R Under development (unstable) (2026-01-12 r89300 ucrt) -- "Unsuffered Consequences"
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> # test_contrast_utils.R
> 
> library(lmerTest)
Loading required package: lme4
Loading required package: Matrix

Attaching package: 'lmerTest'

The following object is masked from 'package:lme4':

    lmer

The following object is masked from 'package:stats':

    step

> 
> ##########
> # Test that a message is printed if some cells have zero data:
> # Missing a single cell:
> data("cake", package="lme4")
> cake4 <- cake
> cake4$temperature <- factor(cake4$temperature, ordered=FALSE)
> cake4 <- droplevels(subset(cake4, !(recipe == "A" & temperature == "175") ))
> with(cake4, table(recipe, temperature))
      temperature
recipe 175 185 195 205 215 225
     A   0  15  15  15  15  15
     B  15  15  15  15  15  15
     C  15  15  15  15  15  15
> 
> fm1 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4)
fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
> an <- anova(fm1)
Missing cells for: recipeA:temperature175.  
Interpret type III hypotheses with care.
> txt <- capture.output(an <- anova(fm1), type = "message")
> stopifnot(length(grep("Missing cells for:", txt)) > 0,
+           length(grep("Interpret type III hypotheses with care.", txt)) > 0)
> 
> ##########
> # Test that a message is printed if some cells have zero data:
> # Missing diagonal:
> cake4 <- cake
> cake4$temperature <- factor(cake4$temperature, ordered=FALSE)
> cake4 <- droplevels(subset(cake4, temperature %in% levels(cake4$temperature)[1:3]))
> cake4 <- droplevels(subset(cake4, !((recipe == "A" & temperature == "175") |
+                                       (recipe == "B" & temperature == "185") |
+                                       (recipe == "C" & temperature == "195") )))
> cake4$temp0 <- cake4$temp - mean(cake4$temp)
> with(cake4, table(recipe, temperature))
      temperature
recipe 175 185 195
     A   0  15  15
     B  15   0  15
     C  15  15   0
> 
> fm1 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4)
fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients
> an <- anova(fm1)
Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195.  
Interpret type III hypotheses with care.
> txt <- capture.output(an <- anova(fm1), type = "message")
> stopifnot(length(grep("Missing cells for:", txt)) > 0,
+           length(grep("Interpret type III hypotheses with care.", txt)) > 0)
> 
> ##########
> # Test that a message is NOT printed with centered covariates:
> fm1 <- lmer(angle ~ recipe * temp0 + (1|recipe:replicate), cake4)
> an <- anova(fm1)
> txt <- capture.output(an <- anova(fm1), type = "message")
> stopifnot(length(grep("Missing cells for:", txt)) == 0,
+           length(grep("Interpret type III hypotheses with care.", txt)) == 0)
> # Note: in many cases a message would not be printed anyway because the
> # columns sums in the rdX design matrix would not be exactly zero but just a
> # small number very close to zero.
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
   2.15    0.17    2.31