Doug, For your examples fm5 and m5 I obtain a very different iteration behavior than the one you sent along in lmer2_test.Rout, but the deviances are the same. I copy the relevant section below. The runs converge much faster (lmer: 37 iterations, lmer2: 53 iterations); in this case lmer2 takes longer than lmer. Let me know if you want the complete output. Best Reinhold # output copied from lmer2_test.Rout (Doug Bates) > data(star, package = "mlmRev") > system.time(fm5 <- lmer(math ~ 0+eth*sx+gr+cltype+(yrs|id)+(1|tch)+ (yrs|sch), + star, control = list(niterEM = 0, + msVerbose = 1, grad = 0))) 0 242697.: 1.16440 0.335239 0.00000 0.149076 0.00867985 0.00249898 0.00000 1 240182.: 1.22398 0.133992 0.0107802 0.486643 0.596311 0.707177 -0.000728211 ... 162 238762.: 3.01226 0.134199 1.49260 0.700875 0.303919 0.133997 1.84893 163 238762.: 3.01186 0.134317 1.49231 0.701712 0.304186 0.134159 1.84523 user system elapsed 124.232 14.540 138.976 > system.time(m5 <- lmer2(math ~ 0+eth*sx+gr+cltype+(yrs|id)+(1|tch)+ (yrs|sch), + star, control = list(msVerbose = 1))) 0 242697.: 1.07907 0.578998 0.00000 0.386104 0.0931657 0.0499898 0.00000 ... 105 238762.: 1.81969 0.349463 -0.0605364 0.837551 0.871528 0.231452 -0.325310 user system elapsed 152.305 0.120 152.514 > dput(deviance(fm5)) 238762.389537803 > dput(unname(deviance(m5))) 238762.389580669 > ## The Cholesky decomposition is chosen to be simplicial. > ## A supernodal decomposition may be faster. > class(m5@L) [1] "dCHMsimpl" attr(,"package") [1] "Matrix" > object.size(fm5) [1] 25493280 > object.size(m5) [1] 16525464 ############################# output from my run R version 2.4.1 Patched (2007-01-26 r40579) i386-apple-darwin8.8.1 8 (MacBook Pro) lme4 0.9975-11; Matrix 0.9975-9) > system.time(fm5 <- lmer(math ~ 0+eth*sx+gr+cltype+(yrs|id)+(1|tch)+ (yrs|sch), + star, control = list(niterEM = 0, + msVerbose = 1, grad = 0))) 0 242697.: 1.16440 0.335239 0.00000 0.149076 0.00867985 0.00249898 0.00000 1 240190.: 1.22511 0.136410 0.0113707 0.486800 0.596531 0.707499 -0.000738651 2 239486.: 1.63543 5.00000e-10 -0.00742053 0.519908 0.618466 0.715359 0.00974589 ... 35 238762.: 3.01045 0.134544 1.49397 0.700177 0.302708 0.134498 1.85304 36 238762.: 3.01192 0.134243 1.49167 0.701853 0.304239 0.133878 1.84529 37 238762.: 3.01170 0.134269 1.49274 0.701456 0.304068 0.134149 1.84515 [1] 48.448 8.914 59.079 0.000 0.000 > system.time(m5 <- lmer2(math ~ 0+eth*sx+gr+cltype+(yrs|id)+(1|tch)+ (yrs|sch), + star, control = list(msVerbose = 1))) 0 242697.: 1.07907 0.578998 0.00000 0.386104 0.0931657 0.0499898 0.00000 1 240177.: 1.41005 0.00000 -0.0992838 1.04542 0.370329 0.228358 0.00647129 2 240177.: 1.45247 0.000138750 0.179498 1.02619 0.371758 0.225824 0.00530791 ... 51 238762.: 1.81942 0.349366 -0.0605206 0.837256 0.871043 0.231642 -0.325055 52 238762.: 1.81944 0.349402 -0.0605135 0.837522 0.871074 0.231529 -0.325294 53 238762.: 1.81949 0.349484 -0.0605134 0.837539 0.871436 0.231562 -0.325248 [1] 104.364 11.791 115.872 0.000 0.000 > dput(deviance(fm5)) 238762.38946746 > dput(unname(deviance(m5))) 238762.389579281 > class(m5@L) [1] "dCHMsimpl" attr(,"package") [1] "Matrix" > object.size(fm5) [1] 23948460 > object.size(m5) [1] 15483912 ---- Reinhold Kliegl, Dept. of Psychology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany phone: +493319772868, fax: +493319772793 http://www.psych.uni-potsdam.de/people/kliegl/ [[alternative HTML version deleted]]