### Eclipse Workspace Patch 1.0
#P pedigreemm
Index: R/AllClass.R
===================================================================
--- R/AllClass.R	(revision 127)
+++ R/AllClass.R	(working copy)
@@ -23,5 +23,4 @@
 	     TRUE
 	 })
 
-setClass("pedigreemm", representation = list(relfac = "list"),
-         contains = "mer")
+setClass("pedigreemm", representation = list(relfac = "list", ans = "merMod", call = "call"))
Index: R/pedigree.R
===================================================================
--- R/pedigree.R	(revision 127)
+++ R/pedigree.R	(working copy)
@@ -163,7 +163,8 @@
 {
     mc <- match.call()
     lmerc <- mc                         # create a call to lmer
-    lmerc[[1]] <- as.name("lmer")
+	l... = list(...)
+	if (!is.null(l...$family)) lmerc[[1]] <- as.name("glmer") else lmerc[[1]] <- as.name("lmer")
     lmerc$pedigree <- NULL
 
     if (!length(pedigree))              # call lmer instead
@@ -172,25 +173,35 @@
     stopifnot(is.list(pedigree),        # check the pedigree argument
               length(names(pedigree)) == length(pedigree),
               all(sapply(pedigree, is, class2 = "pedigree")))
-                                     
+
     lmerc$doFit <- FALSE # call lmer without pedigree and with doFit = FALSE
-    lmf <- eval(lmerc, parent.frame())
+	lmf <- eval(lmerc, parent.frame())
 
-    
     relfac <- pedigree          # copy the pedigree list for relfactor
     pnms <- names(pedigree)
-    stopifnot(all(pnms %in% names(lmf$FL$fl)))
-    asgn <- attr(lmf$FL$fl, "assign")
+    stopifnot(all(pnms %in% names(lmf$reTrms$flist)))
+    asgn <- attr(lmf$reTrms$flist, "assign")
+	bigZt <- lmf$rho$pp$Zt
     for (i in seq_along(pedigree)) {
-        tn <- which(match(pnms[i], names(lmf$FL$fl)) == asgn)
+        tn <- which(match(pnms[i], names(lmf$reTrms$flist)) == asgn)
         if (length(tn) > 1)
             stop("a pedigree factor must be associated with only one r.e. term")
-        Zt <- lmf$FL$trms[[tn]]$Zt
-        relfac[[i]] <- relfactor(pedigree[[i]], rownames(Zt))
-        lmf$FL$trms[[tn]]$Zt <- lmf$FL$trms[[tn]]$A <- relfac[[i]] %*% Zt
+		assg = (lmf$reTrms$Gp[tn] + 1):lmf$reTrms$Gp[tn+1]
+		Zt <- bigZt[assg, ]
+		relfac[[i]] <- relfactor(pedigree[[i]], rownames(Zt))
+        #lmf$FL$trms[[tn]]$Zt <- lmf$FL$trms[[tn]]$A <- relfac[[i]] %*% Zt
+		bigZt[assg, ] <- relfac[[i]] %*% Zt
     }
-    ans <- do.call(if (!is.null(lmf$glmFit)) lme4:::glmer_finalize else lme4:::lmer_finalize, lmf)
-    ans <- new("pedigreemm", relfac = relfac, ans)
+	lmf$reTrms$Zt <- bigZt
+	lmf$rho$pp <- do.call(merPredD$new, c(lmf$reTrms[c("Zt","theta","Lambdat","Lind")], n=nrow(lmf$rho$pp$X), list(X=lmf$rho$pp$X)))
+	if (is(lmf$rho$resp, "lmerResp"))
+	{
+		ans <- lme4:::lmer_finalize(lmf$rho, lmf$optimizer, lmf$devfun, lmf$reTrms, lmf$control, lmf$fr, lmf$mc, lmf$verbose)
+	} else {
+		ans <- lme4:::glmer_finalize(lmf$rho, lmf$optimizer, lmf$devfun, lmf$reTrms, lmf$control, lmf$fr, lmf$mc, lmf$nAGQ, lmf$verbose)
+	}
+    #ans <- do.call(if (is(lmf$rho$resp, "lmerResp")) lme4:::lmer_finalize else lme4:::glmer_finalize, lmf)
+    ans <- new("pedigreemm", relfac = relfac, ans = ans)
     ans@call <- match.call()
     ans
 }
@@ -203,7 +214,8 @@
 {
     mc <- match.call()
     lmerc <- mc                         # create a call to lmer
-    lmerc[[1]] <- as.name("lmer")
+	l... = list(...)
+	if (!is.null(l...$family)) lmerc[[1]] <- as.name("glmer") else lmerc[[1]] <- as.name("lmer")
     lmerc$pre <- NULL
 
     if (!length(pre))              # call lmer instead
@@ -212,22 +224,39 @@
     stopifnot(is.list(pre),        # check the pre argument
               length(names(pre)) == length(pre),
               all(sapply(pre, is, class2 = "Matrix")))
-                                     
-    lmerc$doFit <- FALSE # call lmer without pre and with doFit = FALSE
-    lmf <- eval(lmerc, parent.frame())
 
-    
+	lmerc$doFit <- FALSE # call lmer without pedigree and with doFit = FALSE
+	lmf <- eval(lmerc, parent.frame())
+  
     pnms <- names(pre)
-    stopifnot(all(pnms %in% names(lmf$FL$fl)))
-    asgn <- attr(lmf$FL$fl, "assign")
+    stopifnot(all(pnms %in% names(lmf$reTrms$flist)))
+    asgn <- attr(lmf$reTrms$flist, "assign")
+	bigZt <- lmf$rho$pp$Zt
     for (i in seq_along(pre)) {
-        tn <- which(match(pnms[i], names(lmf$FL$fl)) == asgn)
+        tn <- which(match(pnms[i], names(lmf$reTrms$flist)) == asgn)
         if (length(tn) > 1)
             stop("a pre factor must be associated with only one r.e. term")
-        Zt <- lmf$FL$trms[[tn]]$Zt
-        lmf$FL$trms[[tn]]$Zt <- lmf$FL$trms[[tn]]$A <- pre[[i]] %*% Zt
-    }
-    do.call(if (!is.null(lmf$glmFit)) lme4:::glmer_finalize else lme4:::lmer_finalize, lmf)
+		assg = rownames(bigZt) %in% levels(lmf$reTrms$flist[[tn]])
+		Zt <- bigZt[assg, ]
+		relfac[[i]] <- relfactor(pedigree[[i]], rownames(Zt))
+		#lmf$FL$trms[[tn]]$Zt <- lmf$FL$trms[[tn]]$A <- pre[[i]] %*% Zt
+		bigZt[assg, ] <- pre[[i]] %*% Zt
+	}
+	lmf$reTrms$Zt <- bigZt
+	lmf$rho$pp <- do.call(merPredD$new, c(lmf$reTrms[c("Zt","theta","Lambdat","Lind")], n=nrow(lmf$rho$pp$X), list(X=lmf$rho$pp$X)))
+	#do.call(if (is(lmf$rho$resp, "lmerResp")) lme4:::lmer_finalize else lme4:::glmer_finalize, lmf)
+	if (is(lmf$rho$resp, "lmerResp"))
+	{
+		ans <- lme4:::lmer_finalize(lmf$rho, lmf$optimizer, lmf$devfun, lmf$reTrms, lmf$control, lmf$fr, lmf$mc, lmf$verbose)
+	} else {
+		ans <- lme4:::glmer_finalize(lmf$rho, lmf$optimizer, lmf$devfun, lmf$reTrms, lmf$control, lmf$fr, lmf$mc, lmf$nAGQ, lmf$verbose)
+	}
+	return(ans)
+}
+
+summary.pedigreemm <- function(object, ...)
+{
+	return(summary(object@ans))
 }
 
 setMethod("ranef", signature(object = "pedigreemm"),