Philippe Grosjean wrote:
James Widman wrote:I am trying to duplicate the example by Spencer Graves in the wiki, using lmer with the Nozzle data.http://wiki.r-project.org/rwiki/doku.php?id=guides:lmer-testsHowever the Chisq value and the fitAB values that are calculated are different compared to those in the example. I also get a warning message when I attempt the fitAB. Does anyone have any guidance as to why this might happen and how to correct it?I am using R on Kubutu in case that may be helpful. Thanks---- my code -- [Previously saved workspace restored] > rm(list=ls(all=TRUE)) > list=ls(all=TRUE) > print(list) character(0) > y <- c(6,6,-15, 26,12,5, 11,4,4, 21,14,7, 25,18,25, + 13,6,13, 4,4,11, 17,10,17, -5,2,-5, 15,8,1, + 10,10,-11, -35,0,-14, 11,-10,-17, 12,-2,-16, -4,10,24)> Nozzle <- data.frame(Nozzle=rep(LETTERS[1:3], e=15),Operator=rep(letters[1:5], e=3), flowRate=y)> summary(Nozzle) Nozzle Operator flowRate A:15 a:9 Min. :-35.000 B:15 b:9 1st Qu.: 0.000 C:15 c:9 Median : 7.000 d:9 Mean : 5.511 e:9 3rd Qu.: 13.000 Max. : 26.000 > library(lme4) Loading required package: Matrix Loading required package: lattice> fitAB <- lmer(flowRate~Nozzle+(Nozzle|Operator),data=Nozzle, method="ML")Warning messages: 1: In .local(x, ..., value) : Estimated variance-covariance for factor ‘Operator’ is singular 2: In .local(x, ..., value) : nlminb returned message false convergence (8) > fitB <- lmer(flowRate~1+(1|Operator), data=Nozzle, method="ML") > anova(fitAB, fitB) Data: Nozzle Models: fitB: flowRate ~ 1 + (1 | Operator) fitAB: flowRate ~ Nozzle + (Nozzle | Operator) Df AIC BIC logLik Chisq Chi Df Pr(>Chisq) fitB 2 359.36 362.98 -177.68 fitAB 9 362.13 378.39 -172.06 11.237 7 0.1286 ---------------------------------------------------------------------- Output from Spencer Graves example fitAB 9 359.88 376.14 -170.94 13.479 7 0.06126Now, on a Mac OS X (using the unstable, development version of R 2.9.0, and recompiled version of lme4_0.999375-28... so caution of course!), I got this:First, the method = "ML" argument is deprecated and replaced by REML = TRUE/FALSE, but the doc at ?lmer does not tell exactly what is the equivalence to method = "ML" (and I don't know enough in this field to determine it by myself). Anyway, I tried both:> fitAB <- lmer(flowRate~Nozzle+(Nozzle|Operator),data=Nozzle, REML = TRUE)#Warning messages: #1: In .local(x, ..., value) : #Estimated variance-covariance for factor Operator is singular #2: In .local(x, ..., value) : #nlminb returned message false convergence (8) > fitB <- lmer(flowRate~1+(1|Operator), data=Nozzle, REML = TRUE) > anova(fitAB, fitB) Data: Nozzle Models: fitB: flowRate ~ 1 + (1 | Operator) fitAB: flowRate ~ Nozzle + (Nozzle | Operator) Df AIC BIC logLik Chisq Chi Df Pr(>Chisq) fitB 3 361.36 366.78 -177.68 fitAB 10 362.10 380.17 -171.05 13.261 7 0.06601 . --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1> fitAB <- lmer(flowRate~Nozzle+(Nozzle|Operator),data=Nozzle, REML = FALSE)#Warning messages: #1: In .local(x, ..., value) : #Estimated variance-covariance for factor Operator is singular #2: In .local(x, ..., value) : #nlminb returned message false convergence (8) > fitB <- lmer(flowRate~1+(1|Operator), data=Nozzle, REML = FALSE) > anova(fitAB, fitB) Data: Nozzle Models: fitB: flowRate ~ 1 + (1 | Operator) fitAB: flowRate ~ Nozzle + (Nozzle | Operator) Df AIC BIC logLik Chisq Chi Df Pr(>Chisq) fitB 3 361.36 366.78 -177.68 fitAB 10 361.96 380.03 -170.98 13.402 7 0.0629 . --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1So, I got same error messages as you. I got results closer to the one in the wiki page, BUT, I am puzzled by the degrees of freedom that are different 3/10 in my case, against 2/9 in yours and in the wiki page!Could the authors of lmer(), and/or of the wiki page, or the code cited in the wiki page (in CC) provide some explanation to this? Corrections/updates of the wiki page so that it reflects latest lmer() version would be also very much appreciated.All the best, Philippe Grosjean Just in case: > R.Version() $platform [1] "i386-apple-darwin8.11.1" $arch [1] "i386" $os [1] "darwin8.11.1" $system [1] "i386, darwin8.11.1" $status [1] "Under development (unstable)" $major [1] "2" $minor [1] "9.0" $year [1] "2009" $month [1] "01" $day [1] "22" $`svn rev` [1] "47686" $language [1] "R" $version.string [1] "R version 2.9.0 Under development (unstable) (2009-01-22 r47686)" > sessionInfo() R version 2.9.0 Under development (unstable) (2009-01-22 r47686) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] tcltk stats graphics grDevices utils datasets methods [8] base other attached packages: [1] lme4_0.999375-28 Matrix_0.999375-18 lattice_0.17-20 [4] svGUI_0.9-44 svSocket_0.9-43 svMisc_0.9-47 loaded via a namespace (and not attached): [1] grid_2.9.0 tools_2.9.0
Phillipe,My output from R ver 2.8.1 on a different PC running Windows XP agrees with your output verbatim, including the df difference. I used the kubuntu repository when I installed R on the other machine, I guess I'll have to remove it and reinstall a version from CRAN.
Best Regards, Jim ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
