Last updated on 2024-11-03 15:48:43 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2023.12-4.1 | 18.47 | 208.22 | 226.69 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2023.12-4.1 | 0.33 | 1.63 | 1.96 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2023.12-4.1 | 370.85 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2023.12-4.1 | 353.79 | OK | |||
| r-devel-windows-x86_64 | 2023.12-4.1 | 21.00 | 250.00 | 271.00 | OK | |
| r-patched-linux-x86_64 | 2023.12-4.1 | 15.36 | 196.71 | 212.07 | OK | |
| r-release-linux-x86_64 | 2023.12-4.1 | 16.61 | 194.82 | 211.43 | ERROR | |
| r-release-macos-arm64 | 2023.12-4.1 | 116.00 | OK | |||
| r-release-macos-x86_64 | 2023.12-4.1 | 388.00 | OK | |||
| r-release-windows-x86_64 | 2023.12-4.1 | 19.00 | 259.00 | 278.00 | OK | |
| r-oldrel-macos-arm64 | 2023.12-4.1 | 143.00 | OK | |||
| r-oldrel-macos-x86_64 | 2023.12-4.1 | 233.00 | OK | |||
| r-oldrel-windows-x86_64 | 2023.12-4.1 | 25.00 | 292.00 | 317.00 | OK |
Version: 2023.12-4.1
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2023.12-4.1
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘lme4’
Flavor: r-release-linux-x86_64
Version: 2023.12-4.1
Check: tests
Result: ERROR
Running ‘anova.R’ [2s/2s]
Running ‘clm.fit.R’ [2s/3s]
Running ‘clm.formula.R’ [2s/3s]
Running ‘clmm.R’ [5s/7s]
Running ‘clmm.control.R’ [2s/2s]
Running ‘clmm.formula.R’ [3s/3s]
Running ‘clmm.methods.R’ [2s/2s]
Running ‘confint.R’ [3s/4s]
Running ‘nominal.test.R’ [4s/6s]
Running ‘ranef.loading.R’ [0s/1s]
Running ‘test-all.R’ [12s/16s]
Running ‘test.clm.Theta.R’ [3s/3s]
Running ‘test.clm.convergence.R’ [2s/3s]
Running ‘test.clm.flex.link.R’ [6s/7s]
Running ‘test.clm.model.matrix.R’ [2s/3s]
Running ‘test.clm.predict.R’ [2s/2s]
Running ‘test.clm.profile.R’ [2s/3s]
Running ‘test.clm.single.anova.R’ [2s/3s]
Running ‘test.general.R’ [0s/0s]
Running ‘test.makeThresholds.R’ [2s/2s]
Running ‘test.sign.R’ [2s/3s]
Running ‘test0weights.R’ [3s/4s]
Running ‘testAnova.clm2.R’ [2s/3s]
Running ‘testCLM.R’ [3s/4s]
Running the tests in ‘tests/clmm.methods.R’ failed.
Complete output:
> library(ordinal)
> data(wine)
>
> #################################
> ## model.matrix method for clmm-objects:
> fmm1 <- clmm(rating ~ contact + temp + (1|judge), data=wine)
> mm <- model.matrix(fmm1)
> stopifnot(inherits(mm, "matrix"),
+ dim(mm) == c(72, 3))
>
> #################################
> ## anova.clmm works even if formula does not have an environment:
> fmm1 <- clmm(rating ~ temp * contact + (1|judge), data = wine)
> fmm2 <- clmm(rating ~ temp + contact + (1|judge), data = wine)
> environment(fmm1$formula) <- NULL
> environment(fmm2$formula) <- NULL
> anova(fmm1, fmm2)
Likelihood ratio tests of cumulative link models:
formula: link: threshold:
fmm2 rating ~ temp + contact + (1 | judge) logit flexible
fmm1 rating ~ temp * contact + (1 | judge) logit flexible
no.par AIC logLik LR.stat df Pr(>Chisq)
fmm2 7 177.13 -81.565
fmm1 8 179.07 -81.536 0.0589 1 0.8082
>
>
> #################################
> ## Test that ranef, condVar and VarCorr work as they are supposed to whether or
> ## not nlme and lme4 are loaded:
>
> fm <- clmm(rating ~ temp + contact + (1|judge), data = wine)
> fm
Cumulative Link Mixed Model fitted with the Laplace approximation
formula: rating ~ temp + contact + (1 | judge)
data: wine
link threshold nobs logLik AIC niter max.grad
logit flexible 72 -81.57 177.13 332(999) 1.03e-05
Random effects:
Groups Name Variance Std.Dev.
judge (Intercept) 1.279 1.131
Number of groups: judge 9
Coefficients:
tempwarm contactyes
3.063 1.835
Thresholds:
1|2 2|3 3|4 4|5
-1.624 1.513 4.229 6.089
> ranef(fm)
$judge
(Intercept)
1 1.69617818
2 -0.56578308
3 0.96880828
4 -0.05954989
5 0.23051011
6 0.47703864
7 -1.91097339
8 -0.27294385
9 -0.55467576
> VarCorr(fm)
$judge
(Intercept)
(Intercept) 1.279461
attr(,"stddev")
(Intercept)
1.131133
> condVar(fm)
$judge
(Intercept)
1 0.3067453
2 0.3779358
3 0.3545529
4 0.3651870
5 0.3566066
6 0.3485475
7 0.3435693
8 0.3050453
9 0.3183194
> summary(fm)
Cumulative Link Mixed Model fitted with the Laplace approximation
formula: rating ~ temp + contact + (1 | judge)
data: wine
link threshold nobs logLik AIC niter max.grad cond.H
logit flexible 72 -81.57 177.13 332(999) 1.03e-05 2.8e+01
Random effects:
Groups Name Variance Std.Dev.
judge (Intercept) 1.279 1.131
Number of groups: judge 9
Coefficients:
Estimate Std. Error z value Pr(>|z|)
tempwarm 3.0630 0.5954 5.145 2.68e-07 ***
contactyes 1.8349 0.5125 3.580 0.000344 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Threshold coefficients:
Estimate Std. Error z value
1|2 -1.6237 0.6824 -2.379
2|3 1.5134 0.6038 2.507
3|4 4.2285 0.8090 5.227
4|5 6.0888 0.9725 6.261
>
> library(nlme)
> ranef(fm)
$judge
(Intercept)
1 1.69617818
2 -0.56578308
3 0.96880828
4 -0.05954989
5 0.23051011
6 0.47703864
7 -1.91097339
8 -0.27294385
9 -0.55467576
> VarCorr(fm)
$judge
(Intercept)
(Intercept) 1.279461
attr(,"stddev")
(Intercept)
1.131133
> condVar(fm)
$judge
(Intercept)
1 0.3067453
2 0.3779358
3 0.3545529
4 0.3651870
5 0.3566066
6 0.3485475
7 0.3435693
8 0.3050453
9 0.3183194
> library(lme4)
Error in library(lme4) : there is no package called 'lme4'
Execution halted
Running the tests in ‘tests/ranef.loading.R’ failed.
Complete output:
> # check that ranef and VarCorr work even after loading ordinal:
> library(lme4)
Error in library(lme4) : there is no package called 'lme4'
Execution halted
Flavor: r-release-linux-x86_64
Version: 2023.12-4.1
Check: HTML version of manual
Result: NOTE
Skipping checking math rendering: package 'V8' unavailable
Flavor: r-release-linux-x86_64