R Under development (unstable) (2023-11-01 r85459 ucrt) -- "Unsuffered Consequences"
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> library(lme4)
Loading required package: Matrix
> ## show important current settings {for reference, etc} -- [early, and also on Windows !]:
> str( lmerControl())
List of 8
 $ optimizer      : chr "nloptwrap"
 $ restart_edge   : logi TRUE
 $ boundary.tol   : num 1e-05
 $ calc.derivs    : logi TRUE
 $ use.last.params: logi FALSE
 $ checkControl   :List of 8
  ..$ check.nobs.vs.rankZ: chr "ignore"
  ..$ check.nobs.vs.nlev : chr "stop"
  ..$ check.nlev.gtreq.5 : chr "ignore"
  ..$ check.nlev.gtr.1   : chr "stop"
  ..$ check.nobs.vs.nRE  : chr "stop"
  ..$ check.rankX        : chr "message+drop.cols"
  ..$ check.scaleX       : chr "warning"
  ..$ check.formula.LHS  : chr "stop"
 $ checkConv      :List of 3
  ..$ check.conv.grad    :List of 3
  .. ..$ action: chr "warning"
  .. ..$ tol   : num 0.002
  .. ..$ relTol: NULL
  ..$ check.conv.singular:List of 2
  .. ..$ action: chr "message"
  .. ..$ tol   : num 1e-04
  ..$ check.conv.hess    :List of 2
  .. ..$ action: chr "warning"
  .. ..$ tol   : num 1e-06
 $ optCtrl        : list()
 - attr(*, "class")= chr [1:2] "lmerControl" "merControl"
> str(glmerControl())
List of 11
 $ optimizer      : chr [1:2] "bobyqa" "Nelder_Mead"
 $ restart_edge   : logi FALSE
 $ boundary.tol   : num 1e-05
 $ calc.derivs    : logi TRUE
 $ use.last.params: logi FALSE
 $ checkControl   :List of 9
  ..$ check.nobs.vs.rankZ     : chr "ignore"
  ..$ check.nobs.vs.nlev      : chr "stop"
  ..$ check.nlev.gtreq.5      : chr "ignore"
  ..$ check.nlev.gtr.1        : chr "stop"
  ..$ check.nobs.vs.nRE       : chr "stop"
  ..$ check.rankX             : chr "message+drop.cols"
  ..$ check.scaleX            : chr "warning"
  ..$ check.formula.LHS       : chr "stop"
  ..$ check.response.not.const: chr "stop"
 $ checkConv      :List of 3
  ..$ check.conv.grad    :List of 3
  .. ..$ action: chr "warning"
  .. ..$ tol   : num 0.002
  .. ..$ relTol: NULL
  ..$ check.conv.singular:List of 2
  .. ..$ action: chr "message"
  .. ..$ tol   : num 1e-04
  ..$ check.conv.hess    :List of 2
  .. ..$ action: chr "warning"
  .. ..$ tol   : num 1e-06
 $ optCtrl        : list()
 $ tolPwrss       : num 1e-07
 $ compDev        : logi TRUE
 $ nAGQ0initStep  : logi TRUE
 - attr(*, "class")= chr [1:2] "glmerControl" "merControl"
> str(nlmerControl())
List of 3
 $ optimizer: chr [1:2] "Nelder_Mead" "Nelder_Mead"
 $ tolPwrss : num 1e-10
 $ optCtrl  : list()
 - attr(*, "class")= chr [1:2] "nlmerControl" "merControl"
> ls.str(environment(nloptwrap))
defaultControl : List of 4
 $ algorithm: chr "NLOPT_LN_BOBYQA"
 $ xtol_abs : num 1e-08
 $ ftol_abs : num 1e-08
 $ maxeval  : num 1e+05
> ##
> fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
> fm1ML <- refitML(fm1)
> REMLcrit(fm1)
[1] 1743.628
> deviance(fm1ML)
[1] 1751.939
> deviance(fm1,REML=FALSE)  ## FIXME: not working yet (NA)
[1] 1751.986
> deviance(fm1,REML=TRUE)
[1] 1751.986
> 
> ## from lme4.0
> oldvals <- c(REML=1743.6282722424, ML=1751.98581103058)
> ## leave out ML values for REML fits for now ...
> stopifnot(
+           all.equal(REMLcrit(fm1),deviance(fm1,REML=TRUE),deviance(fm1ML,REML=TRUE),oldvals["REML"]),
+           all.equal(deviance(fm1ML),deviance(fm1ML,REML=FALSE),oldvals["ML"]),
+           all.equal(REMLcrit(fm1)/-2,c(logLik(fm1)),c(logLik(fm1ML,REML=TRUE)),c(logLik(fm1,REML=TRUE))),
+           all.equal(deviance(fm1ML)/-2,c(logLik(fm1ML,REML=FALSE)),
+                     c(logLik(fm1ML,REML=FALSE))))
> 
> ## should be:
> ## stopifnot(
> ##           all.equal(deviance(fm1),deviance(fm1,REML=TRUE),deviance(fm1ML,REML=TRUE),oldvals["REML"]),
> ##           all.equal(deviance(fm1ML),deviance(fm1,REML=FALSE),deviance(fm1ML,REML=FALSE),oldvals["ML"]),
> ##           all.equal(deviance(fm1)/2,c(logLik(fm1)),c(logLik(fm1ML,REML=TRUE)),c(logLik(fm1,REML=TRUE))),
> ##           all.equal(deviance(fm1ML)/2,c(logLik(fm1,REML=FALSE)),c(logLik(fm1ML,REML=FALSE)),
> ##                     c(logLik(fm1ML,REML=FALSE))))
> 
> proc.time()
   user  system elapsed 
   1.21    0.09    1.31