[R-pkg-team] Bug#921938: lme4 breaks r-cran-lmertest autopkgtest
Dirk Eddelbuettel
edd at debian.org
Sun Feb 10 14:39:17 GMT 2019
On 10 February 2019 at 08:20, Dirk Eddelbuettel wrote:
|
| On 10 February 2019 at 13:35, Paul Gevers wrote:
| | Source: lme4, r-cran-lmertest
| | Control: found -1 lme4/1.1-20-1
| | Control: found -1 r-cran-lmertest/3.0-1-2
| | Severity: important
| | X-Debbugs-CC: debian-ci at lists.debian.org
| | User: debian-ci at lists.debian.org
| | Usertags: breaks needs-update
| |
| | Dear maintainers,
| |
| | With a recent upload of lme4 the autopkgtest of r-cran-lmertest fails in
| | testing when that autopkgtest is run with the binary packages of lme4
| | from unstable. It passes when run with only packages from testing. In
| | tabular form:
| | pass fail
| | lme4 from testing 1.1-20-1
| | r-cran-lmertest from testing 3.0-1-2
| | all others from testing from testing
| |
| | I copied some of the output at the bottom of this report.
| |
| | Currently this regression is blocking the migration of lme4 to testing
| | [1]. Due to the nature of this issue, I filed this bug report against
| | both packages. Can you please investigate the situation and reassign the
| | bug to the right package? If needed, please change the bug's severity.
|
| Sorry I don't really have the time for this. I maintain r-cran-lme4; it
| passes. The relevant page for me is
|
| https://cloud.r-project.org/web/checks/check_results_lme4.html
|
| which shows that lme4 builds and passes its checks where it matters (we can
| disregard Solaris and old-Windows here).
|
| The package has MANY reverse dependencies but I am responsible for
| those. Talk to _their_ maintainers. Thanks for your understandind.
A casual glance at this reveals that one of the two packages you mention
(r-cran-mlmrev) is not current as it was updated two days ago:
https://cloud.r-project.org/web/packages/mlmRev/index.html
The other fails ALL its tests at CRAN and needs an upstream fix:
https://cloud.r-project.org/web/checks/check_results_lmerTest.html
So as I suggested earlier: please reassign to the dependee packages.
Dirk
| Dirk
|
| | More information about this bug and the reason for filing it can be found on
| | https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
| |
| | Paul
| |
| | [1] https://qa.debian.org/excuses.php?package=lme4
| |
| | https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-cran-lmertest/1896879/log.gz
| |
| | autopkgtest [04:42:34]: test run-unit-test: [-----------------------
| | BEGIN TEST test_a_utils.R
| |
| | R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
| | Copyright (C) 2018 The R Foundation for Statistical Computing
| | Platform: x86_64-pc-linux-gnu (64-bit)
| |
| | R is free software and comes with ABSOLUTELY NO WARRANTY.
| | You are welcome to redistribute it under certain conditions.
| | Type 'license()' or 'licence()' for distribution details.
| |
| | R is a collaborative project with many contributors.
| | Type 'contributors()' for more information and
| | 'citation()' on how to cite R or R packages in publications.
| |
| | Type 'demo()' for some demos, 'help()' for on-line help, or
| | 'help.start()' for an HTML browser interface to help.
| | Type 'q()' to quit R.
| |
| | > # test_a_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 safeDeparse() - equivalence and differences to deparse():
| | > deparse_args <- formals(deparse)
| | > safeDeparse_args <- formals(lmerTest:::safeDeparse)
| | > stopifnot(
| | + all.equal(names(deparse_args), names(safeDeparse_args)),
| | + all.equal(deparse_args[!names(deparse_args) %in% c("control",
| | "width.cutoff")],
| | + safeDeparse_args[!names(safeDeparse_args) %in%
| | c("control", "width.cutoff")]),
| | + all.equal(deparse_args[["width.cutoff"]], 60L),
| | + all(eval(safeDeparse_args[["control"]]) %in%
| | eval(deparse_args[["control"]])),
| | + all.equal(safeDeparse_args[["width.cutoff"]], 500L)
| | + )
| | >
| | >
| | BEGIN TEST test_anova.R
| |
| | R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
| | Copyright (C) 2018 The R Foundation for Statistical Computing
| | Platform: x86_64-pc-linux-gnu (64-bit)
| |
| | R is free software and comes with ABSOLUTELY NO WARRANTY.
| | You are welcome to redistribute it under certain conditions.
| | Type 'license()' or 'licence()' for distribution details.
| |
| | R is a collaborative project with many contributors.
| | Type 'contributors()' for more information and
| | 'citation()' on how to cite R or R packages in publications.
| |
| | Type 'demo()' for some demos, 'help()' for on-line help, or
| | 'help.start()' for an HTML browser interface to help.
| | Type 'q()' to quit R.
| |
| | > # test_anova.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()
| | >
| | > # 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")
| | > TOL <- 1e-4
| | >
| | > ####################################
| | > ## Basic anova tests
| | > ####################################
| | >
| | > m <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
| | >
| | > ####### ddf argument:
| | > (an1 <- anova(m)) # Also testing print method.
| | Type III Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | Days 30024 30024 1 16.995 45.843 3.273e-06 ***
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an2 <- anova(m, ddf="Satterthwaite"))
| | Type III Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | Days 30024 30024 1 16.995 45.843 3.273e-06 ***
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an2b <- anova(m, ddf="Satterthwaite", type=3))
| | Type III Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | Days 30024 30024 1 16.995 45.843 3.273e-06 ***
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an2c <- anova(m, ddf="Satterthwaite", type=2))
| | Type II Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | Days 30024 30024 1 16.995 45.843 3.273e-06 ***
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > stopifnot(isTRUE(
| | + all.equal(an1, an2, tolerance=TOL)
| | + ))
| | > (an3 <- anova(m, ddf="Sat")) ## Abbreviated argument
| | Type III Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | Days 30024 30024 1 16.995 45.843 3.273e-06 ***
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > stopifnot(isTRUE(
| | + all.equal(an1, an3, tolerance=TOL)
| | + ))
| | > if(has_pbkrtest) {
| | + (anova(m, ddf="Kenward-Roger"))
| | + (anova(m, ddf="Kenward-Roger", type=3))
| | + }
| | Type III Analysis of Variance Table with Kenward-Roger's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | Days 30024 30024 1 17 45.843 3.268e-06 ***
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an1 <- anova(m, ddf="lme4"))
| | Analysis of Variance Table
| | Df Sum Sq Mean Sq F value
| | Days 1 30024 30024 45.843
| | > (an2 <- anova(m, ddf="lme4", type=3)) # 'type' is ignored with ddf="lme4"
| | Analysis of Variance Table
| | Df Sum Sq Mean Sq F value
| | Days 1 30024 30024 45.843
| | > stopifnot(isTRUE(
| | + all.equal(an1, an2, tolerance=TOL)
| | + ))
| | > res <- assertError(anova(m, ddf="KR")) ## Error on incorrect arg.
| | > stopifnot(
| | + grepl("'arg' should be one of ", unlist(res[[1]])$message)
| | + )
| | >
| | > ## lme4 method:
| | > an1 <- anova(m, ddf="lme4")
| | > an2 <- anova(as(m, "lmerMod"))
| | > stopifnot(isTRUE(
| | + all.equal(an1, an2, tolerance=TOL)
| | + ))
| | >
| | > ###### type argument:
| | > (an1 <- anova(m, type="1")) # valid type arg.
| | Type I Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | Days 30024 30024 1 16.995 45.843 3.273e-06 ***
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an2 <- anova(m, type="I")) # same
| | Type I Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | Days 30024 30024 1 16.995 45.843 3.273e-06 ***
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > stopifnot(isTRUE(
| | + all.equal(an1, an2, tolerance=TOL)
| | + ))
| | > (an3 <- anova(m, type=1)) # Not strictly valid, but accepted
| | Type I Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | Days 30024 30024 1 16.995 45.843 3.273e-06 ***
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > stopifnot(isTRUE(
| | + all.equal(an1, an3, tolerance=TOL)
| | + ))
| | >
| | > (an1 <- anova(m, type="2")) # valid type arg.
| | Type II Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | Days 30024 30024 1 16.995 45.843 3.273e-06 ***
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an2 <- anova(m, type="II")) # same
| | Type II Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | Days 30024 30024 1 16.995 45.843 3.273e-06 ***
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > stopifnot(isTRUE(
| | + all.equal(an1, an2, tolerance=TOL)
| | + ))
| | > (an3 <- anova(m, type=3)) # Not strictly valid, but accepted
| | Type III Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | Days 30024 30024 1 16.995 45.843 3.273e-06 ***
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > stopifnot(isTRUE(
| | + all.equal(an1, an3, check.attributes=FALSE, tolerance=TOL)
| | + ))
| | >
| | > (an1 <- anova(m, type="3")) # valid type arg.
| | Type III Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | Days 30024 30024 1 16.995 45.843 3.273e-06 ***
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an2 <- anova(m, type="III")) # same
| | Type III Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | Days 30024 30024 1 16.995 45.843 3.273e-06 ***
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > stopifnot(isTRUE(
| | + all.equal(an1, an2, tolerance=TOL)
| | + ))
| | > (an3 <- anova(m, type=3)) # Not strictly valid, but accepted
| | Type III Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | Days 30024 30024 1 16.995 45.843 3.273e-06 ***
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > stopifnot(isTRUE(
| | + all.equal(an1, an3, tolerance=TOL)
| | + ))
| | > assertError(anova(m, type=0)) # Not valid arg.
| | > assertError(anova(m, type="i")) # Not valid arg.
| | >
| | > ####### Model comparison:
| | > fm <- lm(Reaction ~ Days, sleepstudy)
| | > (an <- anova(m, fm))
| | refitting model(s) with ML (instead of REML)
| | Data: sleepstudy
| | Models:
| | fm: Reaction ~ Days
| | m: Reaction ~ Days + (Days | Subject)
| | Df AIC BIC logLik deviance Chisq Chi Df Pr(>Chisq)
| | fm 3 1906.3 1915.9 -950.15 1900.3
| | m 6 1763.9 1783.1 -875.97 1751.9 148.35 3 < 2.2e-16 ***
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > stopifnot(
| | + nrow(an) == 2L,
| | + rownames(an)[2] == "m"
| | + )
| | >
| | > m2 <- lmer(Reaction ~ Days + I(Days^2) + (Days | Subject), sleepstudy)
| | > (an <- anova(m, m2, refit=FALSE))
| | Data: sleepstudy
| | Models:
| | m: Reaction ~ Days + (Days | Subject)
| | m2: Reaction ~ Days + I(Days^2) + (Days | Subject)
| | Df AIC BIC logLik deviance Chisq Chi Df Pr(>Chisq)
| | m 6 1755.6 1774.8 -871.81 1743.6
| | m2 7 1756.8 1779.2 -871.41 1742.8 0.8127 1 0.3673
| | > stopifnot(
| | + nrow(an) == 2L,
| | + rownames(an)[1] == "m"
| | + )
| | >
| | >
| | > ####################################
| | > ## Example with factor fixef:
| | > ####################################
| | >
| | > ## 'temp' is continuous, 'temperature' an ordered factor with 6 levels
| | > data("cake", package="lme4")
| | > m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake)
| | > (an <- anova(m))
| | Type III Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | recipe 4.00 2.00 2 254.02 0.0957 0.9088
| | temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 ***
| | recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an_lme4 <- anova(m, ddf="lme4"))
| | Analysis of Variance Table
| | Df Sum Sq Mean Sq F value
| | recipe 2 10.39 5.20 0.2488
| | temp 1 1966.71 1966.71 94.1632
| | recipe:temp 2 1.74 0.87 0.0417
| | >
| | > if(has_pbkrtest) {
| | + (an_KR <- anova(m, ddf="Kenward-Roger"))
| | + # res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")],
| | + # an_lme4[, c("Sum Sq", "Mean Sq", "F value")])
| | + # stopifnot(isTRUE(res))
| | + res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")],
| | + an_KR[, c("Sum Sq", "Mean Sq", "F value")],
| | tolerance=TOL)
| | + stopifnot(isTRUE(res))
| | + }
| | > stopifnot(all.equal(c(2, 1, 2), an$NumDF, tol=1e-6),
| | + all.equal(c(254.0157612, 222, 222), an$DenDF, tol=TOL))
| | >
| | > an3 <- anova(m, type=3)
| | > an2 <- anova(m, type=2)
| | > an1 <- anova(m, type=1)
| | >
| | > ## Data is balanced, so Type II and III should be identical:
| | > ## One variable is continuous, so Type I and II/III are different:
| | > stopifnot(
| | + isTRUE(all.equal(an3, an2, check.attributes=FALSE, tolerance=TOL)),
| | + !isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=1e-8))
| | + )
| | >
| | > # Using an ordered factor:
| | > m <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake)
| | > (an1 <- anova(m, type=1))
| | Type I Analysis of Variance Table with Satterthwaite's method
| | 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 5 210 20.5199 <2e-16 ***
| | recipe:temperature 205.98 20.60 10 210 1.0062 0.4393
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an2 <- anova(m, type=2))
| | Type II Analysis of Variance Table with Satterthwaite's method
| | 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 5 210 20.5199 <2e-16 ***
| | recipe:temperature 205.98 20.60 10 210 1.0062 0.4393
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > # Type 3 is also available with ordered factors:
| | > (an3 <- anova(m, type=3))
| | Type III Analysis of Variance Table with Satterthwaite's method
| | 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 5 210 20.5199 <2e-16 ***
| | recipe:temperature 205.98 20.60 10 210 1.0062 0.4393
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > ## Balanced data and only factors: Type I, II and III should be the same:
| | > stopifnot(
| | + isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL)),
| | + isTRUE(all.equal(an1, an3, check.attributes=FALSE, tolerance=TOL))
| | + )
| | >
| | > (an <- anova(m, type=1))
| | Type I Analysis of Variance Table with Satterthwaite's method
| | 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 5 210 20.5199 <2e-16 ***
| | recipe:temperature 205.98 20.60 10 210 1.0062 0.4393
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an_lme4 <- anova(m, type=1, ddf="lme4"))
| | Analysis of Variance Table
| | Df Sum Sq Mean Sq F value
| | recipe 2 10.19 5.09 0.2488
| | temperature 5 2100.30 420.06 20.5199
| | recipe:temperature 10 205.98 20.60 1.0062
| | > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")],
| | + an_lme4[, c("Sum Sq", "Mean Sq", "F value")],
| | tolerance=TOL)
| | > stopifnot(isTRUE(res))
| | > if(has_pbkrtest) {
| | + (an_KR <- anova(m, type=1, ddf="Kenward-Roger"))
| | + res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")],
| | + an_KR[, c("Sum Sq", "Mean Sq", "F value")],
| | tolerance=TOL)
| | + stopifnot(isTRUE(res))
| | + }
| | > stopifnot(all.equal(c(2, 5, 10), an$NumDF, tolerance=TOL),
| | + all.equal(c(42, 210, 210), an$DenDF, tolerance=TOL))
| | >
| | > ########
| | > ## Make case with balanced unordered factors:
| | > cake2 <- cake
| | > cake2$temperature <- factor(cake2$temperature, ordered = FALSE)
| | > # str(cake2)
| | > stopifnot(
| | + !is.ordered(cake2$temperature)
| | + )
| | > m <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2)
| | > (an1 <- anova(m, type=1))
| | Type I Analysis of Variance Table with Satterthwaite's method
| | 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 5 210 20.5199 <2e-16 ***
| | recipe:temperature 205.98 20.60 10 210 1.0062 0.4393
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an2 <- anova(m, type=2))
| | Type II Analysis of Variance Table with Satterthwaite's method
| | 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 5 210 20.5199 <2e-16 ***
| | recipe:temperature 205.98 20.60 10 210 1.0062 0.4393
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an3 <- anova(m, type=3))
| | Type III Analysis of Variance Table with Satterthwaite's method
| | 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 5 210 20.5199 <2e-16 ***
| | recipe:temperature 205.98 20.60 10 210 1.0062 0.4393
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > ## Balanced data and only factors: Type I, II, and III should be the same:
| | > stopifnot(
| | + isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL)),
| | + isTRUE(all.equal(an3, an2, check.attributes=FALSE, tolerance=TOL))
| | + )
| | > ########
| | >
| | > # No intercept:
| | > m <- lmer(angle ~ 0 + recipe * temp + (1|recipe:replicate), cake)
| | > (an <- anova(m, type=1))
| | Type I Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | recipe 21442.9 7147.6 3 42 342.2200 <2e-16 ***
| | temp 1966.7 1966.7 1 222 94.1632 <2e-16 ***
| | recipe:temp 1.7 0.9 2 222 0.0417 0.9592
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an2 <- anova(m, type=2))
| | Type II Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | recipe 4.48 1.49 3 254.02 0.0714 0.9752
| | temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 ***
| | recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an2 <- anova(m, type=3))
| | Type III Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | recipe 4.48 1.49 3 254.02 0.0714 0.9752
| | temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 ***
| | recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > if(has_pbkrtest)
| | + (an_KR <- anova(m, ddf="Kenward-Roger"))
| | Type III Analysis of Variance Table with Kenward-Roger's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | recipe 4.48 1.49 3 254.02 0.0714 0.9752
| | temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 ***
| | recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an_lme4 <- anova(m, ddf="lme4"))
| | Analysis of Variance Table
| | Df Sum Sq Mean Sq F value
| | recipe 3 21442.9 7147.6 342.2200
| | temp 1 1966.7 1966.7 94.1632
| | recipe:temp 2 1.7 0.9 0.0417
| | > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")],
| | + an_lme4[, c("Sum Sq", "Mean Sq", "F value")],
| | tolerance=TOL)
| | > stopifnot(isTRUE(res))
| | >
| | > # ML-fit:
| | > m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake, REML=FALSE)
| | > (an <- anova(m, type=1))
| | Type I Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | recipe 10.99 5.49 2 45 0.2666 0.7672
| | temp 1966.71 1966.71 1 225 95.4357 <2e-16 ***
| | recipe:temp 1.74 0.87 2 225 0.0423 0.9586
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > if(has_pbkrtest)
| | + assertError(an <- anova(m, ddf="Kenward-Roger")) # KR fits should be
| | REML
| | > (an_lme4 <- anova(m, ddf="lme4"))
| | Analysis of Variance Table
| | Df Sum Sq Mean Sq F value
| | recipe 2 10.99 5.49 0.2666
| | temp 1 1966.71 1966.71 95.4357
| | recipe:temp 2 1.74 0.87 0.0423
| | > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")],
| | + an_lme4[, c("Sum Sq", "Mean Sq", "F value")],
| | tolerance=TOL)
| | > stopifnot(isTRUE(res))
| | >
| | > ####################################
| | > ## Using contr.sum:
| | > ####################################
| | >
| | > m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake,
| | + contrasts = list('recipe' = "contr.sum"))
| | > (an <- anova(m, type=1))
| | Type I Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | recipe 10.39 5.20 2 42 0.2488 0.7809
| | temp 1966.71 1966.71 1 222 94.1632 <2e-16 ***
| | recipe:temp 1.74 0.87 2 222 0.0417 0.9592
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an2 <- anova(m, type=2))
| | Type II Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | recipe 4.00 2.00 2 254.02 0.0957 0.9088
| | temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 ***
| | recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an3 <- anova(m, type=3))
| | Type III Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | recipe 4.00 2.00 2 254.02 0.0957 0.9088
| | temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 ***
| | recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > stopifnot(
| | + isTRUE(all.equal(an2, an3, check.attributes=FALSE, tolerance=TOL))
| | + )
| | > if(has_pbkrtest)
| | + (an_KR <- anova(m, type=1, ddf="Kenward-Roger"))
| | Type I Analysis of Variance Table with Kenward-Roger's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | recipe 10.39 5.20 2 42 0.2488 0.7809
| | temp 1966.71 1966.71 1 222 94.1632 <2e-16 ***
| | recipe:temp 1.74 0.87 2 222 0.0417 0.9592
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an_lme4 <- anova(m, ddf="lme4"))
| | Analysis of Variance Table
| | Df Sum Sq Mean Sq F value
| | recipe 2 10.39 5.20 0.2488
| | temp 1 1966.71 1966.71 94.1632
| | recipe:temp 2 1.74 0.87 0.0417
| | > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")],
| | + an_lme4[, c("Sum Sq", "Mean Sq", "F value")],
| | tolerance=TOL)
| | > stopifnot(isTRUE(res))
| | >
| | >
| | > ####################################
| | > ## Example with continuous fixef:
| | > ####################################
| | >
| | > # Example with no fixef:
| | > m <- lmer(Reaction ~ -1 + (Days | Subject), sleepstudy)
| | > # m <- lmer(Reaction ~ 0 + (Days | Subject), sleepstudy) # alternative
| | > stopifnot(length(fixef(m)) == 0L)
| | > (an <- anova(m, type=1))
| | Type I Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | > (an_2 <- anova(m, type=2))
| | Type II Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | > (an_3 <- anova(m, type=3))
| | Type III Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | > stopifnot(nrow(an) == 0L,
| | + nrow(an_2) == 0L,
| | + nrow(an_3) == 0L)
| | > # anova(m, ddf="lme4") # Bug in lme4 it seems
| | > if(has_pbkrtest) {
| | + (an_KR <- anova(m, ddf="Kenward-Roger"))
| | + stopifnot(
| | + nrow(an_KR) == 0L
| | + )
| | + }
| | >
| | > # Example with intercept only:
| | > m <- lmer(Reaction ~ (Days | Subject), sleepstudy)
| | > # m <- lmer(Reaction ~ 1 + (Days | Subject), sleepstudy) # alternative
| | > stopifnot(length(fixef(m)) == 1L,
| | + names(fixef(m)) == "(Intercept)")
| | > (an <- anova(m))
| | Type III Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | > (an_2 <- anova(m, type=2))
| | Type II Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | > (an_3 <- anova(m, type=3))
| | Type III Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | > (an_lme4 <- anova(m, ddf="lme4"))
| | Analysis of Variance Table
| | Df Sum Sq Mean Sq F value
| | > stopifnot(nrow(an) == 0L,
| | + nrow(an_2) == 0L,
| | + nrow(an_3) == 0L,
| | + nrow(an_lme4) == 0L)
| | > if(has_pbkrtest) {
| | + (an_KR <- anova(m, ddf="Kenward-Roger"))
| | + stopifnot(
| | + nrow(an_KR) == 0L
| | + )
| | + }
| | >
| | > # Example with 1 fixef without intercept:
| | > m <- lmer(Reaction ~ Days - 1 + (Days | Subject), sleepstudy)
| | Warning message:
| | In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
| | Model failed to converge with max|grad| = 0.00416642 (tol = 0.002,
| | component 1)
| | > # m <- lmer(Reaction ~ 0 + Days + (Days | Subject), sleepstudy) #
| | alternative
| | > stopifnot(length(fixef(m)) == 1L,
| | + names(fixef(m)) == "Days")
| | > (an <- anova(m))
| | Type III Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | Days 93779 93779 1 16.995 143.19 1.054e-09 ***
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an_2 <- anova(m, type=2))
| | Type II Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | Days 93779 93779 1 16.995 143.19 1.054e-09 ***
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an_3 <- anova(m, type=3))
| | Type III Analysis of Variance Table with Satterthwaite's method
| | Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
| | Days 93779 93779 1 16.995 143.19 1.054e-09 ***
| | ---
| | Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
| | > (an_lme4 <- anova(m, ddf="lme4"))
| | Analysis of Variance Table
| | Df Sum Sq Mean Sq F value
| | Days 1 93779 93779 143.19
| | > stopifnot(nrow(an) == 1L,
| | + nrow(an_2) == 1L,
| | + nrow(an_3) == 1L,
| | + nrow(an_lme4) == 1L)
| | > if(has_pbkrtest) {
| | + (an_KR <- anova(m, ddf="Kenward-Roger"))
| | + stopifnot(
| | + nrow(an_KR) == 1L
| | + )
| | + }
| | >
| | > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")],
| | + an_lme4[, c("Sum Sq", "Mean Sq", "F value")],
| | tolerance=TOL)
| | > stopifnot(isTRUE(res))
| | > stopifnot(isTRUE(all.equal(
| | + c(1, 17), unname(unlist(an[, c("NumDF", "DenDF")])), tolerance=TOL
| | + )))
| | Error: isTRUE(all.equal(c(1, 17), unname(unlist(an[, c("NumDF",
| | "DenDF")])), .... is not TRUE
| | Execution halted
| | autopkgtest [04:42:39]: test run-unit-test: -----------------------]
| |
| | x[DELETED ATTACHMENT signature.asc, application/pgp-signature]
|
| --
| http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
--
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
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