[Lme4-commits] r1687 - in pkg/SASmixed: . inst man vignettes

[noreply at r-forge.r-project.org]

Author: bbolker
Date: 2012-03-22 19:30:20 +0100 (Thu, 22 Mar 2012)
New Revision: 1687

Added:
   pkg/SASmixed/vignettes/
Removed:
   pkg/SASmixed/inst/doc/
Modified:
   pkg/SASmixed/man/Mississippi.Rd
   pkg/SASmixed/man/Multilocation.Rd
   pkg/SASmixed/vignettes/Usinglmer.Rnw
Log:

  moved vignette from inst/doc/ to vignettes/
  fixed some method="ML|REML" to REML=TRUE|FALSE
  (still not quite passing checks; there is one sensivity in refitML ...)



Modified: pkg/SASmixed/man/Mississippi.Rd
===================================================================
--- pkg/SASmixed/man/Mississippi.Rd	2012-03-22 03:18:02 UTC (rev 1686)
+++ pkg/SASmixed/man/Mississippi.Rd	2012-03-22 18:30:20 UTC (rev 1687)
@@ -37,14 +37,14 @@
   ## compare with output 4.1, p. 142
   print(fm1Miss <- lmer(y ~ 1 + (1|influent), Mississippi))
   ## compare with output 4.2, p. 143
-  print(fm1MLMiss <- update(fm1Miss, method = "ML"))
+  print(fm1MLMiss <- update(fm1Miss, REML=FALSE))
   ## BLUP's of random effects on p. 142
   ranef(fm1Miss)            
   ## BLUP's of random effects on p. 144
   print(ranef(fm1MLMiss))
 #intervals(fm1Miss)       # interval estimates of variance components
   ## compare to output 4.8 and 4.9, pp. 150-152
-  print(fm2Miss <- lmer(y ~ Type+(1|influent), Mississippi, method = "REML"))
+  print(fm2Miss <- lmer(y ~ Type+(1|influent), Mississippi, REML=TRUE))
   print(anova(fm2Miss))
 }
 }

Modified: pkg/SASmixed/man/Multilocation.Rd
===================================================================
--- pkg/SASmixed/man/Multilocation.Rd	2012-03-22 03:18:02 UTC (rev 1686)
+++ pkg/SASmixed/man/Multilocation.Rd	2012-03-22 18:30:20 UTC (rev 1687)
@@ -57,7 +57,11 @@
   print(fm4Mult <- lmer(Adj ~ Trt + (1|Grp), Multilocation))
   print(fm5Mult <- lmer(Adj ~ 1 + (1|Grp), Multilocation))
   print(anova(fm2Mult))
+## testing
+  mlist  <- list(fm1Mult, fm2Mult, fm3Mult, fm4Mult, fm5Mult)
+  for (i in seq_along(mlist)) { cat(i,"\n"); refitML(mlist[[i]]) }
   print(anova(fm1Mult, fm2Mult, fm3Mult, fm4Mult, fm5Mult))
+  ## fm3Mult has a zero group variance -- is this true in lme4.0 as well?
   ### Treating the location as a random effect
   print(fm1MultR <- lmer(Adj ~ Trt + (1|Location/Trt) + (1|Grp), Multilocation))
   print(anova(fm1MultR))

Modified: pkg/SASmixed/vignettes/Usinglmer.Rnw
===================================================================
--- pkg/SASmixed/inst/doc/Usinglmer.Rnw	2012-03-20 13:18:30 UTC (rev 1685)
+++ pkg/SASmixed/vignettes/Usinglmer.Rnw	2012-03-22 18:30:20 UTC (rev 1687)
@@ -369,7 +369,7 @@
 ## compare with output 4.1, p. 142
 (fm1Miss <- lmer(y ~ 1 + (1 | influent), Mississippi))
 ## compare with output 4.2, p. 143
-(fm1MLMiss <- lmer(y ~ 1 + (1 | influent), Mississippi, method = "ML"))
+(fm1MLMiss <- lmer(y ~ 1 + (1 | influent), Mississippi, REML=FALSE))
 ranef(fm1MLMiss)          # BLUP's of random effects on p. 144
 ranef(fm1Miss)            # BLUP's of random effects on p. 142
 VarCorr(fm1Miss)          # compare to output 4.7, p. 148