### Eclipse Workspace Patch 1.0
#P lme4Eigen
Index: R/lmer.R
===================================================================
--- R/lmer.R	(revision 1635)
+++ R/lmer.R	(working copy)
@@ -77,7 +77,7 @@
 lmer <- function(formula, data, REML = TRUE, sparseX = FALSE,
                  control = list(), start = NULL,
                  verbose = 0L, subset, weights, na.action, offset,
-                 contrasts = NULL, devFunOnly=FALSE, ...)
+                 contrasts = NULL, devFunOnly=FALSE, optimizer=c("NelderMead","bobyqa"), ...)
 {
     if (sparseX) warning("sparseX = TRUE has no effect at present")
     mf <- mc <- match.call()
@@ -136,21 +136,51 @@
     ## FIXME: this code is replicated in lmer/glmer/nlmer ...
     ## it seems good to have it in R rather than C++ code but maybe it should go within Nelder_Mead() ??
 
-    control$iprint <- switch(as.character(min(verbose,3L)),
-                             "0"=0, "1"=20,"2"=10,"3"=1)
-
-    lower <- reTrms$lower
-    ## FIXME: allow user control of xst, xt ?
-    xst <- rep.int(0.1, length(lower))
-    opt <- Nelder_Mead(devfun, x0=rho$pp$theta, xst=0.2*xst, xt=xst*0.0001,
-                       lower=lower, control=control)
-    if (opt$ierr < 0L) {
-        if (opt$ierr > -4L)
-            stop("convergence failure, code ", opt$ierr, " in NelderMead")
-        else
-            warning("failure to converge in", opt$control$maxfun, "evaluations")
-    }
-    mkMerMod(environment(devfun), opt, reTrms, fr, mc)
+	lower <- reTrms$lower
+	# RJ's changes begin
+	opt <- switch(match.arg(optimizer),
+			bobyqa = {
+				if(!is.numeric(control$rhobeg)) control$rhobeg <- 0.0002
+				if(!is.numeric(control$rhoend)) control$rhoend <- 2e-7
+				rho$control <- control
+				# Delete unused options to prevent warning from showing up
+				control$FtolAbs <- NULL
+				control$FtolRel <- NULL
+				bobyqa(rho$pp$theta, devfun, lower, control=control)
+			},
+			NelderMead = {
+				## FIXME: this code is replicated in lmer/glmer/nlmer ...
+				## it seems good to have it in R rather than C++ code but maybe it should go within Nelder_Mead() ??
+				control$iprint <- switch(as.character(min(verbose,3L)), "0"=0, "1"=20,"2"=10,"3"=1)
+				xst <- rep.int(0.1, length(lower))
+				# RJ -- allow user control of xst, xt
+				ctl <- control
+				if(!is.numeric(control$xstFactor))
+					xstFactor <- 0.2
+				else
+					xstFactor <- control$xstFactor
+				if(!is.numeric(control$xtFactor))
+					xtFactor <- 0.0001
+				else
+					xtFactor <- control$xtFactor
+				ctl$xstFactor <- NULL
+				ctl$xtFactor <- NULL
+				Nelder_Mead(devfun, x0=rho$pp$theta, xst=xstFactor*xst, xt=xst*xtFactor, lower=lower, control=ctl)
+			})
+	
+	if(optimizer=="NelderMead") {
+		if (opt$ierr < 0L) {
+			if (opt$ierr > -4L)
+				stop("convergence failure, code ", opt$ierr, " in NelderMead")
+			else
+				warning("failure to converge in", opt$control$maxfun, "evaluations")
+		}
+	} else if (optimizer=="bobyqa") {
+		if (opt$ierr > 0L)
+			warning("convergence problem, code ", opt$ierr, " in bobyqa")
+	}
+	# RJ's changes end
+	mkMerMod(environment(devfun), opt, reTrms, fr, mc)
 }## { lmer }
 
 ##' Fit a generalized linear mixed model (GLMM)