$irwls.initial,
@@ -469,7 +503,7 @@
 
 georob.control <- 
   function(
-    initial.method = c("lmrob", "rq"),
+    initial.method = c("lmrob", "rq", "lm"),
     bhat = NULL,
     param.tf = param.transf(),
     fwd.tf = fwd.transf(), 
@@ -486,8 +520,8 @@
     cov.bhat = FALSE, full.cov.bhat = FALSE,
     cov.betahat = TRUE, 
     cov.bhat.betahat = FALSE,
-    cov.delta.bhat = TRUE, full.cov.delta.bhat = TRUE,
-    cov.delta.bhat.betahat = TRUE,
+    cov.deltabhat = TRUE, full.cov.deltabhat = TRUE,
+    cov.deltabhat.betahat = TRUE,
     cov.ehat = TRUE, full.cov.ehat = FALSE,
     cov.ehat.p.bhat = FALSE, full.cov.ehat.p.bhat = FALSE,
     aux.cov.pred.target = FALSE,
@@ -535,10 +569,10 @@
   ##                   should be computed
   ## cov.bhat.betahat  logical, flag controlling whether the covariance matrix of 
   ##                   bhat and betahat should be computed
-  ## cov.delta.bhat      logical, flag controlling whether the covariances of z-bhat should be computed
-  ## full.cov.delta.bhat logical, flag controlling whether the full covariance matrix of z-bhat 
+  ## cov.deltabhat      logical, flag controlling whether the covariances of z-bhat should be computed
+  ## full.cov.deltabhat logical, flag controlling whether the full covariance matrix of z-bhat 
   ##                   is computed (TRUE) or only the diagonal elements (FALSE)
-  ## cov.delta.bhat.betahat    logical, flag controlling whether the covariance matrix of z-bhat
+  ## cov.deltabhat.betahat    logical, flag controlling whether the covariance matrix of z-bhat
   ##                    and betahat should be computed
   ## cov.ehat        logical, flag controlling whether the covariances of the resdiuals should be computed
   ## full.cov.ehat   logical, flag controlling whether the full covariance matrix of the residuals 
@@ -587,8 +621,8 @@
     cov.bhat = cov.bhat, full.cov.bhat = full.cov.bhat,
     cov.betahat = cov.betahat, 
     cov.bhat.betahat = cov.bhat.betahat,
-    cov.delta.bhat = cov.delta.bhat, full.cov.delta.bhat = full.cov.delta.bhat,
-    cov.delta.bhat.betahat = cov.delta.bhat.betahat,
+    cov.deltabhat = cov.deltabhat, full.cov.deltabhat = full.cov.deltabhat,
+    cov.deltabhat.betahat = cov.deltabhat.betahat,
     cov.ehat = cov.ehat, full.cov.ehat = full.cov.ehat,
     cov.ehat.p.bhat = cov.ehat.p.bhat, full.cov.ehat.p.bhat = full.cov.ehat.p.bhat,
     aux.cov.pred.target = aux.cov.pred.target,

Modified: pkg/R/georob.predict.R
===================================================================
--- pkg/R/georob.predict.R	2013-05-23 15:41:57 UTC (rev 5)
+++ pkg/R/georob.predict.R	2013-06-06 13:28:13 UTC (rev 6)
@@ -93,7 +93,7 @@
       locations.coords, betahat, bhat,
       pred.X, pred.coords, newdata,
       variogram.model, param, aniso,
-      cov.dbhat.betahat.l, cov.betahat.l, cov.bhat.betahat, cov.p.t, Valpha.objects,
+      cov.deltabhat.betahat.l, cov.betahat.l, cov.bhat.betahat, cov.p.t, Valpha.objects,
       pwidth, pheight, napp,
       signif,
       extended.output, full.covmat
@@ -385,8 +385,8 @@
         ## compute uk variance (= (co-)variance of prediction errors)
         
         aux <- cbind(
-          gammaValphai %*% cov.dbhat.betahat.l[1:n, 1:n] - pred.X[!ex, , drop = FALSE ] %*% cov.dbhat.betahat.l[-(1:n), 1:n],
-          - pred.X[!ex, , drop = FALSE ] %*% cov.dbhat.betahat.l[-(1:n), -(1:n)]
+          gammaValphai %*% cov.deltabhat.betahat.l[1:n, 1:n] - pred.X[!ex, , drop = FALSE ] %*% cov.deltabhat.betahat.l[-(1:n), 1:n],
+          - pred.X[!ex, , drop = FALSE ] %*% cov.deltabhat.betahat.l[-(1:n), -(1:n)]
         )
         
         if( full.covmat ){
@@ -630,16 +630,16 @@
   ## if needed compute missing covariance matrices
   
   cov.betahat    <- is.null( object[["cov"]][["cov.betahat"]] )
-  cov.dbhat   <- is.null( object[["cov"]][["cov.delta.bhat"]] ) ||
-  !is.matrix( object[["cov"]][["cov.delta.bhat"]] )
-  cov.dbhat.betahat <- is.null( object[["cov"]][["cov.delta.bhat.betahat"]] )
+  cov.deltabhat   <- is.null( object[["cov"]][["cov.deltabhat"]] ) ||
+    !is.matrix( object[["cov"]][["cov.deltabhat"]] )
+  cov.deltabhat.betahat <- is.null( object[["cov"]][["cov.deltabhat.betahat"]] )
   cov.bhat    <- extended.output & (
     is.null( object[["cov"]]$cov.bhat ) || !is.matrix( object[["cov"]]$cov.bhat )
   )
   cov.bhat.betahat  <-  extended.output & is.null( object[["cov"]]$cov.bhat.betahat )
   cov.p.t  <-  extended.output & is.null( object[["cov"]]$aux.cov.pred.target )
   
-  if( any( c( cov.betahat, cov.dbhat, cov.dbhat.betahat, 
+  if( any( c( cov.betahat, cov.deltabhat, cov.deltabhat.betahat, 
         extended.output & ( cov.bhat || cov.bhat.betahat || cov.p.t )
       )
     )
@@ -676,8 +676,8 @@
       cov.bhat = cov.bhat, full.cov.bhat = cov.bhat,
       cov.betahat = cov.betahat, 
       cov.bhat.betahat = cov.bhat.betahat,
-      cov.delta.bhat = cov.dbhat, full.cov.delta.bhat = cov.dbhat,
-      cov.delta.bhat.betahat = cov.dbhat.betahat,
+      cov.deltabhat = cov.deltabhat, full.cov.deltabhat = cov.deltabhat,
+      cov.deltabhat.betahat = cov.deltabhat.betahat,
       cov.ehat = FALSE, full.cov.ehat = FALSE,
       cov.ehat.p.bhat = FALSE, full.cov.ehat.p.bhat = FALSE,
       aux.cov.pred.target = cov.p.t,
@@ -691,9 +691,9 @@
     if( is.null( object[["cov"]] ) ) object[["cov"]] <- list()
     
     if( cov.betahat )    object[["cov"]][["cov.betahat"]]    <- r.cov[["cov.betahat"]]
-    if( cov.dbhat )   object[["cov"]][["cov.delta.bhat"]] <- r.cov[["cov.delta.bhat"]]
-    if( cov.dbhat.betahat ) object[["cov"]][["cov.delta.bhat.betahat"]] <- 
-      r.cov[["cov.delta.bhat.betahat"]]
+    if( cov.deltabhat )   object[["cov"]][["cov.delta"]] <- r.cov[["cov.delta"]]
+    if( cov.deltabhat.betahat ) object[["cov"]][["cov.deltabhat.betahat"]] <- 
+      r.cov[["cov.deltabhat.betahat"]]
     if( extended.output && cov.bhat )   object[["cov"]][["cov.bhat"]] <- r.cov[["cov.bhat"]]
     if( extended.output && cov.bhat.betahat ) object[["cov"]][["cov.bhat.betahat"]] <- 
       r.cov[["cov.bhat.betahat"]]
@@ -702,26 +702,26 @@
     
   } ## end cov
   
-  ## compute lower cholesky factor of covariance matrix of delta.bhat = (b -
+  ## compute lower cholesky factor of covariance matrix of delta = (b -
   ## bhat) and betahat - beta
   
-  cov.dbhat.betahat.l <- try( 
+  cov.deltabhat.betahat.l <- try( 
     t(
       chol(
         rbind(
           cbind( 
-            object[["cov"]][["cov.delta.bhat"]], 
-            object[["cov"]][["cov.delta.bhat.betahat"]] 
+            object[["cov"]][["cov.delta"]], 
+            object[["cov"]][["cov.deltabhat.betahat"]] 
           ),
           cbind( 
-            t( object[["cov"]][["cov.delta.bhat.betahat"]] ), 
+            t( object[["cov"]][["cov.deltabhat.betahat"]] ), 
             object[["cov"]][["cov.betahat"]]
           )
         )
       )
     ), silent = TRUE
   )
-  if( identical( class( cov.dbhat.betahat.l ), "try-error" ) ) stop(
+  if( identical( class( cov.deltabhat.betahat.l ), "try-error" ) ) stop(
     "covariance matrix of kriging errors 'b-bhat' and 'betahat' not positive definite"  
   )
   
@@ -890,8 +890,8 @@
         },
         signal = {    ## signal
           aux <- cbind( 
-            cov.dbhat.betahat.l[1:n,1:n] - X %*% cov.dbhat.betahat.l[-(1:n),1:n],
-            - X  %*% cov.dbhat.betahat.l[-(1:n),-(1:n)]
+            cov.deltabhat.betahat.l[1:n,1:n] - X %*% cov.deltabhat.betahat.l[-(1:n),1:n],
+            - X  %*% cov.deltabhat.betahat.l[-(1:n),-(1:n)]
           )
           aux <- aux[object[["Tmat"]], , drop = FALSE]
           if( full.covmat ){
@@ -1137,7 +1137,7 @@
       locations.coords, betahat, bhat,
       pred.X, pred.coords, newdata, 
       variogram.model, param, aniso,
-      cov.dbhat.betahat.l, cov.betahat.l, cov.bhat.betahat, cov.p.t, Valpha.objects,
+      cov.deltabhat.betahat.l, cov.betahat.l, cov.bhat.betahat, cov.p.t, Valpha.objects,
       pwidth, pheight, napp,
       signif,
       extended.output, full.covmat,
@@ -1164,7 +1164,7 @@
         bhat = bhat,
         pred.X = pred.X, pred.coords = pred.coords, newdata = newdata,
         variogram.model = variogram.model, param = param, aniso = aniso,
-        cov.dbhat.betahat.l = cov.dbhat.betahat.l,
+        cov.deltabhat.betahat.l = cov.deltabhat.betahat.l,
         cov.betahat.l = cov.betahat.l, 
         cov.bhat.betahat = cov.bhat.betahat,
         cov.p.t = cov.p.t,
@@ -1205,7 +1205,7 @@
           variogram.model = object[["variogram.model"]],
           param = object[["param"]],
           aniso = object[["aniso"]],
-          cov.dbhat.betahat.l = cov.dbhat.betahat.l,
+          cov.deltabhat.betahat.l = cov.deltabhat.betahat.l,
           cov.betahat.l = cov.betahat.l,
           cov.bhat.betahat = cov.bhat.betahat,
           cov.p.t = cov.p.t,
@@ -1235,7 +1235,7 @@
           variogram.model = object[["variogram.model"]],
           param = object[["param"]],
           aniso = object[["aniso"]],
-          cov.dbhat.betahat.l = cov.dbhat.betahat.l,
+          cov.deltabhat.betahat.l = cov.deltabhat.betahat.l,
           cov.betahat.l = cov.betahat.l,
           cov.bhat.betahat = cov.bhat.betahat,
           cov.p.t = cov.p.t,
@@ -1264,7 +1264,7 @@
         variogram.model = object[["variogram.model"]],
         param = object[["param"]],
         aniso = object[["aniso"]],
-        cov.dbhat.betahat.l = cov.dbhat.betahat.l,
+        cov.deltabhat.betahat.l = cov.deltabhat.betahat.l,
         cov.betahat.l = cov.betahat.l,
         cov.bhat.betahat = cov.bhat.betahat,
         cov.p.t = cov.p.t,

Modified: pkg/R/georob.private.functions.R
===================================================================
--- pkg/R/georob.private.functions.R	2013-05-23 15:41:57 UTC (rev 5)
+++ pkg/R/georob.private.functions.R	2013-06-06 13:28:13 UTC (rev 6)
@@ -9,15 +9,15 @@
 compute.covariances <- 
   function(
     Valpha.objects, 
-#     Valpha.inverse.Palpha, Palpha,
+    Aalpha, Palpha,
     rweights, XX, TT, names.yy,
     nugget, eta, 
     expectations,
     cov.bhat, full.cov.bhat,
     cov.betahat, 
     cov.bhat.betahat,
-    cov.delta.bhat, full.cov.delta.bhat,
-    cov.delta.bhat.betahat,
+    cov.deltabhat, full.cov.deltabhat,
+    cov.deltabhat.betahat,
     cov.ehat, full.cov.ehat,
     cov.ehat.p.bhat, full.cov.ehat.p.bhat,
     aux.cov.pred.target,
@@ -48,486 +48,698 @@
   ## 2012-11-04 AP unscaled psi-function
   ## 2013-02-05 AP covariance matrix of xihat
   ## 2013-04-23 AP new names for robustness weights
+  ## 2013-05-06 AP changes for solving estimating equations for xi
   
-  n <- nrow( XX )
-  sel <- 1:n
   
-  result <- list( error = FALSE )
-  a <- expectations["psi2"] 
-  b <- expectations["dpsi"]
+  ## adjust flags for computing covariance matrices
   
-  TtWiT <- b
-  TtDT  <- a
-  TtT <- as.vector( table( TT ) )
+  cov.bhat.b       <- FALSE
+  cov.bhat.e       <- FALSE
+  cov.betahat.b    <- FALSE
+  cov.betahat.e    <- FALSE
   
-  ##  ... aggregate elements of Wi and D for replicated observations
-  
-  if( sum( duplicated( TT ) ) > 0 ){
-    TtWiT  <- TtWiT * TtT
-    TtDT   <- TtDT * TtT
+  if( any( c( cov.deltabhat, aux.cov.pred.target )))                          cov.bhat.b <- TRUE
+  if( any( c( cov.ehat, aux.cov.pred.target )))                               cov.bhat.e <- TRUE
+  if( any( c( cov.deltabhat.betahat, cov.ehat.p.bhat, aux.cov.pred.target ))) cov.betahat.b <- TRUE
+  if( any( c( cov.ehat, cov.ehat.p.bhat, aux.cov.pred.target )))              cov.betahat.e <- TRUE
+  if( any( c( cov.ehat, cov.ehat.p.bhat ) ) )                             cov.betahat <- TRUE
+  if( any( c( cov.deltabhat, cov.deltabhat.betahat ))){
+                                                                          cov.bhat <- TRUE
+    if( full.cov.deltabhat )                                              full.cov.bhat <- TRUE
   }
+  if( cov.deltabhat.betahat )                                             cov.bhat.betahat <- TRUE
+  if( cov.ehat ){
+                                                                          cov.deltabhat.betahat <- TRUE
+                                                                          cov.deltabhat <- TRUE
+    if( full.cov.ehat )                                                   full.cov.deltabhat <- TRUE
+  }
   
-  ##  construct matrix M
+  ## compute required auxiliary items 
+    
+  result.new <- list( error = FALSE )
   
-  TtWiTXX <- TtWiT * XX
-  aux <- Valpha.objects$Valpha.inverse / eta
-  diag( aux ) <- diag( aux ) + TtWiT
+  a <- expectations["psi2"] 
+  b <- expectations["dpsi"]
   
-  M <- rbind(
-    cbind( aux,        TtWiTXX ),
-    cbind( t(TtWiTXX), crossprod( XX , TtWiTXX ) )
+  TtT <- as.vector( table( TT ) )
+
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/georob -r 6

From noreply at r-forge.r-project.org  Mon Jun 10 12:49:41 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 10 Jun 2013 12:49:41 +0200 (CEST)
Subject: [Georob-commits] r7 - in pkg: R man
Message-ID: <20130610104941.A83CF18458F@r-forge.r-project.org>

Author: papritz
Date: 2013-06-10 12:49:41 +0200 (Mon, 10 Jun 2013)
New Revision: 7

Modified:
   pkg/R/georob.S3methods.R
   pkg/R/georob.exported.functions.R
   pkg/R/georob.predict.R
   pkg/R/georob.private.functions.R
   pkg/man/georob.control.Rd
   pkg/man/georobObject.Rd
Log:
error in predict.georob corrected, old names of flags for computing covariances restored

M    pkg/R/georob.S3methods.R
M    pkg/R/georob.predict.R
M    pkg/R/georob.exported.functions.R
M    pkg/R/georob.private.functions.R
M    pkg/man/georob.control.Rd
M    pkg/man/georobObject.Rd



Modified: pkg/R/georob.S3methods.R
===================================================================
--- pkg/R/georob.S3methods.R	2013-06-06 13:28:13 UTC (rev 6)
+++ pkg/R/georob.S3methods.R	2013-06-10 10:49:41 UTC (rev 7)
@@ -229,8 +229,8 @@
         cov.bhat = TRUE, full.cov.bhat = FALSE,
         cov.betahat = FALSE, 
         cov.bhat.betahat = FALSE,
-        cov.deltabhat = FALSE, full.cov.deltabhat = FALSE,
-        cov.deltabhat.betahat = FALSE,
+        cov.delta.bhat = FALSE, full.cov.delta.bhat = FALSE,
+        cov.delta.bhat.betahat = FALSE,
         cov.ehat = FALSE, full.cov.ehat = FALSE,
         cov.ehat.p.bhat = FALSE, full.cov.ehat.p.bhat = FALSE,
         aux.cov.pred.target = FALSE,
@@ -425,8 +425,8 @@
       cov.bhat = FALSE, full.cov.bhat = FALSE,
       cov.betahat = FALSE, 
       cov.bhat.betahat = FALSE,
-      cov.deltabhat = FALSE, full.cov.deltabhat = FALSE,
-      cov.deltabhat.betahat = FALSE,
+      cov.delta.bhat = FALSE, full.cov.delta.bhat = FALSE,
+      cov.delta.bhat.betahat = FALSE,
       cov.ehat = level == 1, full.cov.ehat = FALSE,
       cov.ehat.p.bhat = level == 0, full.cov.ehat.p.bhat = FALSE,
       aux.cov.pred.target = FALSE,

Modified: pkg/R/georob.exported.functions.R
===================================================================
--- pkg/R/georob.exported.functions.R	2013-06-06 13:28:13 UTC (rev 6)
+++ pkg/R/georob.exported.functions.R	2013-06-10 10:49:41 UTC (rev 7)
@@ -368,9 +368,9 @@
       cov.bhat = control$cov.bhat, full.cov.bhat = control$full.cov.bhat,
       cov.betahat = control$cov.betahat, 
       cov.bhat.betahat = control$cov.bhat.betahat,
-      cov.deltabhat = control$cov.deltabhat,
-      full.cov.deltabhat = control$full.cov.deltabhat,
-      cov.deltabhat.betahat = control$cov.deltabhat.betahat,
+      cov.delta.bhat = control$cov.delta.bhat,
+      full.cov.delta.bhat = control$full.cov.delta.bhat,
+      cov.delta.bhat.betahat = control$cov.delta.bhat.betahat,
       cov.ehat = control$cov.ehat, full.cov.ehat = control$full.cov.ehat,
       cov.ehat.p.bhat = control$cov.ehat.p.bhat, full.cov.ehat.p.bhat = control$full.cov.ehat.p.bhat,
       aux.cov.pred.target = control$aux.cov.pred.target,
@@ -433,9 +433,9 @@
     cov.bhat = control$cov.bhat, full.cov.bhat = control$full.cov.bhat,
     cov.betahat = control$cov.betahat, 
     cov.bhat.betahat = control$cov.bhat.betahat,
-    cov.deltabhat = control$cov.deltabhat,
-    full.cov.deltabhat = control$full.cov.deltabhat,
-    cov.deltabhat.betahat = control$cov.deltabhat.betahat,
+    cov.delta.bhat = control$cov.delta.bhat,
+    full.cov.delta.bhat = control$full.cov.delta.bhat,
+    cov.delta.bhat.betahat = control$cov.delta.bhat.betahat,
     cov.ehat = control$cov.ehat, full.cov.ehat = control$full.cov.ehat,
     cov.ehat.p.bhat = control$cov.ehat.p.bhat, full.cov.ehat.p.bhat = control$full.cov.ehat.p.bhat,
     aux.cov.pred.target = control$aux.cov.pred.target,
@@ -520,8 +520,8 @@
     cov.bhat = FALSE, full.cov.bhat = FALSE,
     cov.betahat = TRUE, 
     cov.bhat.betahat = FALSE,
-    cov.deltabhat = TRUE, full.cov.deltabhat = TRUE,
-    cov.deltabhat.betahat = TRUE,
+    cov.delta.bhat = TRUE, full.cov.delta.bhat = TRUE,
+    cov.delta.bhat.betahat = TRUE,
     cov.ehat = TRUE, full.cov.ehat = FALSE,
     cov.ehat.p.bhat = FALSE, full.cov.ehat.p.bhat = FALSE,
     aux.cov.pred.target = FALSE,
@@ -569,10 +569,10 @@
   ##                   should be computed
   ## cov.bhat.betahat  logical, flag controlling whether the covariance matrix of 
   ##                   bhat and betahat should be computed
-  ## cov.deltabhat      logical, flag controlling whether the covariances of z-bhat should be computed
-  ## full.cov.deltabhat logical, flag controlling whether the full covariance matrix of z-bhat 
+  ## cov.delta.bhat      logical, flag controlling whether the covariances of z-bhat should be computed
+  ## full.cov.delta.bhat logical, flag controlling whether the full covariance matrix of z-bhat 
   ##                   is computed (TRUE) or only the diagonal elements (FALSE)
-  ## cov.deltabhat.betahat    logical, flag controlling whether the covariance matrix of z-bhat
+  ## cov.delta.bhat.betahat    logical, flag controlling whether the covariance matrix of z-bhat
   ##                    and betahat should be computed
   ## cov.ehat        logical, flag controlling whether the covariances of the resdiuals should be computed
   ## full.cov.ehat   logical, flag controlling whether the full covariance matrix of the residuals 
@@ -621,8 +621,8 @@
     cov.bhat = cov.bhat, full.cov.bhat = full.cov.bhat,
     cov.betahat = cov.betahat, 
     cov.bhat.betahat = cov.bhat.betahat,
-    cov.deltabhat = cov.deltabhat, full.cov.deltabhat = full.cov.deltabhat,
-    cov.deltabhat.betahat = cov.deltabhat.betahat,
+    cov.delta.bhat = cov.delta.bhat, full.cov.delta.bhat = full.cov.delta.bhat,
+    cov.delta.bhat.betahat = cov.delta.bhat.betahat,
     cov.ehat = cov.ehat, full.cov.ehat = full.cov.ehat,
     cov.ehat.p.bhat = cov.ehat.p.bhat, full.cov.ehat.p.bhat = full.cov.ehat.p.bhat,
     aux.cov.pred.target = aux.cov.pred.target,

Modified: pkg/R/georob.predict.R
===================================================================
--- pkg/R/georob.predict.R	2013-06-06 13:28:13 UTC (rev 6)
+++ pkg/R/georob.predict.R	2013-06-10 10:49:41 UTC (rev 7)
@@ -93,7 +93,7 @@
       locations.coords, betahat, bhat,
       pred.X, pred.coords, newdata,
       variogram.model, param, aniso,
-      cov.deltabhat.betahat.l, cov.betahat.l, cov.bhat.betahat, cov.p.t, Valpha.objects,
+      cov.delta.bhat.betahat.l, cov.betahat.l, cov.bhat.betahat, cov.p.t, Valpha.objects,
       pwidth, pheight, napp,
       signif,
       extended.output, full.covmat
@@ -385,8 +385,8 @@
         ## compute uk variance (= (co-)variance of prediction errors)
         
         aux <- cbind(
-          gammaValphai %*% cov.deltabhat.betahat.l[1:n, 1:n] - pred.X[!ex, , drop = FALSE ] %*% cov.deltabhat.betahat.l[-(1:n), 1:n],
-          - pred.X[!ex, , drop = FALSE ] %*% cov.deltabhat.betahat.l[-(1:n), -(1:n)]
+          gammaValphai %*% cov.delta.bhat.betahat.l[1:n, 1:n] - pred.X[!ex, , drop = FALSE ] %*% cov.delta.bhat.betahat.l[-(1:n), 1:n],
+          - pred.X[!ex, , drop = FALSE ] %*% cov.delta.bhat.betahat.l[-(1:n), -(1:n)]
         )
         
         if( full.covmat ){
@@ -630,16 +630,16 @@
   ## if needed compute missing covariance matrices
   
   cov.betahat    <- is.null( object[["cov"]][["cov.betahat"]] )
-  cov.deltabhat   <- is.null( object[["cov"]][["cov.deltabhat"]] ) ||
-    !is.matrix( object[["cov"]][["cov.deltabhat"]] )
-  cov.deltabhat.betahat <- is.null( object[["cov"]][["cov.deltabhat.betahat"]] )
+  cov.delta.bhat   <- is.null( object[["cov"]][["cov.delta.bhat"]] ) ||
+    !is.matrix( object[["cov"]][["cov.delta.bhat"]] )
+  cov.delta.bhat.betahat <- is.null( object[["cov"]][["cov.delta.bhat.betahat"]] )
   cov.bhat    <- extended.output & (
     is.null( object[["cov"]]$cov.bhat ) || !is.matrix( object[["cov"]]$cov.bhat )
   )
   cov.bhat.betahat  <-  extended.output & is.null( object[["cov"]]$cov.bhat.betahat )
   cov.p.t  <-  extended.output & is.null( object[["cov"]]$aux.cov.pred.target )
   
-  if( any( c( cov.betahat, cov.deltabhat, cov.deltabhat.betahat, 
+  if( any( c( cov.betahat, cov.delta.bhat, cov.delta.bhat.betahat, 
         extended.output & ( cov.bhat || cov.bhat.betahat || cov.p.t )
       )
     )
@@ -676,8 +676,8 @@
       cov.bhat = cov.bhat, full.cov.bhat = cov.bhat,
       cov.betahat = cov.betahat, 
       cov.bhat.betahat = cov.bhat.betahat,
-      cov.deltabhat = cov.deltabhat, full.cov.deltabhat = cov.deltabhat,
-      cov.deltabhat.betahat = cov.deltabhat.betahat,
+      cov.delta.bhat = cov.delta.bhat, full.cov.delta.bhat = cov.delta.bhat,
+      cov.delta.bhat.betahat = cov.delta.bhat.betahat,
       cov.ehat = FALSE, full.cov.ehat = FALSE,
       cov.ehat.p.bhat = FALSE, full.cov.ehat.p.bhat = FALSE,
       aux.cov.pred.target = cov.p.t,
@@ -691,9 +691,9 @@
     if( is.null( object[["cov"]] ) ) object[["cov"]] <- list()
     
     if( cov.betahat )    object[["cov"]][["cov.betahat"]]    <- r.cov[["cov.betahat"]]
-    if( cov.deltabhat )   object[["cov"]][["cov.delta"]] <- r.cov[["cov.delta"]]
-    if( cov.deltabhat.betahat ) object[["cov"]][["cov.deltabhat.betahat"]] <- 
-      r.cov[["cov.deltabhat.betahat"]]
+    if( cov.delta.bhat )   object[["cov"]][["cov.delta.bhat"]] <- r.cov[["cov.delta.bhat"]]
+    if( cov.delta.bhat.betahat ) object[["cov"]][["cov.delta.bhat.betahat"]] <- 
+      r.cov[["cov.delta.bhat.betahat"]]
     if( extended.output && cov.bhat )   object[["cov"]][["cov.bhat"]] <- r.cov[["cov.bhat"]]
     if( extended.output && cov.bhat.betahat ) object[["cov"]][["cov.bhat.betahat"]] <- 
       r.cov[["cov.bhat.betahat"]]
@@ -704,24 +704,23 @@
   
   ## compute lower cholesky factor of covariance matrix of delta = (b -
   ## bhat) and betahat - beta
-  
-  cov.deltabhat.betahat.l <- try( 
+  cov.delta.bhat.betahat.l <- try( 
     t(
       chol(
         rbind(
           cbind( 
-            object[["cov"]][["cov.delta"]], 
-            object[["cov"]][["cov.deltabhat.betahat"]] 
+            object[["cov"]][["cov.delta.bhat"]], 
+            object[["cov"]][["cov.delta.bhat.betahat"]] 
           ),
           cbind( 
-            t( object[["cov"]][["cov.deltabhat.betahat"]] ), 
+            t( object[["cov"]][["cov.delta.bhat.betahat"]] ), 
             object[["cov"]][["cov.betahat"]]
           )
         )
       )
     ), silent = TRUE
   )
-  if( identical( class( cov.deltabhat.betahat.l ), "try-error" ) ) stop(
+  if( identical( class( cov.delta.bhat.betahat.l ), "try-error" ) ) stop(
     "covariance matrix of kriging errors 'b-bhat' and 'betahat' not positive definite"  
   )
   
@@ -890,8 +889,8 @@
         },
         signal = {    ## signal
           aux <- cbind( 
-            cov.deltabhat.betahat.l[1:n,1:n] - X %*% cov.deltabhat.betahat.l[-(1:n),1:n],
-            - X  %*% cov.deltabhat.betahat.l[-(1:n),-(1:n)]
+            cov.delta.bhat.betahat.l[1:n,1:n] - X %*% cov.delta.bhat.betahat.l[-(1:n),1:n],
+            - X  %*% cov.delta.bhat.betahat.l[-(1:n),-(1:n)]
           )
           aux <- aux[object[["Tmat"]], , drop = FALSE]
           if( full.covmat ){
@@ -1137,7 +1136,7 @@
       locations.coords, betahat, bhat,
       pred.X, pred.coords, newdata, 
       variogram.model, param, aniso,
-      cov.deltabhat.betahat.l, cov.betahat.l, cov.bhat.betahat, cov.p.t, Valpha.objects,
+      cov.delta.bhat.betahat.l, cov.betahat.l, cov.bhat.betahat, cov.p.t, Valpha.objects,
       pwidth, pheight, napp,
       signif,
       extended.output, full.covmat,
@@ -1164,7 +1163,7 @@
         bhat = bhat,
         pred.X = pred.X, pred.coords = pred.coords, newdata = newdata,
         variogram.model = variogram.model, param = param, aniso = aniso,
-        cov.deltabhat.betahat.l = cov.deltabhat.betahat.l,
+        cov.delta.bhat.betahat.l = cov.delta.bhat.betahat.l,
         cov.betahat.l = cov.betahat.l, 
         cov.bhat.betahat = cov.bhat.betahat,
         cov.p.t = cov.p.t,
@@ -1205,7 +1204,7 @@
           variogram.model = object[["variogram.model"]],
           param = object[["param"]],
           aniso = object[["aniso"]],
-          cov.deltabhat.betahat.l = cov.deltabhat.betahat.l,
+          cov.delta.bhat.betahat.l = cov.delta.bhat.betahat.l,
           cov.betahat.l = cov.betahat.l,
           cov.bhat.betahat = cov.bhat.betahat,
           cov.p.t = cov.p.t,
@@ -1235,7 +1234,7 @@
           variogram.model = object[["variogram.model"]],
           param = object[["param"]],
           aniso = object[["aniso"]],
-          cov.deltabhat.betahat.l = cov.deltabhat.betahat.l,
+          cov.delta.bhat.betahat.l = cov.delta.bhat.betahat.l,
           cov.betahat.l = cov.betahat.l,
           cov.bhat.betahat = cov.bhat.betahat,
           cov.p.t = cov.p.t,
@@ -1264,7 +1263,7 @@
         variogram.model = object[["variogram.model"]],
         param = object[["param"]],
         aniso = object[["aniso"]],
-        cov.deltabhat.betahat.l = cov.deltabhat.betahat.l,
+        cov.delta.bhat.betahat.l = cov.delta.bhat.betahat.l,
         cov.betahat.l = cov.betahat.l,
         cov.bhat.betahat = cov.bhat.betahat,
         cov.p.t = cov.p.t,

Modified: pkg/R/georob.private.functions.R
===================================================================
--- pkg/R/georob.private.functions.R	2013-06-06 13:28:13 UTC (rev 6)
+++ pkg/R/georob.private.functions.R	2013-06-10 10:49:41 UTC (rev 7)
@@ -16,8 +16,8 @@
     cov.bhat, full.cov.bhat,
     cov.betahat, 
     cov.bhat.betahat,
-    cov.deltabhat, full.cov.deltabhat,
-    cov.deltabhat.betahat,
+    cov.delta.bhat, full.cov.delta.bhat,
+    cov.delta.bhat.betahat,
     cov.ehat, full.cov.ehat,
     cov.ehat.p.bhat, full.cov.ehat.p.bhat,
     aux.cov.pred.target,
@@ -58,20 +58,20 @@
   cov.betahat.b    <- FALSE
   cov.betahat.e    <- FALSE
   
-  if( any( c( cov.deltabhat, aux.cov.pred.target )))                          cov.bhat.b <- TRUE
+  if( any( c( cov.delta.bhat, aux.cov.pred.target )))                          cov.bhat.b <- TRUE
   if( any( c( cov.ehat, aux.cov.pred.target )))                               cov.bhat.e <- TRUE
-  if( any( c( cov.deltabhat.betahat, cov.ehat.p.bhat, aux.cov.pred.target ))) cov.betahat.b <- TRUE
+  if( any( c( cov.delta.bhat.betahat, cov.ehat.p.bhat, aux.cov.pred.target ))) cov.betahat.b <- TRUE
   if( any( c( cov.ehat, cov.ehat.p.bhat, aux.cov.pred.target )))              cov.betahat.e <- TRUE
   if( any( c( cov.ehat, cov.ehat.p.bhat ) ) )                             cov.betahat <- TRUE
-  if( any( c( cov.deltabhat, cov.deltabhat.betahat ))){
+  if( any( c( cov.delta.bhat, cov.delta.bhat.betahat ))){
                                                                           cov.bhat <- TRUE
-    if( full.cov.deltabhat )                                              full.cov.bhat <- TRUE
+    if( full.cov.delta.bhat )                                              full.cov.bhat <- TRUE
   }
-  if( cov.deltabhat.betahat )                                             cov.bhat.betahat <- TRUE
+  if( cov.delta.bhat.betahat )                                             cov.bhat.betahat <- TRUE
   if( cov.ehat ){
-                                                                          cov.deltabhat.betahat <- TRUE
-                                                                          cov.deltabhat <- TRUE
-    if( full.cov.ehat )                                                   full.cov.deltabhat <- TRUE
+                                                                          cov.delta.bhat.betahat <- TRUE
+                                                                          cov.delta.bhat <- TRUE
+    if( full.cov.ehat )                                                   full.cov.delta.bhat <- TRUE
   }
   
   ## compute required auxiliary items 
@@ -169,8 +169,8 @@
   
   ## ... of (b - bhat) (debugging status ok)
   
-  if( cov.deltabhat ){
-    result.new$cov.deltabhat <- if( full.cov.deltabhat )
+  if( cov.delta.bhat ){
+    result.new$cov.delta.bhat <- if( full.cov.delta.bhat )
     {
       aux <- V + result.new$cov.bhat - cov.bhat.b - t( cov.bhat.b )
       attr( aux, "struc" ) <- "sym"
@@ -189,18 +189,18 @@
   
   ## ... of (b - bhat) and betahat (debugging status ok)
   
-  if( cov.deltabhat.betahat ){
-    result.new$cov.deltabhat.betahat <- t( cov.betahat.b ) - result.new$cov.bhat.betahat
-    dimnames( result.new$cov.deltabhat.betahat ) <- dimnames( XX )
+  if( cov.delta.bhat.betahat ){
+    result.new$cov.delta.bhat.betahat <- t( cov.betahat.b ) - result.new$cov.bhat.betahat
+    dimnames( result.new$cov.delta.bhat.betahat ) <- dimnames( XX )
   }
   
   ## ... of ehat (debugging status ok)
  
   if( cov.ehat ){
-    aux1 <- tcrossprod( result.new$cov.deltabhat.betahat, XX )[TT,TT]
+    aux1 <- tcrossprod( result.new$cov.delta.bhat.betahat, XX )[TT,TT]
     result.new$cov.ehat <- if( full.cov.ehat )
     {
-      aux <- bla <- result.new$cov.deltabhat[TT,TT] + 
+      aux <- bla <- result.new$cov.delta.bhat[TT,TT] + 
         tcrossprod( tcrossprod( XX, result.new$cov.betahat ), XX )[TT,TT] -
         aux1 - t(aux1) - cov.bhat.e[TT,] - t(cov.bhat.e)[,TT] - 
         TX.cov.betahat.e - t(TX.cov.betahat.e)
@@ -209,10 +209,10 @@
       dimnames( aux ) <- list( names.yy, names.yy )
       aux   
     } else {
-      aux <- (if( full.cov.deltabhat ){
-        diag( result.new$cov.deltabhat )[TT] 
+      aux <- (if( full.cov.delta.bhat ){
+        diag( result.new$cov.delta.bhat )[TT] 
       } else {
-        result.new$cov.deltabhat[TT]
+        result.new$cov.delta.bhat[TT]
       }) + rowSums( XX * (XX %*% result.new$cov.betahat) )[TT] -
         2 * diag( aux1 ) - 2 * diag( cov.bhat.e[TT,] ) - 2 * diag( TX.cov.betahat.e ) + 
         nugget
@@ -502,20 +502,20 @@
   ##   
   ##   ##  ... of delta.z = (z - bhat)  (debugging status: ok)
   ##   
-  ##   if( cov.deltabhat ){
+  ##   if( cov.delta.bhat ){
   ##     
-  ##     if( full.cov.deltabhat ){
+  ##     if( full.cov.delta.bhat ){
   ##       
   ##       ##  full matrix
   ##       
-  ##       result$cov.deltabhat <- nugget * ( 
+  ##       result$cov.delta.bhat <- nugget * ( 
   ##         M.inverse[sel, sel] %*% ValphaiP / eta +
   ##         crossprod( sqrtD * PpXQt )
   ##       )
-  ##       dimnames( result$cov.deltabhat ) <- list(
+  ##       dimnames( result$cov.delta.bhat ) <- list(
   ##         rownames( XX ), rownames( XX )
   ##       )
-  ##       attr( result$cov.deltabhat, "struc" ) <- "sym"
+  ##       attr( result$cov.delta.bhat, "struc" ) <- "sym"
   ##       
   ##       ##       ##  zur Kontrolle: Kovarianzmatrix UK-Vorhersagefehler
   ##       ##       
@@ -523,26 +523,26 @@
   ##       ##       t.Sigma <- t.V + nugget * diag( n )
   ##       ##       t.iSigma <- solve( t.Sigma )
   ##       ##       
-  ##       ##       t.cov.deltabhat <- t.V - t.V %*% t.iSigma %*% t.V + t.V %*% t.iSigma %*% XX %*% solve( 
+  ##       ##       t.cov.delta.bhat <- t.V - t.V %*% t.iSigma %*% t.V + t.V %*% t.iSigma %*% XX %*% solve( 
   ##       ##         t( XX ) %*% t.iSigma %*% XX 
   ##       ##       ) %*% t(XX) %*% t.iSigma %*% t.V
   ##       ##       
-  ##       ##       print( summary( c( result$cov.deltabhat - t.cov.deltabhat ) ) )
+  ##       ##       print( summary( c( result$cov.delta.bhat - t.cov.delta.bhat ) ) )
   ##       
   ##     } else {
   ##       
   ##       ##  diagonal elements only 
   ##       
-  ##       result$cov.deltabhat <- nugget * (
+  ##       result$cov.delta.bhat <- nugget * (
   ##         colSums( 
   ##           drop( 
   ##             Valpha.objects$Valpha.ilcf %*% M.inverse[sel, sel] 
   ##           )^2
   ##         ) / eta + colSums( (sqrtD * PpXQt)^2 )
   ##       )
-  ##       names( result$cov.deltabhat ) <- rownames( XX )
+  ##       names( result$cov.delta.bhat ) <- rownames( XX )
   ##       
-  ##       ##       print( summary( c( result$cov.deltabhat - diag( t.cov.deltabhat ) ) ) )
+  ##       ##       print( summary( c( result$cov.delta.bhat - diag( t.cov.delta.bhat ) ) ) )
   ##   
   ##     }
   ##     
@@ -551,9 +551,9 @@
   ##   
   ##   ##  ... of delta.z = (z - bhat) and betahat (debugging status: ok)
   ##   
-  ##   if( cov.deltabhat.betahat ){
+  ##   if( cov.delta.bhat.betahat ){
   ##     
-  ##     result$cov.deltabhat.betahat <- -nugget * (
+  ##     result$cov.delta.bhat.betahat <- -nugget * (
   ##       t(ValphaiP) %*% M.inverse[sel,-sel] / eta +
   ##       crossprod( PpXQt, TtDT * QpXS )
   ##     )
@@ -564,11 +564,11 @@
   ##     ##     t.Sigma <- t.V + nugget * diag( n )
   ##     ##     t.iSigma <- solve( t.Sigma )
   ##     ##     
-  ##     ##     t.cov.deltabhat.betahat <- t.V %*% t.iSigma %*% XX %*% solve( 
+  ##     ##     t.cov.delta.bhat.betahat <- t.V %*% t.iSigma %*% XX %*% solve( 
   ##     ##         t( XX ) %*% t.iSigma %*% XX
   ##     ##     )
   ##     ##     
-  ##     ##     print( summary( c( result$cov.deltabhat.betahat - t.cov.deltabhat.betahat ) ) )
+  ##     ##     print( summary( c( result$cov.delta.bhat.betahat - t.cov.delta.bhat.betahat ) ) )
   ##     
   ##   }
   ##   
@@ -2454,8 +2454,8 @@
       cov.bhat = TRUE, full.cov.bhat = TRUE,
       cov.betahat = FALSE,
       cov.bhat.betahat = FALSE,
-      cov.deltabhat = FALSE, full.cov.deltabhat = FALSE,
-      cov.deltabhat.betahat = FALSE,
+      cov.delta.bhat = FALSE, full.cov.delta.bhat = FALSE,
+      cov.delta.bhat.betahat = FALSE,
       cov.ehat = FALSE, full.cov.ehat = FALSE,
       cov.ehat.p.bhat = FALSE, full.cov.ehat.p.bhat = FALSE,
       aux.cov.pred.target = FALSE,
@@ -3183,8 +3183,8 @@
     cov.bhat, full.cov.bhat,
     cov.betahat, 
     cov.bhat.betahat,
-    cov.deltabhat, full.cov.deltabhat,
-    cov.deltabhat.betahat,
+    cov.delta.bhat, full.cov.delta.bhat,
+    cov.delta.bhat.betahat,
     cov.ehat, full.cov.ehat,
     cov.ehat.p.bhat, full.cov.ehat.p.bhat,
     aux.cov.pred.target,
@@ -4020,7 +4020,7 @@
   
   if( any( c( 
         cov.bhat, cov.betahat, cov.bhat.betahat, 
-        cov.deltabhat, cov.deltabhat.betahat, 
+        cov.delta.bhat, cov.delta.bhat.betahat, 
         cov.ehat, cov.ehat.p.bhat,
         aux.cov.pred.target
       ) 
@@ -4041,8 +4041,8 @@
       cov.bhat = cov.bhat, full.cov.bhat = full.cov.bhat,
       cov.betahat = cov.betahat, 
       cov.bhat.betahat = cov.bhat.betahat,
-      cov.deltabhat = cov.deltabhat, full.cov.deltabhat = full.cov.deltabhat,
-      cov.deltabhat.betahat = cov.deltabhat.betahat,
+      cov.delta.bhat = cov.delta.bhat, full.cov.delta.bhat = full.cov.delta.bhat,
+      cov.delta.bhat.betahat = cov.delta.bhat.betahat,
       cov.ehat = cov.ehat, full.cov.ehat = full.cov.ehat, 
       cov.ehat.p.bhat = cov.ehat.p.bhat, full.cov.ehat.p.bhat = full.cov.ehat.p.bhat,
       aux.cov.pred.target = aux.cov.pred.target,
@@ -4087,7 +4087,7 @@
   
   if( any( c( 
         cov.bhat, cov.betahat, cov.bhat.betahat, 
-        cov.deltabhat, cov.deltabhat.betahat, 
+        cov.delta.bhat, cov.delta.bhat.betahat, 
         cov.ehat, cov.ehat.p.bhat, aux.cov.pred.target
       ) 
     ) 

Modified: pkg/man/georob.control.Rd
===================================================================
--- pkg/man/georob.control.Rd	2013-06-06 13:28:13 UTC (rev 6)
+++ pkg/man/georob.control.Rd	2013-06-10 10:49:41 UTC (rev 7)
@@ -32,8 +32,8 @@
     force.gradient = FALSE, zero.dist = sqrt(.Machine$double.eps),
     cov.bhat = FALSE, full.cov.bhat = FALSE, cov.betahat = TRUE, 
     cov.bhat.betahat = FALSE, 
-    cov.deltabhat = TRUE, full.cov.deltabhat = TRUE,
-    cov.deltabhat.betahat = TRUE,
+    cov.delta.bhat = TRUE, full.cov.delta.bhat = TRUE,
+    cov.delta.bhat.betahat = TRUE,
     cov.ehat = TRUE, full.cov.ehat = FALSE,
     cov.ehat.p.bhat = FALSE, full.cov.ehat.p.bhat = FALSE,
     aux.cov.pred.target = FALSE, min.condnum = 1.e-12,
@@ -173,16 +173,16 @@
   \eqn{\widehat{\mbox{\boldmath$\beta$\unboldmath}}}{hat\beta} is returned
   (default \code{FALSE}).}
   
-  \item{cov.deltabhat}{logical controlling whether the covariances of
+  \item{cov.delta.bhat}{logical controlling whether the covariances of
   \eqn{\mbox{\boldmath$B$\unboldmath}-
   \widehat{\mbox{\boldmath$B$\unboldmath}}}{B-hatB} are returned (default \code{TRUE}).}
   
-  \item{full.cov.deltabhat}{logical controlling whether the full covariance
+  \item{full.cov.delta.bhat}{logical controlling whether the full covariance
   matrix (\code{TRUE}) or only the variance vector of
   \eqn{\mbox{\boldmath$B$\unboldmath}-
   \widehat{\mbox{\boldmath$B$\unboldmath}}}{B-hatB} is returned (default \code{TRUE}).}
   
-  \item{cov.deltabhat.betahat}{logical controlling whether the covariance
+  \item{cov.delta.bhat.betahat}{logical controlling whether the covariance
   matrix of \eqn{\mbox{\boldmath$B$\unboldmath}-
   \widehat{\mbox{\boldmath$B$\unboldmath}}}{B-hatB} and
   \eqn{\widehat{\mbox{\boldmath$\beta$\unboldmath}}}{hat\beta} is returned

Modified: pkg/man/georobObject.Rd
===================================================================
--- pkg/man/georobObject.Rd	2013-06-06 13:28:13 UTC (rev 6)
+++ pkg/man/georobObject.Rd	2013-06-10 10:49:41 UTC (rev 7)
@@ -125,10 +125,10 @@
       \eqn{\widehat{\mbox{\boldmath$B$\unboldmath}}}{hatB} and
       \eqn{\widehat{\mbox{\boldmath$\beta$\unboldmath}}}{hat\beta}.
       
-      \item \code{cov.deltabhat}: the covariances of 
+      \item \code{cov.delta.bhat}: the covariances of 
       \eqn{\mbox{\boldmath$B$\unboldmath}- \widehat{\mbox{\boldmath$B$\unboldmath}}}{B-hatB}.
       
-      \item \code{cov.deltabhat.betahat}: the covariances of 
+      \item \code{cov.delta.bhat.betahat}: the covariances of 
       \eqn{\mbox{\boldmath$B$\unboldmath}- \widehat{\mbox{\boldmath$B$\unboldmath}}}{B-hatB}
       and 
       \eqn{\widehat{\mbox{\boldmath$\beta$\unboldmath}}}{hat\beta}.


From noreply at r-forge.r-project.org  Tue Jun 11 21:44:56 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 11 Jun 2013 21:44:56 +0200 (CEST)
Subject: [Georob-commits] r8 - in pkg: . R
Message-ID: <20130611194456.99BC8185894@r-forge.r-project.org>

Author: papritz
Date: 2013-06-11 21:44:56 +0200 (Tue, 11 Jun 2013)
New Revision: 8

Modified:
   pkg/ChangeLog
   pkg/R/georob.exported.functions.R
   pkg/R/georob.private.functions.R
Log:
non-robust estimation with rank deficient fixed effects design matrix

M    pkg/R/georob.exported.functions.R
M    pkg/R/georob.private.functions.R
M    pkg/ChangeLog


Modified: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog	2013-06-10 10:49:41 UTC (rev 7)
+++ pkg/ChangeLog	2013-06-11 19:44:56 UTC (rev 8)
@@ -85,8 +85,13 @@
 
 2013-06-06  Andreas Papritz  <papritz at env.ethz.ch>
 
-* georob.exported.function.R (georob, georob.control): handling fixed effects model matrices with rank < ncol(x)
-* georob.private.function.R (prepare.likelihood.calculations, compute.estimating.equations, negative.restr.loglikelihood, negative.restr.loglikelihood, gradient.negative.restricted.loglikelihood, georob.fit) : solving estimating equations for xi
+* georob.exported.function.R (georob, georob.control): handling fixed effects model matrices with rank < ncol(x) for robust estimation
+* georob.private.function.R (prepare.likelihood.calculations, compute.estimating.equations, negative.restr.loglikelihood, gradient.negative.restricted.loglikelihood, georob.fit) : solving estimating equations for xi
 * georob.S3methods.R ranef.georob, rstandard.georob) : solving estimating equations for xi
-* georob.private.function.R (compute.covariances, estimate.xihat, update.xihat, negative.restr.loglikelihood): solving estimating equations for xi
+* georob.private.function.R (estimate.xihat, prepare.likelihood.calculations, compute.estimating.equations, negative.restr.loglikelihood, gradient.negative.restricted.loglikelihood, georob.fit): handling fixed effects model matrices with rank < ncol(x) for robust estimation
 
+
+2013-06-11  Andreas Papritz  <papritz at env.ethz.ch>
+
+* georob.exported.function.R (georob): handling fixed effects model matrices with rank < ncol(x) for non-robust estimation
+* georob.private.function.R (estimate.xihat, prepare.likelihood.calculations, compute.estimating.equations, negative.restr.loglikelihood, gradient.negative.restricted.loglikelihood, georob.fit): handling fixed effects model matrices with rank < ncol(x) for non-robust estimation

Modified: pkg/R/georob.exported.functions.R
===================================================================
--- pkg/R/georob.exported.functions.R	2013-06-10 10:49:41 UTC (rev 7)
+++ pkg/R/georob.exported.functions.R	2013-06-11 19:44:56 UTC (rev 8)
@@ -175,22 +175,22 @@
   
   ## check whether design matrix has full column rank
   
+  rankdef.x <- FALSE
+  
   min.max.sv <- range( svd( crossprod( x ) )$d )
   condnum <- min.max.sv[1] / min.max.sv[2] 
   
   if( condnum <= control$min.condnum ){
-    if( initial.param || tuning.psi >= control$tuning.psi.nr ) stop(
-      "singular fixed effects design matrices cannot be handled if 'initial.param = TRUE'",
-      "or for Gaussian REML estimation"
-    )
+    rankdef.x <- TRUE
     cat( 
       "design matrix has not full column rank (condition number of X^T X: ", 
-      signif( condnum, 2 ), ")\ninitial values of regression coefficients are computed by 'lm\n\n'"
+      signif( condnum, 2 ), ")\ninitial values of fixed effects coefficients are computed by 'lm'\n\n"
     )
     control$initial.method <- "lm"
+    initial.param <- FALSE
     warning( 
       "design matrix has not full column rank (condition number of X^T X: ", 
-      signif( condnum, 2 ), ")\ninitial values of regression coefficients are computed by 'lm'"
+      signif( condnum, 2 ), ")\ninitial values of fixed effects coefficients are computed by 'lm'"
     )
   }
   
@@ -375,6 +375,7 @@
       cov.ehat.p.bhat = control$cov.ehat.p.bhat, full.cov.ehat.p.bhat = control$full.cov.ehat.p.bhat,
       aux.cov.pred.target = control$aux.cov.pred.target,
       min.condnum = control$min.condnum,
+      rankdef.x = rankdef.x,
       psi.func = control$psi.func,
       tuning.psi.nr = control$tuning.psi.nr,
       irwls.initial = control$irwls.initial,
@@ -440,6 +441,7 @@
     cov.ehat.p.bhat = control$cov.ehat.p.bhat, full.cov.ehat.p.bhat = control$full.cov.ehat.p.bhat,
     aux.cov.pred.target = control$aux.cov.pred.target,
     min.condnum = control$min.condnum,
+    rankdef.x = rankdef.x,
     psi.func = control$psi.func,
     tuning.psi.nr = control$tuning.psi.nr,
     irwls.initial = control$irwls.initial,

Modified: pkg/R/georob.private.functions.R
===================================================================
--- pkg/R/georob.private.functions.R	2013-06-10 10:49:41 UTC (rev 7)
+++ pkg/R/georob.private.functions.R	2013-06-11 19:44:56 UTC (rev 8)
@@ -798,7 +798,7 @@
 
 estimate.xihat <- 
   function(
-    XX, min.condnum, yy, betahat, TT, xihat, 
+    XX, min.condnum, rankdef.x, yy, betahat, TT, xihat, 
     psi.function, tuning.psi, tuning.psi.nr, 
     maxit, reltol,
     nugget, eta, Valpha.inverse,
@@ -834,15 +834,23 @@
   
   ##  compute projection matrix Palpha and related items
   
-#   browser()
-#   
   result <- list( error = FALSE )
   
   aux <- t( XX ) %*% Valpha.inverse
   
-  s <- svd( aux %*% XX )
-  s$d <- ifelse( s$d / max( s$d ) <= min.condnum, 0., 1. / s$d )
-  Palpha <- s$v %*% ( s$d * t( s$u ) )
+  if( rankdef.x ){
+    s <- svd( aux %*% XX )
+    s$d <- ifelse( s$d / max( s$d ) <= min.condnum, 0., 1. / s$d )
+    Palpha <- s$v %*% ( s$d * t( s$u ) )                # Moore-Penrose inverse
+  } else {
+    t.chol <- try( chol( aux %*% XX ), silent = TRUE )
+    if( !identical( class( t.chol ), "try-error" ) ){
+      Palpha <- chol2inv( t.chol )    
+    } else {
+      result$error <- TRUE
+      return( result )    
+    }
+  }
   
   result$Aalpha             <- Palpha %*% aux
   dimnames( result$Aalpha ) <- dimnames( t(XX) )
@@ -1055,7 +1063,7 @@
     adjustable.param, variogram.model, fixed.param, param.name, aniso.name,
     param.tf, bwd.tf, safe.param,
     lag.vectors,
-    XX, min.condnum, yy, betahat, TT, bhat, 
+    XX, min.condnum, rankdef.x, yy, betahat, TT, bhat, 
     psi.function, dpsi.function, tuning.psi, tuning.psi.nr, 
     irwls.initial, irwls.maxiter, irwls.reltol,
     compute.Q,
@@ -1282,7 +1290,7 @@
     }
     
     lik.item$effects <- estimate.xihat( 
-      XX, min.condnum, yy, betahat, TT, bhat, 
+      XX, min.condnum, rankdef.x, yy, betahat, TT, bhat, 
       psi.function, tuning.psi, tuning.psi.nr, 
       irwls.maxiter, irwls.reltol,
       lik.item$param["nugget"], lik.item$eta, lik.item$Valpha$Valpha.inverse,
@@ -1318,27 +1326,38 @@
       Q <- rbind( 
         cbind( aux,      TtDTX                 ),
         cbind( t(TtDTX), crossprod( XX, TtDTX) )
-      )
+      ) / lik.item$param["nugget"]
       
       lik.item$Q <- list( error = TRUE )
       
-      ##  compute log(det(Q)) and inverse of Q by cholesky decomposition
-      
-      t.chol <- try( 
-        chol( Q / lik.item$param["nugget"] ), 
-        silent = TRUE
-      )
-      
-      if( !identical( class( t.chol ), "try-error" ) ) {
+      if( rankdef.x ){
         
+        ## compute log(pseudo.det(Q)) and (Moore-Penrose) pseudo inverse of Q by svd
+        
         lik.item$Q$error <- FALSE
-        lik.item$Q$log.det.Q <- 2 * sum( log( diag( t.chol) ) )
-        lik.item$Q$Q.inverse <- chol2inv( t.chol )
+        s <- svd( Q )
+        lik.item$Q$log.det.Q <- sum( log( s$d[s$d / max( s$d ) > min.condnum] ) )
+        s$d <- ifelse( s$d / max( s$d ) <= min.condnum, 0., 1. / s$d )
+        lik.item$Q$Q.inverse <- s$v %*% ( s$d * t( s$u ) )
         
       } else {
         
-        return( lik.item )
+        ##  compute log(det(Q)) and inverse of Q by cholesky decomposition
         
+        t.chol <- try( chol( Q ), silent = TRUE )
+        
+        if( !identical( class( t.chol ), "try-error" ) ) {
+          
+          lik.item$Q$error <- FALSE
+          lik.item$Q$log.det.Q <- 2 * sum( log( diag( t.chol) ) )
+          lik.item$Q$Q.inverse <- chol2inv( t.chol )
+          
+        } else {
+          
+          return( lik.item )
+          
+        }
+        
       }
       
     }
@@ -2370,7 +2389,7 @@
     variogram.model, fixed.param, param.name, aniso.name,
     param.tf, bwd.tf, safe.param,
     lag.vectors,
-    XX, min.condnum, yy, betahat, TT, bhat, 
+    XX, min.condnum, rankdef.x, yy, betahat, TT, bhat, 
     psi.function, dpsi.function, 
     tuning.psi, tuning.psi.nr,
     irwls.initial, irwls.maxiter, irwls.reltol,
@@ -2397,7 +2416,7 @@
     adjustable.param, variogram.model, fixed.param, param.name, aniso.name,
     param.tf, bwd.tf, safe.param,
     lag.vectors,
-    XX, min.condnum, yy, betahat, TT, bhat, 
+    XX, min.condnum, rankdef.x, yy, betahat, TT, bhat, 
     psi.function, dpsi.function, tuning.psi, tuning.psi.nr,
     irwls.initial, irwls.maxiter, irwls.reltol,
     compute.Q = FALSE,
@@ -2628,7 +2647,7 @@
     variogram.model, fixed.param, param.name, aniso.name,
     param.tf, bwd.tf, safe.param,
     lag.vectors,
-    XX, min.condnum, yy, betahat, TT, bhat, 
+    XX, min.condnum, rankdef.x, yy, betahat, TT, bhat, 
     psi.function, dpsi.function, 
     tuning.psi, tuning.psi.nr, 
     irwls.initial, irwls.maxiter, irwls.reltol,
@@ -2657,7 +2676,7 @@
     adjustable.param, variogram.model, fixed.param, param.name, aniso.name,
     param.tf, bwd.tf, safe.param,
     lag.vectors,
-    XX, min.condnum, yy, betahat, TT, bhat, 
+    XX, min.condnum, rankdef.x, yy, betahat, TT, bhat, 
     psi.function, dpsi.function, tuning.psi, tuning.psi.nr,
     irwls.initial, irwls.maxiter, irwls.reltol,
     compute.Q = TRUE,
@@ -2743,7 +2762,7 @@
     variogram.model, fixed.param, param.name, aniso.name,
     param.tf, deriv.fwd.tf, bwd.tf, safe.param,
     lag.vectors,
-    XX, min.condnum, yy, betahat, TT, bhat, 
+    XX, min.condnum, rankdef.x, yy, betahat, TT, bhat, 
     psi.function, dpsi.function, d2psi.function, 
     tuning.psi, tuning.psi.nr,
     irwls.initial, irwls.maxiter, irwls.reltol,
@@ -2773,7 +2792,7 @@
     adjustable.param, variogram.model, fixed.param, param.name, aniso.name,
     param.tf, bwd.tf, safe.param,
     lag.vectors,
-    XX, min.condnum, yy, betahat, TT, bhat, 
+    XX, min.condnum, rankdef.x, yy, betahat, TT, bhat, 
     psi.function, dpsi.function, tuning.psi, tuning.psi.nr,
     irwls.initial, irwls.maxiter, irwls.reltol,
     compute.Q = TRUE,
@@ -3188,7 +3207,7 @@
     cov.ehat, full.cov.ehat,
     cov.ehat.p.bhat, full.cov.ehat.p.bhat,
     aux.cov.pred.target,
-    min.condnum,
+    min.condnum, rankdef.x,
     psi.func,
     tuning.psi.nr,
     irwls.initial,
@@ -3780,7 +3799,7 @@
         bwd.tf = bwd.tf,
         safe.param = safe.param,
         lag.vectors = lag.vectors,
-        XX = XX, min.condnum = min.condnum, 
+        XX = XX, min.condnum = min.condnum, rankdef.x = rankdef.x,
         yy = yy, betahat = betahat, TT = TT, bhat = bhat, 
         psi.function = rho.psi.etc$psi.function, 
         dpsi.function = rho.psi.etc$dpsi.function, 
@@ -3831,7 +3850,7 @@
         bwd.tf = bwd.tf,
         safe.param = safe.param,
         lag.vectors = lag.vectors,
-        XX = XX, min.condnum = min.condnum, 
+        XX = XX, min.condnum = min.condnum, rankdef.x = rankdef.x,
         yy = yy, betahat = betahat, TT = TT, bhat = bhat, 
         psi.function = rho.psi.etc$psi.function, 
         dpsi.function = rho.psi.etc$dpsi.function, 
@@ -3885,7 +3904,7 @@
         bwd.tf = bwd.tf,
         safe.param = safe.param,
         lag.vectors = lag.vectors,
-        XX = XX, min.condnum = min.condnum, 
+        XX = XX, min.condnum = min.condnum, rankdef.x = rankdef.x,
         yy = yy, betahat = betahat, TT = TT, bhat = bhat, 
         psi.function = rho.psi.etc$psi.function, 
         dpsi.function = rho.psi.etc$dpsi.function, 
@@ -3922,7 +3941,7 @@
         bwd.tf = bwd.tf,
         safe.param = safe.param,
         lag.vectors = lag.vectors,
-        XX = XX, min.condnum = min.condnum, 
+        XX = XX, min.condnum = min.condnum, rankdef.x = rankdef.x,
         yy = yy, betahat = betahat, TT = TT, bhat = bhat, 
         psi.function = rho.psi.etc$psi.function, 
         dpsi.function = rho.psi.etc$dpsi.function, 
@@ -3960,7 +3979,7 @@
         bwd.tf = bwd.tf,
         safe.param = safe.param,
         lag.vectors = lag.vectors,
-        XX = XX, min.condnum = min.condnum, 
+        XX = XX, min.condnum = min.condnum, rankdef.x = rankdef.x,
         yy = yy, betahat = betahat, TT = TT, bhat = bhat, 
         psi.function = rho.psi.etc$psi.function, 
         dpsi.function = rho.psi.etc$dpsi.function, 
@@ -3990,7 +4009,7 @@
         bwd.tf = bwd.tf,
         safe.param = safe.param,
         lag.vectors = lag.vectors,
-        XX = XX, min.condnum = min.condnum, 
+        XX = XX, min.condnum = min.condnum, rankdef.x = rankdef.x,
         yy = yy, betahat = betahat, TT = TT, bhat = bhat, 
         psi.function = rho.psi.etc$psi.function, 
         dpsi.function = rho.psi.etc$dpsi.function, 


From noreply at r-forge.r-project.org  Wed Jun 12 15:24:40 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 12 Jun 2013 15:24:40 +0200 (CEST)
Subject: [Georob-commits] r9 - in pkg: . R man
Message-ID: <20130612132440.8C3B9185671@r-forge.r-project.org>

Author: papritz
Date: 2013-06-12 15:24:39 +0200 (Wed, 12 Jun 2013)
New Revision: 9

Modified:
   pkg/ChangeLog
   pkg/DESCRIPTION
   pkg/NAMESPACE
   pkg/R/georob.S3methods.R
   pkg/R/georob.cv.R
   pkg/R/georob.exported.functions.R
   pkg/R/georob.lgnpp.R
   pkg/R/georob.predict.R
   pkg/R/georob.private.functions.R
   pkg/R/variogram.R
   pkg/man/compress.Rd
   pkg/man/cv.georob.Rd
   pkg/man/fit.variogram.model.Rd
   pkg/man/georob.Rd
   pkg/man/georob.control.Rd
   pkg/man/lgnpp.Rd
   pkg/man/predict.georob.Rd
   pkg/man/sample.variogram.Rd
Log:
substituting [["x"]] for $x in all lists

M    pkg/R/georob.cv.R
M    pkg/R/georob.S3methods.R
M    pkg/R/georob.predict.R
M    pkg/R/variogram.R
M    pkg/R/georob.lgnpp.R
M    pkg/R/georob.exported.functions.R
M    pkg/R/georob.private.functions.R
M    pkg/DESCRIPTION
M    pkg/ChangeLog
M    pkg/man/georob.Rd
M    pkg/man/lgnpp.Rd
M    pkg/man/cv.georob.Rd
M    pkg/man/compress.Rd
M    pkg/man/georob.control.Rd
M    pkg/man/predict.georob.Rd
M    pkg/man/fit.variogram.model.Rd
M    pkg/man/sample.variogram.Rd
M    pkg/NAMESPACE



Modified: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog	2013-06-11 19:44:56 UTC (rev 8)
+++ pkg/ChangeLog	2013-06-12 13:24:39 UTC (rev 9)
@@ -95,3 +95,14 @@
 
 * georob.exported.function.R (georob): handling fixed effects model matrices with rank < ncol(x) for non-robust estimation
 * georob.private.function.R (estimate.xihat, prepare.likelihood.calculations, compute.estimating.equations, negative.restr.loglikelihood, gradient.negative.restricted.loglikelihood, georob.fit): handling fixed effects model matrices with rank < ncol(x) for non-robust estimation
+
+
+2013-06-12  Andreas Papritz  <papritz at env.ethz.ch>
+
+* georob.cv.R (all functions): substituting [["x"]] for $x in all lists
+* georob.exported.functions.R (all functions): substituting [["x"]] for $x in all lists
+* georob.lgnpp.R (all functions): substituting [["x"]] for $x in all lists
+* georob.predict.R (all functions): substituting [["x"]] for $x in all lists
+* georob.private.functions.R (all functions): substituting [["x"]] for $x in all lists
+* georob.S3methods.R (all functions): substituting [["x"]] for $x in all lists
+* variogram.R (all functions): substituting [["x"]] for $x in all lists

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2013-06-11 19:44:56 UTC (rev 8)
+++ pkg/DESCRIPTION	2013-06-12 13:24:39 UTC (rev 9)
@@ -7,8 +7,7 @@
   person( "Andreas", "Papritz", role = c( "cre", "aut" ), 
           email =  "andreas.papritz at env.ethz.ch" ),
   person( "Cornelia", "Schwierz", role = "ctb" ))
-Depends: R(>= 2.14.0), lmtest, nlme, 
-         robustbase, sp(>= 0.9-60), parallel
+Depends: R(>= 2.14.0), lmtest, nlme, robustbase, sp(>= 0.9-60)
 Imports: constrainedKriging(>= 0.1-9), nleqslv, quantreg, 
          RandomFields(>= 2.0.55), spatialCovariance(>= 0.6-4)
 Suggests: geoR

Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE	2013-06-11 19:44:56 UTC (rev 8)
+++ pkg/NAMESPACE	2013-06-12 13:24:39 UTC (rev 9)
@@ -1,4 +1,4 @@
-import( stats )
+import( stats, parallel )
 
 importFrom( constrainedKriging, covmodel, f.point.block.cov, K, preCKrige )
 importFrom( lmtest, waldtest, waldtest.default )

Modified: pkg/R/georob.S3methods.R
===================================================================
--- pkg/R/georob.S3methods.R	2013-06-11 19:44:56 UTC (rev 8)
+++ pkg/R/georob.S3methods.R	2013-06-12 13:24:39 UTC (rev 9)
@@ -25,9 +25,6 @@
 
 # 2011-08-11 A. Papritz
 
-# ToDos:
-# - ...$xy durch ...[["xy"]] ersetzen
-
 ## ##############################################################################
 
 model.frame.georob <- 
@@ -92,6 +89,7 @@
   ## 2011-08-13 A. Papritz
   ## 2012-02-07 AP change for anisotropic variograms 
   ## 2012-12-18 AP invisible(x)
+  ## 2013-06-12 AP substituting [["x"]] for $x in all lists
   
   ## code borrowed from print.lmrob for printing fixed effects coeffcients
   
@@ -107,10 +105,10 @@
   ## print variogram parameters
   
   cat("\n")
-  cat( "Variogram: ", x$variogram.model, "\n" )
-  param <- x$param
+  cat( "Variogram: ", x[["variogram.model"]], "\n" )
+  param <- x[["param"]]
   names( param ) <- ifelse(
-    x$initial.objects$fit.param,
+    x[["initial.objects"]][["fit.param"]],
     names( param ),
     paste( names( param ), "(fixed)", sep = "" )
   )
@@ -121,13 +119,13 @@
   
   ## print anisotropy parameters
   
-  if( !x$aniso$isotropic ){
+  if( !x[["aniso"]][["isotropic"]] ){
     
     cat("\n")
     cat( "Anisotropy parameters: ", "\n" )
-    aniso <- x$aniso$aniso * c( rep(1, 2), rep( 180/pi, 3 ) )
+    aniso <- x[["aniso"]][["aniso"]] * c( rep(1, 2), rep( 180/pi, 3 ) )
     names( aniso ) <- ifelse(
-      x$initial.objects$fit.aniso,
+      x[["initial.objects"]][["fit.aniso"]],
       names( aniso ),
       paste( names( aniso ), "(fixed)", sep = "" )
     )
@@ -172,60 +170,40 @@
   ## 2013-05-31 AP correct handling of missing observations
   ## 2013-05-31 AP revised expansion of covariance matrices
   ## 2013-05-06 AP changes for solving estimating equations for xi
+  ## 2013-06-12 AP substituting [["x"]] for $x in all lists
   
   ## temporarily redefine na.action component of object
   
-  object.na <- object$na.action
-  if( identical( class( object$na.action ), "exclude" ) ){
-    class( object$na.action ) <- "omit"
+  object.na <- object[["na.action"]]
+  if( identical( class( object[["na.action"]] ), "exclude" ) ){
+    class( object[["na.action"]] ) <- "omit"
   }
 
-  Valpha.objects <- expand( object$Valpha.objects )
-  covmat         <- expand( object$cov )
+  Valpha.objects <- expand( object[["Valpha.objects"]] )
+  covmat         <- expand( object[["cov"]] )
   
-  bhat <- object$bhat   
+  bhat <- object[["bhat"]]   
   
   if( standard ){
     
-    if( is.null( covmat$cov.bhat ) ){
+    if( is.null( covmat[["cov.bhat"]] ) ){
       
       ## compute standard errors of residuals
       
-      if( is.null( Valpha.objects$Valpha.inverse ) || 
-        is.null( Valpha.objects$Valpha.ilcf ) 
-      ) stop( 
-        "'Valpha.objects' incomplete or missing in georob object;\n", 
-        "'Valpha.objects' must include components 'Valpha.inverse' and 'Valpha.ilcf'"
-      )
-      if( is.null( object$expectations ) ) stop( 
-        "'expectations' missing in georob object;\n",
-        "use 'full.output = TRUE' when fitting the object"
-      )
-      
-      
-      if( is.null( Valpha.objects$Valpha.ucf ) ){
-        
-        ## compute upper cholesky factor of correlation matrix Valpha
-        ## which is needed to compute cov( bhat )
-        
-        Valpha.objects$Valpha.ucf <- t( solve( Valpha.objects$Valpha.ilcf ) )
-        
-      }            
-      
       X <- model.matrix( 
         terms( object ),
         model.frame( object ) 
-      )[!duplicated( object$Tmat ), , drop = FALSE]
+      )[!duplicated( object[["Tmat"]] ), , drop = FALSE]
       
       r.cov <- compute.covariances(
         Valpha.objects = Valpha.objects,
         Aalpha = object[["Aalpha"]],
-        Palpha = expand( object[["Palpha"]] ),
-        rweights = object$rweights,
-        XX = X, TT = object$Tmat, names.yy = rownames( model.frame( object ) ),
-        nugget = object$param["nugget"],
-        eta = sum( object$param[c( "variance", "snugget")] ) / object$param["nugget"],
-        expectations = object$expectations,
+        Palpha = object[["Palpha"]],
+        rweights = object[["rweights"]],
+        XX = X, TT = object[["Tmat"]], names.yy = rownames( model.frame( object ) ),
+        nugget = object[["param"]]["nugget"],
+        eta = sum( object[["param"]][c( "variance", "snugget")] ) / object[["param"]]["nugget"],
+        expectations = object[["expectations"]],
         cov.bhat = TRUE, full.cov.bhat = FALSE,
         cov.betahat = FALSE, 
         cov.bhat.betahat = FALSE,
@@ -237,20 +215,20 @@
         verbose = 0
       )
       
-      if( r.cov$error ) stop( 
+      if( r.cov[["error"]] ) stop( 
         "an error occurred when computing the variances of the random effects" 
       )
       
-      se <- sqrt( r.cov$cov.bhat )       
+      se <- sqrt( r.cov[["cov.bhat"]] )       
       
     } else {
       
       ## extract standard errors of residuals from georob object
       
-      if( is.matrix( covmat$cov.bhat ) ){
-        se <- sqrt( diag( covmat$cov.bhat ) )
+      if( is.matrix( covmat[["cov.bhat"]] ) ){
+        se <- sqrt( diag( covmat[["cov.bhat"]] ) )
       } else {
-        se <- sqrt( covmat$cov.bhat )
+        se <- sqrt( covmat[["cov.bhat"]] )
       }
       
     }
@@ -281,8 +259,9 @@
   ## ...       further arguments passed to methods
   
   ## 2012-11-26 A. Papritz    
+  ## 2013-06-12 AP substituting [["x"]] for $x in all lists
 
-  object$coef 
+  object[["coef"]] 
 
 }
 
@@ -314,6 +293,7 @@
   ## 2011-10-13 A. Papritz    
   ## 2011-12-14 AP modified for replicated observations
   ## 2013-05-31 AP modified for computing partial residuals for single terms
+  ## 2013-06-12 AP substituting [["x"]] for $x in all lists
   
   type <- match.arg( type )
   
@@ -321,28 +301,28 @@
   
   ## temporarily redefine na.action component of object
   
-  object.na <- object$na.action
-  if( identical( class( object$na.action ), "exclude" ) ){
-    class( object$na.action ) <- "omit"
+  object.na <- object[["na.action"]]
+  if( identical( class( object[["na.action"]] ), "exclude" ) ){
+    class( object[["na.action"]] ) <- "omit"
   }
   
-  r <- object$residuals
+  r <- object[["residuals"]]
   res <- switch(
     type, 
     working = , 
     response = r, 
     deviance = , 
-    pearson = if( is.null(object$weights) ) r else r * sqrt(object$weights), 
+    pearson = if( is.null(object[["weights"]]) ) r else r * sqrt(object[["weights"]]), 
     partial = r
   )
   
     
   if( level == 0 && any( type %in% c( "working", "response", "partial" ) ) ){
-    res <- res + ranef( object, standard = FALSE )[object$Tmat]
+    res <- res + ranef( object, standard = FALSE )[object[["Tmat"]]]
   }
   
   if( type == "partial" ) 
-    res <- res + predict( object, type = "terms", terms = terms )$fit
+    res <- res + predict( object, type = "terms", terms = terms )[["fit"]]
   drop( res )
   
   naresid( object.na, res )
@@ -373,55 +353,41 @@
   ## 2013-05-31 AP correct handling of missing observations
   ## 2013-05-31 AP revised expansion of covariance matrices
   ## 2013-05-06 AP changes for solving estimating equations for xi
+  ## 2013-06-12 AP substituting [["x"]] for $x in all lists
   
   ## temporarily redefine na.action component of model
   
-  model.na <- model$na.action
-  if( identical( class( model$na.action ), "exclude" ) ){
-    class( model$na.action ) <- "omit"
+  model.na <- model[["na.action"]]
+  if( identical( class( model[["na.action"]] ), "exclude" ) ){
+    class( model[["na.action"]] ) <- "omit"
   }
   
-  Valpha.objects <- expand( model$Valpha.objects )
-  covmat         <- expand( model$cov )
+  Valpha.objects <- expand( model[["Valpha.objects"]] )
+  covmat         <- expand( model[["cov"]] )
   
   if( !level %in% 1:0 ) stop( "wrong level: must be either 1 or 0" )
   
   if( 
-    ( is.null( covmat$cov.ehat ) & level == 1 ) ||
-    ( is.null( covmat$cov.ehat.p.bhat ) & level == 0 ) 
+    ( is.null( covmat[["cov.ehat"]] ) & level == 1 ) ||
+    ( is.null( covmat[["cov.ehat.p.bhat"]] ) & level == 0 ) 
   ){
     
     ## compute standard errors of residuals
     
-    if( is.null( Valpha.objects$Valpha.inverse ) || 
-      is.null( Valpha.objects$Valpha.ilcf ) 
-    ) stop( 
-      "'Valpha.objects' incomplete or missing in georob object;\n", 
-      "'Valpha.objects' must include components 'Valpha.inverse' and 'Valpha.ilcf'"
-    )
-    if( is.null( model$expectations ) ) stop( 
-      "'expectations' missing in georob object;\n",
-      "use 'full.output = TRUE' when fitting the model"
-    )
-    
     X <- model.matrix( 
       terms( model), 
       model.frame( model ) 
-    )[!duplicated( model$Tmat ), , drop = FALSE]
+    )[!duplicated( model[["Tmat"]] ), , drop = FALSE]
     
-    if( is.null( Valpha.objects$Valpha.ucf ) ){
-      Valpha.objects$Valpha.ucf <- t( solve( Valpha.objects$Valpha.ilcf ) )
-    }
-    
     r.cov <- compute.covariances(
       Valpha.objects = Valpha.objects,
       Aalpha = model[["Aalpha"]],
-      Palpha = expand( model[["Palpha"]] ),
-      rweights = model$rweights,
-      XX = X, TT = model$Tmat, names.yy = rownames( model.frame( model ) ),
-      nugget = model$param["nugget"],
-      eta = sum( model$param[c( "variance", "snugget")] ) / model$param["nugget"],
-      expectations = model$expectations,
+      Palpha = model[["Palpha"]],
+      rweights = model[["rweights"]],
+      XX = X, TT = model[["Tmat"]], names.yy = rownames( model.frame( model ) ),
+      nugget = model[["param"]]["nugget"],
+      eta = sum( model[["param"]][c( "variance", "snugget")] ) / model[["param"]]["nugget"],
+      expectations = model[["expectations"]],
       cov.bhat = FALSE, full.cov.bhat = FALSE,
       cov.betahat = FALSE, 
       cov.bhat.betahat = FALSE,
@@ -433,14 +399,14 @@
       verbose = 0
     )
     
-    if( r.cov$error ) stop( 
+    if( r.cov[["error"]] ) stop( 
       "an error occurred when computing the variance of the residuals" 
     )
     
     if( level == 1 ){
-      covmat$cov.ehat <-r.cov$cov.ehat 
+      covmat[["cov.ehat"]] <-r.cov[["cov.ehat"]] 
     } else {
-      covmat$cov.ehat.p.bhat <-r.cov$cov.ehat.p.bhat 
+      covmat[["cov.ehat.p.bhat"]] <-r.cov[["cov.ehat.p.bhat"]] 
     }
     
   } 
@@ -448,9 +414,9 @@
   ## extract standard errors of residuals from georob object
   
   if( level == 1 ){
-    se <- covmat$cov.ehat
+    se <- covmat[["cov.ehat"]]
   } else {
-    se <- covmat$cov.ehat.p.bhat
+    se <- covmat[["cov.ehat.p.bhat"]]
   }
   if( is.matrix( se ) ){
     se <- sqrt( diag( se ) )
@@ -479,6 +445,7 @@
   ## ...       further arguments passed to cv.georob
   
   ## 2011-12-22 A. Papritz    
+  ## 2013-06-12 AP substituting [["x"]] for $x in all lists
   
   if( !identical( class( model )[1], "georob" ) ) stop(
     "model is not of class 'georob'" 
@@ -516,74 +483,75 @@
   ## 2012-11-27 AP changes in parameter back-transformation
   ## 2013-04-23 AP new names for robustness weights
   ## 2013-05-31 AP revised expansion of covariance matrices
+  ## 2013-06-12 AP substituting [["x"]] for $x in all lists
   
-  covmat       <- expand( object$cov )
+  covmat       <- expand( object[["cov"]] )
   
   ans <- object[c(
     "call", "residuals", "bhat", "rweights", "converged", "convergence.code", 
     "iter", "loglik", "variogram.model", "gradient",
     "tuning.psi", "df.residual"
   )]
-  ans <- c( ans, object$initial.objects["fit.param"] )
+  ans <- c( ans, object[["initial.objects"]]["fit.param"] )
   
-  if( !object$aniso$isotropic ) ans$fit.param <- c( 
-    ans$fit.param, object$initial.objects$fit.aniso
+  if( !object[["aniso"]][["isotropic"]] ) ans[["fit.param"]] <- c( 
+    ans[["fit.param"]], object[["initial.objects"]][["fit.aniso"]]
   )
     
-  ans$terms <- NA
-  ans$scale <- sqrt(object$param["nugget"])
-  ans$control$method <- "TODO: PRINT GLSROB CONTROL PARAMETERS HERE"
+  ans[["terms"]] <- NA
+  ans[["scale"]] <- sqrt(object[["param"]]["nugget"])
+  ans[["control"]][["method"]] <- "TODO: PRINT GLSROB CONTROL PARAMETERS HERE"
   
-  se <- sqrt(diag(covmat$cov.betahat))
-  est <- object$coefficients
+  se <- sqrt(diag(covmat[["cov.betahat"]]))
+  est <- object[["coefficients"]]
   tval <- est/se
   
-  ans$coefficients <- cbind( 
-    est, se, tval, 2 * pt( abs(tval), object$df.residual, lower.tail = FALSE ) 
+  ans[["coefficients"]] <- cbind( 
+    est, se, tval, 2 * pt( abs(tval), object[["df.residual"]], lower.tail = FALSE ) 
   )
-  dimnames( ans$coefficients ) <- list( 
+  dimnames( ans[["coefficients"]] ) <- list( 
     names(est), c("Estimate", "Std. Error", "t value", "Pr(>|t|)")
   )
   
   if( correlation ){
-    ans$correlation <- covmat$cov.betahat / outer(se, se)
+    ans[["correlation"]] <- covmat[["cov.betahat"]] / outer(se, se)
   }
   
-  ans$param <- as.matrix( object$param, ncol = 1 )
+  ans[["param"]] <- as.matrix( object[["param"]], ncol = 1 )
   
-  if( !object$aniso$isotropic ) ans$param <- rbind( 
-    ans$param,
-    as.matrix( object$aniso$aniso, ncol = 1 ) * c( rep( 1, 2 ), rep( 180/pi, 3 ) )
+  if( !object[["aniso"]][["isotropic"]] ) ans[["param"]] <- rbind( 
+    ans[["param"]],
+    as.matrix( object[["aniso"]][["aniso"]], ncol = 1 ) * c( rep( 1, 2 ), rep( 180/pi, 3 ) )
   )
   
-  colnames( ans$param ) <- "Estimate"
+  colnames( ans[["param"]] ) <- "Estimate"
   
   ## compute confidence intervals of variogram parameters from observed
   ## Fisher information matrix (Gaussian REML only)
   
-  if( !is.null( object$hessian ) ){
+  if( !is.null( object[["hessian"]] ) ){
     
     ## initialization
     
     cor.tf.param <- cov.tf.param <- matrix( 
-      NA, nrow = nrow( object$hessian ), ncol = nrow( object$hessian ),
-      dimnames = dimnames( object$hessian )
+      NA, nrow = nrow( object[["hessian"]] ), ncol = nrow( object[["hessian"]] ),
+      dimnames = dimnames( object[["hessian"]] )
     )
     
-    se <- rep( NA, nrow( object$hessian ) )
-    names( se ) <- rownames( object$hessian)
+    se <- rep( NA, nrow( object[["hessian"]] ) )
+    names( se ) <- rownames( object[["hessian"]])
     
-    ci <- matrix( NA, nrow = nrow( ans$param ), ncol = 2 )
+    ci <- matrix( NA, nrow = nrow( ans[["param"]] ), ncol = 2 )
     colnames( ci ) <- c( "Lower", "Upper" )
-    rownames( ci ) <- rownames( ans$param )
+    rownames( ci ) <- rownames( ans[["param"]] )
     
     ## select parameters that are not on boundary of parameter space
     
-    sr  <- !apply( object$hessian, 1, function( x ) all( is.na( x ) ) )
+    sr  <- !apply( object[["hessian"]], 1, function( x ) all( is.na( x ) ) )
     
     if( sum( sr ) > 0 ){
       
-      t.chol <- try( chol( object$hessian[sr, sr] ), silent = TRUE )
+      t.chol <- try( chol( object[["hessian"]][sr, sr] ), silent = TRUE )
       
       if( !identical( class( t.chol ), "try-error" ) ){
         
@@ -604,15 +572,15 @@
         
         ## compute confidence interval on original scale of parameters
         
-        sel.names <- names( object$param[object$initial.objects$fit.param] )
-        if( !object$aniso$isotropic ) sel.names <- c( 
+        sel.names <- names( object[["param"]][object[["initial.objects"]][["fit.param"]]] )
+        if( !object[["aniso"]][["isotropic"]] ) sel.names <- c( 
           sel.names,
-          names( object$aniso$aniso[object$initial.objects$fit.aniso] )
+          names( object[["aniso"]][["aniso"]][object[["initial.objects"]][["fit.aniso"]]] )
         )
         sel.names <- sel.names[sr]
         
-        ff <- c( rep( 1, length( object$param ) + 2 ), rep( 180/pi, 3 ) )
-        names( ff ) <- names( c( object$param, object$aniso$aniso ) )
+        ff <- c( rep( 1, length( object[["param"]] ) + 2 ), rep( 180/pi, 3 ) )
+        names( ff ) <- names( c( object[["param"]], object[["aniso"]][["aniso"]] ) )
         
         ci[sel.names, ] <- t( 
           sapply(
@@ -623,19 +591,19 @@
                 c(-1, 1) * se[x] * qnorm( (1-signif)/2, lower.tail = FALSE ) 
               )
             },
-            param         = c( object$param, object$aniso$aniso ),
+            param         = c( object[["param"]], object[["aniso"]][["aniso"]] ),
             f             = ff,
             se            = se,
-            param.tf      = object$param.tf,
-            trafo.fct     = object$fwd.tf,
-            inv.trafo.fct = object$bwd.tf
+            param.tf      = object[["param.tf"]],
+            trafo.fct     = object[["fwd.tf"]],
+            inv.trafo.fct = object[["bwd.tf"]]
           )
         )
         is.angle <- rownames( ci ) %in% c( "omega", "phi", "zeta" )
         if( sum(is.angle) > 0 ) ci[is.angle, ] <- ci[is.angle, ] * 180/pi
         
-        ans$param <- cbind( ans$param, ci )
-        if( correlation ) ans$cor.tf.param <- cor.tf.param
+        ans[["param"]] <- cbind( ans[["param"]], ci )
+        if( correlation ) ans[["cor.tf.param"]] <- cor.tf.param
         
       } else {
         warning(
@@ -646,12 +614,12 @@
     } 
   }
   
-  ans$se.residuals <- if( !is.null( covmat$cov.ehat ) ){
+  ans[["se.residuals"]] <- if( !is.null( covmat[["cov.ehat"]] ) ){
     
-    if( is.matrix( covmat$cov.ehat ) ){
-      sqrt( diag( covmat$cov.ehat ) )
+    if( is.matrix( covmat[["cov.ehat"]] ) ){
+      sqrt( diag( covmat[["cov.ehat"]] ) )
     } else {
-      sqrt( covmat$cov.ehat )
+      sqrt( covmat[["cov.ehat"]] )
     }
     
   } else NULL
@@ -682,48 +650,48 @@
   ## 2012-02-07 AP change for anisotropic variograms
   ## 2012-12-18 AP invisible(x)
   ## 2013-04-23 AP new names for robustness weights
+  ## 2013-06-12 AP substituting [["x"]] for $x in all lists
   
-  
   cat("\nCall:")
-  cat( paste( deparse(x$call), sep = "\n", collapse = "\n"),  "\n", sep = "" )
+  cat( paste( deparse(x[["call"]]), sep = "\n", collapse = "\n"),  "\n", sep = "" )
   
   
   cat("\nTuning constant: ", x[["tuning.psi"]], "\n" )
   
-  if( is.na( x$converged ) ){
+  if( is.na( x[["converged"]] ) ){
     cat( "\nEstimation with fixed variogram parameters\n" )
     
   } else {
     
-    if(!(x$converged)) {
+    if(!(x[["converged"]])) {
       cat( 
         "\nAlgorithm did not converge, diagnostic code: ", 
-        x$convergence.code, "\n"
+        x[["convergence.code"]], "\n"
       )
     } else {
       cat(
-        "\nConvergence in", x$iter[1], "function and", 
-        x$iter[2], "Jacobian/gradient evaluations\n"
+        "\nConvergence in", x[["iter"]][1], "function and", 
+        x[["iter"]][2], "Jacobian/gradient evaluations\n"
       )
     }
     
-    attr( x$gradient, "eeq.emp" ) <- NULL
-    attr( x$gradient, "eeq.exp" ) <- NULL
+    attr( x[["gradient"]], "eeq.emp" ) <- NULL
+    attr( x[["gradient"]], "eeq.exp" ) <- NULL
     
     cat( "\nEstimating equations (gradient)\n")
-    print( x$gradient, digits = digits, ... )
+    print( x[["gradient"]], digits = digits, ... )
     
-    if( x$tuning.psi >= 
-      georob.control()$tuning.psi.nr ) cat(
+    if( x[["tuning.psi"]] >= 
+      georob.control()[["tuning.psi.nr"]] ) cat(
       "\nMaximized restricted log-likelihood:", 
-      x$loglik, "\n"
+      x[["loglik"]], "\n"
     )
     
   }
   
-  df <- x$df.residual
+  df <- x[["df.residual"]]
   
-  bhat <- x$bhat
+  bhat <- x[["bhat"]]
   cat( "\nPredicted latent variable (z):\n")
   if(df > 5){
     nam <- c("Min", "1Q", "Median", "3Q", "Max")
@@ -732,7 +700,7 @@
   }
   else print( bhat, digits = digits, ...)
   
-  resid <- x$residuals
+  resid <- x[["residuals"]]
   cat( "\nResiduals (epsilon):\n")
   if(df > 5){
     nam <- c("Min", "1Q", "Median", "3Q", "Max")
@@ -741,8 +709,8 @@
   }
   else print( resid, digits = digits, ...)
   
-  if( !is.null( x$se.residuals ) ){
-    resid <- x$residuals / x$se.residuals
+  if( !is.null( x[["se.residuals"]] ) ){
+    resid <- x[["residuals"]] / x[["se.residuals"]]
     cat( "\nStandardized residuals:\n")
     if(df > 5){
       nam <- c("Min", "1Q", "Median", "3Q", "Max")
@@ -752,21 +720,21 @@
     else print( resid, digits = digits, ...)
   }
   
-  cat( "\nVariogram: ", x$variogram.model, "\n" )
-  rownames( x$param ) <- ifelse(
-    x$fit.param,
-    rownames( x$param ),
-    paste( rownames( x$param ), "(fixed)", sep = "" )
+  cat( "\nVariogram: ", x[["variogram.model"]], "\n" )
+  rownames( x[["param"]] ) <- ifelse(
+    x[["fit.param"]],
+    rownames( x[["param"]] ),
+    paste( rownames( x[["param"]] ), "(fixed)", sep = "" )
   )
-  ##        print( format( x$param, digits = digits ), print.gap = 2, quote = FALSE )
+  ##        print( format( x[["param"]], digits = digits ), print.gap = 2, quote = FALSE )
   printCoefmat(
-    x$param, digits = digits, signif.stars = FALSE, ...
+    x[["param"]], digits = digits, signif.stars = FALSE, ...
   )
   
   
-  if( !is.null( x$cor.tf.param ) ){
+  if( !is.null( x[["cor.tf.param"]] ) ){
     
-    correl <- x$cor.tf.param
+    correl <- x[["cor.tf.param"]]
     p <- NCOL(correl)
     if( p > 1 ){
       cat("\nCorrelation of (transformed) variogram parameters:\n")
@@ -780,15 +748,15 @@
   
   cat( "\nFixed effects coefficients:\n" )
   printCoefmat(
-    x$coefficients, digits = digits, signif.stars = signif.stars, ...
+    x[["coefficients"]], digits = digits, signif.stars = signif.stars, ...
   )
   
   cat(
     "\nResidual standard error (sqrt(nugget)):",
-    format(signif(x$scale,  digits)), "\n"
+    format(signif(x[["scale"]],  digits)), "\n"
   )
   
-  correl <- x$correlation
+  correl <- x[["correlation"]]
   if( !is.null(correl) ){
     p <- NCOL(correl)
     if( p > 1 ){
@@ -801,7 +769,7 @@
   }
   
   cat("\n")
-  summarizeRobWeights(x$rweights, digits = digits, ... )
+  summarizeRobWeights(x[["rweights"]], digits = digits, ... )
   
   invisible( x )
 }
@@ -812,9 +780,10 @@
   function( object, ... )
 {
   
-    ## 2012-11-04 AP handling compressed cov.betahat
+  ## 2012-11-04 AP handling compressed cov.betahat
+  ## 2013-06-12 AP substituting [["x"]] for $x in all lists
 
-    result <- expand( object$cov$cov.betahat )
+    result <- expand( object[["cov"]][["cov.betahat"]] )
     attr( result, "struc" ) <- NULL
     result
     
@@ -830,6 +799,7 @@
 {
 
   ## 2012-02-08 AP change for anisotropic variograms
+  ## 2013-06-12 AP substituting [["x"]] for $x in all lists
 
   ## refit model with fixed variogram parameters
   
@@ -841,13 +811,13 @@
     
     object <- update( 
       object, 
-      param = object$param,
-      aniso = object$aniso$aniso,
+      param = object[["param"]],
+      aniso = object[["aniso"]][["aniso"]],
       fit.param = c( 
         variance = FALSE, snugget = FALSE, nugget = FALSE, scale = FALSE, 
         a = FALSE, alpha = FALSE, beta = FALSE, delta = FALSE, 
         gamma = FALSE, lambda = FALSE, n = FALSE, nu = FALSE
-      )[names( object$param )],
+      )[names( object[["param"]] )],
       fit.aniso = c(
         f1 = FALSE, f2 = FALSE, omega = FALSE, phi = FALSE, zeta = FALSE 
       ),
@@ -871,21 +841,22 @@
 {
   
   ## 2012-12-22 method for extracting (restricted) loglikelihood
+  ## 2013-06-12 AP substituting [["x"]] for $x in all lists
   
    val <- if( REML ){
-    val <- object$loglik 
+    val <- object[["loglik"]] 
   } else if( object[["tuning.psi"]] >= georob.control()[["tuning.psi.nr"]] ){
     D <- deviance( object )
     -0.5 * ( 
-      D + attr( D, "log.det.covmat" ) + length( object$residuals ) * log( 2 * pi )
+      D + attr( D, "log.det.covmat" ) + length( object[["residuals"]] ) * log( 2 * pi )
     ) 
   } else NA_real_
   
-  attr(val, "nall") <- length(object$residuals)
-  attr(val, "nobs") <- object$df.residual
-  attr(val, "df") <- length(object$coefficients) + 
-    sum( object$initial.objects$fit.param ) +
-    sum( object$initial.objects$fit.aniso)
+  attr(val, "nall") <- length(object[["residuals"]])
+  attr(val, "nobs") <- object[["df.residual"]]
+  attr(val, "df") <- length(object[["coefficients"]]) + 
+    sum( object[["initial.objects"]][["fit.param"]] ) +
+    sum( object[["initial.objects"]][["fit.aniso"]])
   
   class(val) <- "logLik"
   val
@@ -904,19 +875,19 @@
   ## 2012-12-22 A. Papritz
   ## 2013-05-23 AP correct handling of missing observations
   ## 2013-05-31 AP revised expansion of covariance matrices
+  ## 2013-06-12 AP substituting [["x"]] for $x in all lists
   
   ## redefine na.action component of object
   
-  if( identical( class( object$na.action ), "exclude" ) ){
-    class( object$na.action ) <- "omit"
+  if( identical( class( object[["na.action"]] ), "exclude" ) ){
+    class( object[["na.action"]] ) <- "omit"
   }
   
   if( object[["tuning.psi"]] < georob.control()[["tuning.psi.nr"]] ){
     result <- NA_real_
   } else {
     Valpha.objects <- expand( object[["Valpha.objects"]] )
-    G <- sum( object[["param"]][c("variance", "snugget")] ) *
-      t(Valpha.objects[["Valpha.ucf"]]) %*% Valpha.objects[["Valpha.ucf"]]
+    G <- sum( object[["param"]][c("variance", "snugget")] ) * Valpha.objects[["Valpha"]]
       
     diag( G ) <- diag( G ) + object[["param"]]["nugget"]
     G <- G[object[["Tmat"]], object[["Tmat"]]]

Modified: pkg/R/georob.cv.R
===================================================================
--- pkg/R/georob.cv.R	2013-06-11 19:44:56 UTC (rev 8)
+++ pkg/R/georob.cv.R	2013-06-12 13:24:39 UTC (rev 9)
@@ -10,8 +10,8 @@
     formula = NULL, subset = NULL,
     nset = 10, seed = NULL, sets = NULL,
     duplicates.in.same.set = TRUE,
-    re.estimate = TRUE, param = object$param, 
-    fit.param = object$initial.objects$fit.param,
+    re.estimate = TRUE, param = object[["param"]], 
+    fit.param = object[["initial.objects"]][["fit.param"]],
     return.fit = FALSE, reduced.output = TRUE,
     lgn = FALSE,
     ncores = min( nset, detectCores() ),
@@ -20,6 +20,7 @@
   )
 {
   
+#  \$([[:alnum:]\.]+)([\^\r,$\[\] \(\)])          [["\1"]]\2
   ## Function computes nset-fold cross-validation predictions from a
   ## fitted georob object
   
@@ -72,6 +73,7 @@
   ## 2013-04-24 AP changes for parallelization on windows os
   ## 2013-05-23 AP correct handling of missing observations
   ## 2013-05-24 AP separate initial variogram parameters for each cross-validation set
+  ## 2013-06-12 AP substituting [["x"]] for $x in all lists
     
   ## auxiliary function that fits the model and computes the predictions of
   ## a cross-validation set
@@ -96,7 +98,7 @@
     ## change environment of terms and formula so that subset selection works for update            
     
     environment( formula ) <- environment()
-    environment( object$terms ) <- environment()
+    environment( object[["terms"]] ) <- environment()
     
     ## read-off initial values of variogram parameters
     
@@ -148,8 +150,8 @@
     
     if( reduced.output ){
       
-      if( !is.null( t.georob$cov$cov.betahat ) ){
-        t.se.coef <- sqrt( diag( expand( t.georob$cov$cov.betahat ) ) )
+      if( !is.null( t.georob[["cov"]][["cov.betahat"]] ) ){
+        t.se.coef <- sqrt( diag( expand( t.georob[["cov"]][["cov.betahat"]] ) ) )
       } else {
         t.se.coef <- NULL
       }
@@ -160,9 +162,9 @@
         "coefficients"
       )]
       
-      t.georob$aniso <- t.georob$aniso$aniso
+      t.georob[["aniso"]] <- t.georob[["aniso"]][["aniso"]]
       
-      if( !is.null( t.se.coef ) ) t.georob$se.coefficients <- t.se.coef
+      if( !is.null( t.se.coef ) ) t.georob[["se.coefficients"]] <- t.se.coef
       
     }
     
@@ -172,15 +174,15 @@
   
   ## redefine na.action component of object
   
-  if( identical( class( object$na.action ), "exclude" ) ){
-    class( object$na.action ) <- "omit"
+  if( identical( class( object[["na.action"]] ), "exclude" ) ){
+    class( object[["na.action"]] ) <- "omit"
   }
   
   ## update terms of object is formula is provided
   
   if( !is.null( formula ) ){
     formula <- update( formula( object ), formula )
-    object$terms <- terms( formula )
+    object[["terms"]] <- terms( formula )
   } else {
     formula <- formula( object )
   }
@@ -189,20 +191,20 @@
   ## as data argument to georob must exist in GlobalEnv)
   
   data <- cbind(
-    get_all_vars( formula( object ), eval( getCall(object)$data ) ),
-    get_all_vars( object$locations.objects$locations, eval( getCall(object)$data ) )
+    get_all_vars( formula( object ), eval( getCall(object)[["data"]] ) ),
+    get_all_vars( object[["locations.objects"]][["locations"]], eval( getCall(object)[["data"]] ) )
   )
   
   ## select subset if appropriate
   
   if( !is.null( subset ) ){
     data <- data[subset, ]
-    object$Tmat <- object$Tmat[subset]
-  } else if( !is.null( getCall(object)$subset ) ){
-   data <- data[eval( getCall(object)$subset ), ]
+    object[["Tmat"]] <- object[["Tmat"]][subset]
+  } else if( !is.null( getCall(object)[["subset"]] ) ){
+   data <- data[eval( getCall(object)[["subset"]] ), ]
   }
   
-#   if( !is.null( getCall(object)$subset ) )
+#   if( !is.null( getCall(object)[["subset"]] ) )
    
   ## define cross-validation sets
   
@@ -226,8 +228,8 @@
   }
   
   if( duplicates.in.same.set ){
-    dups <- duplicated( object$Tmat )
-    idups <- match( object$Tmat[dups], object$Tmat[!dups] )
+    dups <- duplicated( object[["Tmat"]] )
+    idups <- match( object[["Tmat"]][dups], object[["Tmat"]][!dups] )
     sets[dups] <- (sets[!dups])[idups]
   }
   
@@ -249,7 +251,7 @@
     
   ## loop over all cross-validation sets
   
-  if( .Platform$OS.type == "windows" ){
+  if( .Platform[["OS.type"]] == "windows" ){
     
     ## create a SNOW cluster on windows OS
     
@@ -302,25 +304,25 @@
     
   ## create single data frame with cross-validation results 
   
-  result <- t.result[[1]]$pred
-  result$subset <- rep( 1, nrow( t.result[[1]]$pred ) )
+  result <- t.result[[1]][["pred"]]
+  result[["subset"]] <- rep( 1, nrow( t.result[[1]][["pred"]] ) )
   
   for( t.i in 2:length( t.result ) ) {
     result <- rbind( 
       result, 
       data.frame( 
-        t.result[[t.i]]$pred,
-        subset = rep( t.i, nrow( t.result[[t.i]]$pred ) )
+        t.result[[t.i]][["pred"]],
+        subset = rep( t.i, nrow( t.result[[t.i]][["pred"]] ) )
       )
     )
   }
-  t.ix <- sort( result$i, index.return = T )$ix
+  t.ix <- sort( result[["i"]], index.return = T )[["ix"]]
   result <- result[t.ix, ]
-  result$data <- model.response( 
+  result[["data"]] <- model.response( 
     model.frame( formula( object), data, na.action = na.pass ) 
   )
   
-  if( lgn ) result$lgn.data <- exp( result$data )
+  if( lgn ) result[["lgn.data"]] <- exp( result[["data"]] )
   
   result <- result[, -match("i", colnames( result) )]
   
@@ -335,11 +337,11 @@
     result[,  c(isubset, idata, ipred, ise)]
   )
   
-  t.fit <- lapply( t.result, function( x ) return( x$fit ) )
+  t.fit <- lapply( t.result, function( x ) return( x[["fit"]] ) )
   
-  if( re.estimate && !all( sapply( t.fit, function(x) x$converged ) ) ) warning(
+  if( re.estimate && !all( sapply( t.fit, function(x) x[["converged"]] ) ) ) warning(
     "lack of covergence for  ", 
-    sum( !sapply( t.fit, function(x) x$converged ) ), " cross-validation sets"
+    sum( !sapply( t.fit, function(x) x[["converged"]] ) ), " cross-validation sets"
   )
   
   result <- list( 
@@ -369,8 +371,9 @@
   ## plot method for class "cv.georob"  
   
   ## 2011-12-21 A. Papritz
+  ## 2013-06-12 AP substituting [["x"]] for $x in all lists
   
-  x <- x$pred
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/georob -r 9