[R-sig-ME] Timing for lmer2 versus lmer for chocolate cake data (WinXP)

Andrew Robinson A.Robinson at ms.unimelb.edu.au
Sun Jan 28 20:01:25 CET 2007


I've switched from FreeBSD to WinXP temporarily :)

I've attached a comparison of lmer and lmer2 upon the analysis of
Cochran and Cox's chocolate cake data.  Here, it seems that lmer2 is
faster (0.08 vs. 0.15) but the AIC of the fitted model for lmer2 is
higher (1643 vs 1635).  The models are quite different in the random
effects.

The data, script, and output are attached.

Cheers,

Andrew
-- 
Andrew Robinson  
Department of Mathematics and Statistics            Tel: +61-3-8344-9763
University of Melbourne, VIC 3010 Australia         Fax: +61-3-8344-4599
http://www.ms.unimelb.edu.au/~andrewpr
http://blogs.mbs.edu/fishing-in-the-bay/ 
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# The chocolate cake breakage data are referred to in section 5.5 of
# \citet{lee+nelder+pawitan-2006} as an example of a normal-normal
# hiearchical generalized linear model. The data are originally from
# \citet{cochran+cox-1957}.

require(lme4)

cake <- read.csv("cake.csv")
names(cake) <- c("replicate","batch","recipe","temperature","angle")
cake$recipe <- factor(cake$recipe)
cake$replicate <- factor(cake$replicate)
cake$batch <- factor(cake$batch)
cake$temperature <- factor(cake$temperature)
dim(cake)
head(cake)

system.time(cake.lmer <- lmer(angle ~ recipe * temperature + 
                  (1 | replicate/batch),
                  data = cake))
summary(cake.lmer)
system.time(cake.lmer2 <- lmer2(angle ~ recipe * temperature + 
                  (1 | replicate/batch),
                  data = cake))
summary(cake.lmer2)

sessionInfo()

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> require(lme4)
[1] TRUE

> cake <- read.csv("cake.csv")

> names(cake) <- c("replicate", "batch", "recipe", "temperature", 
    "angle")

> cake$recipe <- factor(cake$recipe)

> cake$replicate <- factor(cake$replicate)

> cake$batch <- factor(cake$batch)

> cake$temperature <- factor(cake$temperature)

> dim(cake)
[1] 270   5

> head(cake)
  replicate batch recipe temperature angle
1         1     1      1         175    42
2         1     1      1         185    46
3         1     1      1         195    47
4         1     1      1         205    39
5         1     1      1         215    53
6         1     1      1         225    42

> system.time(cake.lmer <- lmer(angle ~ recipe * temperature + 
    (1 | replicate/batch), data = cake))
[1] 0.15 0.00 0.16   NA   NA

> summary(cake.lmer)
Linear mixed-effects model fit by REML 
Formula: angle ~ recipe * temperature + (1 | replicate/batch) 
   Data: cake 
  AIC  BIC logLik MLdeviance REMLdeviance
 1635 1707 -797.7       1638         1595
Random effects:
 Groups          Name        Variance Std.Dev.
 batch:replicate (Intercept)  3.7384  1.9335  
 replicate       (Intercept) 38.2278  6.1829  
 Residual                    20.4613  4.5234  
number of obs: 270, groups: batch:replicate, 45; replicate, 15

Fixed effects:
                       Estimate Std. Error t value
(Intercept)             29.1333     2.0401  14.281
recipe2                 -2.2667     1.7963  -1.262
recipe3                 -1.2000     1.7963  -0.668
temperature185           2.4000     1.6517   1.453
temperature195           1.6667     1.6517   1.009
temperature205           4.4000     1.6517   2.664
temperature215           9.5333     1.6517   5.772
temperature225           5.9333     1.6517   3.592
recipe2:temperature185   0.1333     2.3359   0.057
recipe3:temperature185  -1.4000     2.3359  -0.599
recipe2:temperature195   3.2000     2.3359   1.370
recipe3:temperature195   2.1333     2.3359   0.913
recipe2:temperature205   0.8667     2.3359   0.371
recipe3:temperature205  -1.4667     2.3359  -0.628
recipe2:temperature215  -1.9333     2.3359  -0.828
recipe3:temperature215  -3.0667     2.3359  -1.313
recipe2:temperature225   2.4667     2.3359   1.056
recipe3:temperature225   1.8667     2.3359   0.799

Correlation of Fixed Effects:
            (Intr) recip2 recip3 tmp185 tmp195 tmp205 tmp215 tmp225 r2:185
recipe2     -0.440                                                        
recipe3     -0.440  0.500                                                 
tempertr185 -0.405  0.460  0.460                                          
tempertr195 -0.405  0.460  0.460  0.500                                   
tempertr205 -0.405  0.460  0.460  0.500  0.500                            
tempertr215 -0.405  0.460  0.460  0.500  0.500  0.500                     
tempertr225 -0.405  0.460  0.460  0.500  0.500  0.500  0.500              
rcp2:tmp185  0.286 -0.650 -0.325 -0.707 -0.354 -0.354 -0.354 -0.354       
rcp3:tmp185  0.286 -0.325 -0.650 -0.707 -0.354 -0.354 -0.354 -0.354  0.500
rcp2:tmp195  0.286 -0.650 -0.325 -0.354 -0.707 -0.354 -0.354 -0.354  0.500
rcp3:tmp195  0.286 -0.325 -0.650 -0.354 -0.707 -0.354 -0.354 -0.354  0.250
rcp2:tmp205  0.286 -0.650 -0.325 -0.354 -0.354 -0.707 -0.354 -0.354  0.500
rcp3:tmp205  0.286 -0.325 -0.650 -0.354 -0.354 -0.707 -0.354 -0.354  0.250
rcp2:tmp215  0.286 -0.650 -0.325 -0.354 -0.354 -0.354 -0.707 -0.354  0.500
rcp3:tmp215  0.286 -0.325 -0.650 -0.354 -0.354 -0.354 -0.707 -0.354  0.250
rcp2:tmp225  0.286 -0.650 -0.325 -0.354 -0.354 -0.354 -0.354 -0.707  0.500
rcp3:tmp225  0.286 -0.325 -0.650 -0.354 -0.354 -0.354 -0.354 -0.707  0.250
            r3:185 r2:195 r3:195 r2:205 r3:205 r2:215 r3:215 r2:225
recipe2                                                            
recipe3                                                            
tempertr185                                                        
tempertr195                                                        
tempertr205                                                        
tempertr215                                                        
tempertr225                                                        
rcp2:tmp185                                                        
rcp3:tmp185                                                        
rcp2:tmp195  0.250                                                 
rcp3:tmp195  0.500  0.500                                          
rcp2:tmp205  0.250  0.500  0.250                                   
rcp3:tmp205  0.500  0.250  0.500  0.500                            
rcp2:tmp215  0.250  0.500  0.250  0.500  0.250                     
rcp3:tmp215  0.500  0.250  0.500  0.250  0.500  0.500              
rcp2:tmp225  0.250  0.500  0.250  0.500  0.250  0.500  0.250       
rcp3:tmp225  0.500  0.250  0.500  0.250  0.500  0.250  0.500  0.500

> system.time(cake.lmer2 <- lmer2(angle ~ recipe * temperature + 
    (1 | replicate/batch), data = cake))
[1] 0.08 0.00 0.06   NA   NA

> summary(cake.lmer2)
Linear mixed-effects model fit by REML 
  AIC  BIC logLik MLdeviance REMLdeviance
 1643 1715 -801.7       1647         1603
Random effects:
 Groups          Name        Variance   Std.Dev. 
 batch:replicate (Intercept) 2.2454e-06 0.0014985
 replicate       (Intercept) 3.9195e+01 6.2605709
 Residual                    2.3099e+01 4.8061038
Number of obs: 270, groups: batch:replicate, 45; replicate, 15

Fixed effects:
                       Estimate Std. Error t value
(Intercept)             29.1333     2.0379  14.296
recipe2                 -2.2667     1.7549  -1.292
recipe3                 -1.2000     1.7549  -0.684
temperature185           2.4000     1.7549   1.368
temperature195           1.6667     1.7549   0.950
temperature205           4.4000     1.7549   2.507
temperature215           9.5333     1.7549   5.432
temperature225           5.9333     1.7549   3.381
recipe2:temperature185   0.1333     2.4819   0.054
recipe3:temperature185  -1.4000     2.4819  -0.564
recipe2:temperature195   3.2000     2.4819   1.289
recipe3:temperature195   2.1333     2.4819   0.860
recipe2:temperature205   0.8667     2.4819   0.349
recipe3:temperature205  -1.4667     2.4819  -0.591
recipe2:temperature215  -1.9333     2.4819  -0.779
recipe3:temperature215  -3.0667     2.4819  -1.236
recipe2:temperature225   2.4667     2.4819   0.994
recipe3:temperature225   1.8667     2.4819   0.752

Correlation of Fixed Effects:
            (Intr) recip2 recip3 tmp185 tmp195 tmp205 tmp215 tmp225 r2:185
recipe2     -0.431                                                        
recipe3     -0.431  0.500                                                 
tempertr185 -0.431  0.500  0.500                                          
tempertr195 -0.431  0.500  0.500  0.500                                   
tempertr205 -0.431  0.500  0.500  0.500  0.500                            
tempertr215 -0.431  0.500  0.500  0.500  0.500  0.500                     
tempertr225 -0.431  0.500  0.500  0.500  0.500  0.500  0.500              
rcp2:tmp185  0.304 -0.707 -0.354 -0.707 -0.354 -0.354 -0.354 -0.354       
rcp3:tmp185  0.304 -0.354 -0.707 -0.707 -0.354 -0.354 -0.354 -0.354  0.500
rcp2:tmp195  0.304 -0.707 -0.354 -0.354 -0.707 -0.354 -0.354 -0.354  0.500
rcp3:tmp195  0.304 -0.354 -0.707 -0.354 -0.707 -0.354 -0.354 -0.354  0.250
rcp2:tmp205  0.304 -0.707 -0.354 -0.354 -0.354 -0.707 -0.354 -0.354  0.500
rcp3:tmp205  0.304 -0.354 -0.707 -0.354 -0.354 -0.707 -0.354 -0.354  0.250
rcp2:tmp215  0.304 -0.707 -0.354 -0.354 -0.354 -0.354 -0.707 -0.354  0.500
rcp3:tmp215  0.304 -0.354 -0.707 -0.354 -0.354 -0.354 -0.707 -0.354  0.250
rcp2:tmp225  0.304 -0.707 -0.354 -0.354 -0.354 -0.354 -0.354 -0.707  0.500
rcp3:tmp225  0.304 -0.354 -0.707 -0.354 -0.354 -0.354 -0.354 -0.707  0.250
            r3:185 r2:195 r3:195 r2:205 r3:205 r2:215 r3:215 r2:225
recipe2                                                            
recipe3                                                            
tempertr185                                                        
tempertr195                                                        
tempertr205                                                        
tempertr215                                                        
tempertr225                                                        
rcp2:tmp185                                                        
rcp3:tmp185                                                        
rcp2:tmp195  0.250                                                 
rcp3:tmp195  0.500  0.500                                          
rcp2:tmp205  0.250  0.500  0.250                                   
rcp3:tmp205  0.500  0.250  0.500  0.500                            
rcp2:tmp215  0.250  0.500  0.250  0.500  0.250                     
rcp3:tmp215  0.500  0.250  0.500  0.250  0.500  0.500              
rcp2:tmp225  0.250  0.500  0.250  0.500  0.250  0.500  0.250       
rcp3:tmp225  0.500  0.250  0.500  0.250  0.500  0.250  0.500  0.500

> sessionInfo()
R version 2.4.1 (2006-12-18) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"  
[7] "base"     

other attached packages:
       lme4      Matrix     lattice 
"0.9975-11"  "0.9975-8"   "0.14-16" 


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