DataData is from nine batches from which three samples were selected (A, B and C) and each a duplicate measurement. I am not sure about copyright of these data, so I will not reprint the data here. The problem is to determine the measurement ans sampling error in a chemical process.
facet_wrap(~ batch )
AnalysisAt the time of writing the book, the only approach was to do a classical ANOVA and calculate the estimates from there.
aov(x~ batch + batch:Sample,data=r4) %>%
Analysis of Variance Table
Df Sum Sq Mean Sq F value Pr(>F)
batch 8 792.88 99.110 132.6710 < 2e-16 ***
batch:Sample 18 25.30 1.406 1.8818 0.06675 .
Residuals 27 20.17 0.747
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
In this case the residual variation is 0.75. The batch:Sample variation estimates is, due to the design, twice the sapling variation plus residual variation. Hence it is estimated as 0.33. How lucky we are to have tools (lme4) which can do this estimate directly. In this case, as it was a well designed experiment, these estimates are the same as from the ANOVA.
l1 <- lmer(x ~1+ (1 | batch) + (1|batch:Sample) ,data=r4 )
Linear mixed model fit by REML ['lmerMod']
Formula: x ~ 1 + (1 | batch) + (1 | batch:Sample)
REML criterion at convergence: 189.4
Min 1Q Median 3Q Max
-1.64833 -0.50283 -0.06649 0.55039 1.57801
Groups Name Variance Std.Dev.
batch:Sample (Intercept) 0.3294 0.5739
batch (Intercept) 16.2841 4.0354
Residual 0.7470 0.8643
Number of obs: 54, groups: batch:Sample, 27; batch, 9
Estimate Std. Error t value
(Intercept) 47.148 1.355 34.8
A next step is confidence intervals around the estimates. Davies uses limits from a Chi-squared distribution for the residual variation, leading to a 90% interval 0.505 to 1.25. In contrast lme4 has two estimators, profile (computing a likelihood profile and finding the appropriate cutoffs based on the likelihood ratio test;) and bootstrap (perform parametric bootstrapping with confidence intervals computed from the bootstrap distribution according to boot.type). Each of these takes one or few second on my laptop, not feasible for the pre computer age. The estimates are different, to my surprise more narrow:
Computing profile confidence intervals ...
5 % 95 %
.sig01 0.0000000 0.9623748
.sig02 2.6742109 5.9597328
.sigma 0.7017849 1.1007261
(Intercept) 44.8789739 49.4173227
Computing bootstrap confidence intervals ...
5 % 95 %
sd_(Intercept)|batch:Sample 0.000000 0.8880414
sd_(Intercept)|batch 2.203608 5.7998348
sigma 0.664149 1.0430984
(Intercept) 45.140652 49.4931109
Davies continues to estimate the ratio to residual for sampling variation, which was the best available for that time. This I won't repeat.