R Under development (unstable) (2026-01-12 r89300 ucrt) -- "Unsuffered Consequences"
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> # test_drop1.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

> 
> # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible."
> # even in tests:
> assertError <- function(expr, ...)
+   if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible()
> assertWarning <- function(expr, ...)
+   if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible()
> 
> TOL <- 1e-4
> # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3
> # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest)
> has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3"
> 
> data("sleepstudy", package="lme4")
> 
> ######### Basic usage
> 
> data("cake", package="lme4")
> cake2 <- cake
> cake2$temperature <- factor(cake2$temperature, ordered = FALSE)
> fm <- lmer(angle ~ recipe + temperature + (1|recipe:replicate), cake2)
> (an1 <- drop1(fm))
Single term deletions using Satterthwaite's method:

Model:
angle ~ recipe + temperature + (1 | recipe:replicate)
             Sum Sq Mean Sq NumDF DenDF F value Pr(>F)    
recipe        10.19    5.09     2    42  0.2488 0.7809    
temperature 2100.30  420.06     5   220 20.5141 <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> (an2 <- drop1(fm, force_get_contrasts = TRUE))
Single term deletions using Satterthwaite's method:

Model:
angle ~ recipe + temperature + (1 | recipe:replicate)
             Sum Sq Mean Sq NumDF DenDF F value Pr(>F)    
recipe        10.19    5.09     2    42  0.2488 0.7809    
temperature 2100.30  420.06     5   220 20.5141 <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> drop1(fm, ddf="lme4", test="Chi")
Single term deletions

Model:
angle ~ recipe + temperature + (1 | recipe:replicate)
            npar    AIC    LRT Pr(Chi)    
<none>           1709.6                   
recipe         2 1706.1  0.530  0.7672    
temperature    5 1785.7 86.106  <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> if(has_pbkrtest)
+   drop1(fm, ddf="Kenward-Roger")
Single term deletions using Kenward-Roger's method:

Model:
angle ~ recipe + temperature + (1 | recipe:replicate)
             Sum Sq Mean Sq NumDF DenDF F value Pr(>F)    
recipe        10.19    5.09     2    42  0.2488 0.7809    
temperature 2100.30  420.06     5   220 20.5141 <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> 
> tests1 <- show_tests(an1)
> tests2 <- show_tests(an2)
> 
> stopifnot(
+   # Tests are the same:
+   isTRUE(all.equal(an1, an2, check.attributes = FALSE, tolerance=TOL)),
+   # But contrast matrices are not:
+   all(!mapply(function(x, y) isTRUE(all.equal(x, y)), tests1, tests2))
+ )
> 
> fm <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2)
> drop1(fm)
Single term deletions using Satterthwaite's method:

Model:
angle ~ recipe * temperature + (1 | recipe:replicate)
                   Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
recipe:temperature 205.98  20.598    10   210  1.0062 0.4393
> drop1(fm, ddf="lme4")
Single term deletions

Model:
angle ~ recipe * temperature + (1 | recipe:replicate)
                   npar    AIC
<none>                  1719.0
recipe:temperature   10 1709.6
> if(has_pbkrtest)
+   drop1(fm, ddf="Kenward-Roger")
Single term deletions using Kenward-Roger's method:

Model:
angle ~ recipe * temperature + (1 | recipe:replicate)
                   Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
recipe:temperature 205.98  20.598    10   210  1.0062 0.4393
> 
> # Incorrect arguments:
> assertError(drop1(fm, scope="recipe")) # Correct Error
> assertError(drop1(fm, scope=3)) # Correct Error
> assertError(drop1(fm, scope=list("recipe"))) # Correct Error
> 
> # Polynomial terms:
> 
> fm <- lmer(Reaction ~ 0 + (Days|Subject), sleepstudy)
> (an0 <- drop1(fm)) # No fixef!
Single term deletions using Satterthwaite's method:

Model:
Reaction ~ 0 + (Days | Subject)
     Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
> fm <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
> (an1 <- drop1(fm))
Single term deletions using Satterthwaite's method:

Model:
Reaction ~ Days + (Days | Subject)
     Sum Sq Mean Sq NumDF DenDF F value    Pr(>F)    
Days  30031   30031     1    17  45.853 3.264e-06 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> fm <- lmer(Reaction ~ Days + I(Days^2) + (Days|Subject), sleepstudy)
> (an2 <- (drop1(fm)))
Single term deletions using Satterthwaite's method:

Model:
Reaction ~ Days + I(Days^2) + (Days | Subject)
          Sum Sq Mean Sq NumDF  DenDF F value  Pr(>F)   
Days      4534.5  4534.5     1 114.43  6.9551 0.00952 **
I(Days^2) 1079.5  1079.5     1 143.00  1.6558 0.20026   
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> fm <- lmer(Reaction ~ poly(Days, 2) + (Days|Subject), sleepstudy)
> (an3 <- drop1(fm))
Single term deletions using Satterthwaite's method:

Model:
Reaction ~ poly(Days, 2) + (Days | Subject)
              Sum Sq Mean Sq NumDF  DenDF F value    Pr(>F)    
poly(Days, 2)  30974   15487     2 29.115  23.754 7.625e-07 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> stopifnot(
+   nrow(an0) == 0L,
+   nrow(an1) == 1L,
+   nrow(an2) == 2L,
+   nrow(an3) == 1L
+ )
> 
> # Consider a rank-deficient design matrix:
> fm <- lmer(angle ~ recipe + temp + temperature + (1|recipe:replicate), cake)
fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
> # Here temp accounts for the linear effect of temperature, and
> # temperature is an (ordered) factor that accounts for the remaining
> # variation between temperatures (4 df).
> (an4 <- drop1(fm))
Single term deletions using Satterthwaite's method:

Model:
angle ~ recipe + temp + temperature + (1 | recipe:replicate)
             Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
recipe       10.189   5.094     2    42  0.2488 0.7809
temp                                                  
temperature 133.595  33.399     4   220  1.6311 0.1674
> # While temperature is in the model, we cannot test the effect of dropping
> # temp. After removing temperature we can test the effect of dropping temp:
> (an5 <- drop1(update(fm, ~.-temperature)))
Single term deletions using Satterthwaite's method:

Model:
angle ~ recipe + temp + (1 | recipe:replicate)
       Sum Sq Mean Sq NumDF DenDF F value Pr(>F)    
recipe   10.3    5.15     2    42  0.2488 0.7809    
temp   1966.7 1966.71     1   224 94.9759 <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> 
> stopifnot(
+   nrow(an4) == 3,
+   rownames(an4)[2] == "temp",
+   all(is.na(an4[2, ])),
+   all(!is.na(an4[-2, ])),
+   all(rownames(an5) == c("recipe", "temp"))
+ )
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
   3.07    0.37    3.45