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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 900, Sat Sep 3 22:00:07 2005 UTC revision 901, Tue Sep 6 01:26:11 2005 UTC
# Line 100  Line 100 
100  setMethod("lmer", signature(formula = "formula"),  setMethod("lmer", signature(formula = "formula"),
101            function(formula, data, family,            function(formula, data, family,
102                     method = c("REML", "ML", "PQL", "Laplace", "AGQ"),                     method = c("REML", "ML", "PQL", "Laplace", "AGQ"),
103                     control = list(),                     control = list(), start,
104                     subset, weights, na.action, offset,                     subset, weights, na.action, offset,
105                     model = TRUE, x = FALSE, y = FALSE , ...)                     model = TRUE, x = FALSE, y = FALSE , ...)
106            ## x, y : not dealt with at all -- FIXME ? .NotYetImplemented(            ## x, y : not dealt with at all -- FIXME ? .NotYetImplemented(
# Line 180  Line 180 
180            mer <- .Call("lmer_create", lapply(random, "[[", 2),            mer <- .Call("lmer_create", lapply(random, "[[", 2),
181                         mmats, method, PACKAGE = "Matrix")                         mmats, method, PACKAGE = "Matrix")
182            if (lmm) {                    ## linear mixed model            if (lmm) {                    ## linear mixed model
183                .Call("lmer_initial", mer, PACKAGE="Matrix")                if (missing(start)) .Call("lmer_initial", mer, PACKAGE="Matrix")
184                  else .Call("lmer_set_initial", mer, start, PACKAGE = "Matrix")
185                .Call("lmer_ECMEsteps", mer, cv$niterEM, cv$EMverbose, PACKAGE = "Matrix")                .Call("lmer_ECMEsteps", mer, cv$niterEM, cv$EMverbose, PACKAGE = "Matrix")
186                LMEoptimize(mer) <- cv                LMEoptimize(mer) <- cv
187                fits <- .Call("lmer_fitted", mer, mmats, TRUE, PACKAGE = "Matrix")                fits <- .Call("lmer_fitted", mer, mmats, TRUE, PACKAGE = "Matrix")

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