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

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revision 808, Mon Jul 11 15:05:40 2005 UTC revision 809, Tue Jul 12 23:00:50 2005 UTC
# Line 188  Line 188 
188            LMEopt <- get("LMEoptimize<-")            LMEopt <- get("LMEoptimize<-")
189            doLMEopt <- quote(LMEopt(x = mer, value = cv))            doLMEopt <- quote(LMEopt(x = mer, value = cv))
190    
191            GSpt <- .Call("glmer_init", environment())            GSpt <- .Call("glmer_init", environment(), PACKAGE = "Matrix")
192            .Call("glmer_PQL", GSpt)  # obtain PQL estimates            .Call("glmer_PQL", GSpt, PACKAGE = "Matrix")  # obtain PQL estimates
193    
194            fixInd <- seq(ncol(x))            fixInd <- seq(ncol(x))
195            ## pars[fixInd] == beta, pars[-fixInd] == theta            ## pars[fixInd] == beta, pars[-fixInd] == theta
# Line 250  Line 250 
250                    cat(paste("convergence message", optimRes$message, "\n"))                    cat(paste("convergence message", optimRes$message, "\n"))
251                }                }
252                fxd[] <- optpars[fixInd]  ## preserve the names                fxd[] <- optpars[fixInd]  ## preserve the names
253                .Call("lmer_coefGets", mer, optpars[-fixInd], 2,                .Call("lmer_coefGets", mer, optpars[-fixInd], 2, PACKAGE = "Matrix")
                     PACKAGE = "Matrix")  
254            }            }
255    
256            .Call("glmer_finalize", GSpt, PACKAGE = "Matrix")            .Call("glmer_finalize", GSpt, PACKAGE = "Matrix")
# Line 860  Line 859 
859      LMEopt <- getAnywhere("LMEoptimize<-")      LMEopt <- getAnywhere("LMEoptimize<-")
860      doLMEopt <- quote(LMEopt(x = mer, value = cv))      doLMEopt <- quote(LMEopt(x = mer, value = cv))
861    
862      GSpt <- .Call("glmer_init", environment())      GSpt <- .Call("glmer_init", environment(), PACKAGE = "Matrix")
863      nf <- length(obj@flist)      nf <- length(obj@flist)
864      fixed <- obj@fixed      fixed <- obj@fixed
865      varc <- .Call("lmer_coef", mer, 2, PACKAGE = "Matrix")      varc <- .Call("lmer_coef", mer, 2, PACKAGE = "Matrix")

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