R Under development (unstable) (2024-08-31 r87082 ucrt) -- "Unsuffered Consequences"
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> library(testthat)
> library(afex)
Loading required package: lme4
Loading required package: Matrix
************
Welcome to afex. For support visit: http://afex.singmann.science/
- Functions for ANOVAs: aov_car(), aov_ez(), and aov_4()
- Methods for calculating p-values with mixed(): 'S', 'KR', 'LRT', and 'PB'
- 'afex_aov' and 'mixed' objects can be passed to emmeans() for follow-up tests
- Get and set global package options with: afex_options()
- Set sum-to-zero contrasts globally: set_sum_contrasts()
- For example analyses see: browseVignettes("afex")
************
Attaching package: 'afex'
The following object is masked from 'package:lme4':
lmer
>
> test_check("afex")
Mixed Model Anova Table (Type 3 tests, S-method)
Model: value ~ treatment + (1 | id)
Data: obk.long
Effect df F p.value
1 treatment 2, 13.00 2.91 + .090
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1
Mixed Model Anova Table (Type 3 tests, S-method)
Model: value ~ treatment + phase + (1 | id)
Data: obk.long
Effect df F p.value
1 treatment 2, 13.00 2.91 + .090
2 phase 2, 222.00 38.48 *** <.001
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1
Mixed Model Anova Table (Type 3 tests, LRT-method)
Model: value ~ treatment + (1 | id)
Data: obk.long
Df full model: 5
Effect df Chisq p.value
1 treatment 2 5.93 + .052
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1
Mixed Model Anova Table (Type 3 tests, LRT-method)
Model: value ~ treatment + phase + (1 | id)
Data: obk.long
Df full model: 7
Effect df Chisq p.value
1 treatment 2 5.93 + .052
2 phase 2 66.67 *** <.001
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1
Mixed Model Anova Table (Type 3 tests, PB-method)
Model: use ~ urban + (1 | district)
Data: Contraception
Effect df Chisq p.value
1 urban 1 31.28 .333
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1
Mixed Model Anova Table (Type 3 tests, PB-method)
Model: use ~ urban + livch + (1 | district)
Data: Contraception
Effect df Chisq p.value
1 urban 1 36.33 .333
2 livch 3 77.91 .333
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1
[ FAIL 0 | WARN 1 | SKIP 29 | PASS 341 ]
══ Skipped tests (29) ══════════════════════════════════════════════════════════
• On CRAN (28): 'test-afex_plot-basics.R:11:3', 'test-afex_plot-basics.R:76:3',
'test-afex_plot-basics.R:111:3', 'test-afex_plot-basics.R:140:3',
'test-afex_plot-basics.R:346:3', 'test-afex_plot-basics.R:360:3',
'test-afex_plot-bugs.R:6:3', 'test-afex_plot-bugs.R:21:3',
'test-afex_plot-bugs.R:43:3', 'test-afex_plot-bugs.R:79:3',
'test-afex_plot-default-support.R:11:3',
'test-afex_plot-default-support.R:20:3',
'test-afex_plot-default-support.R:38:3',
'test-afex_plot-default-support.R:66:3', 'test-afex_plot-vignette.R:4:3',
'test-afex_plot-vignette.R:38:3', 'test-afex_plot-vignette.R:114:3',
'test-aov_car-bugs.R:253:3', 'test-emmeans-interface.R:144:3',
'test-emmeans-interface.R:209:3', 'test-mixed-bugs.R:6:3',
'test-mixed-bugs.R:19:3', 'test-mixed-structure.R:214:5',
'test-mixed-structure.R:242:3', 'test-mixed-structure.R:264:3',
'test-mixed-structure.R:305:3', 'test-mixed-structure.R:349:3',
'test-mixed-structure.R:369:3'
• empty test (1): 'test-mixed-structure.R:86:1'
[ FAIL 0 | WARN 1 | SKIP 29 | PASS 341 ]
Deleting unused snapshots:
• afex_plot-basics/afex-plot-connecting-individual-points-works.svg
• afex_plot-basics/geoms-work-box-plot.svg
• afex_plot-basics/geoms-work-boxjitter-1.svg
• afex_plot-basics/geoms-work-boxjitter-2.svg
• afex_plot-basics/geoms-work-boxjitter-3.svg
• afex_plot-basics/geoms-work-geom-count.svg
• afex_plot-basics/geoms-work-ggbeeswarm-geom-beeswarm.svg
• afex_plot-basics/geoms-work-ggbeeswarm-geom-quasirandom.svg
• afex_plot-basics/geoms-work-jitterdodge.svg
• afex_plot-basics/geoms-work-violin-with-colour.svg
• afex_plot-basics/geoms-work-violin.svg
• afex_plot-basics/lme4-mermod-plot-2.svg
• afex_plot-basics/lme4-mermod-plot-3.svg
• afex_plot-basics/mixed-model-1.svg
• afex_plot-basics/mixed-model-2.svg
• afex_plot-basics/mixed-model-3.svg
• afex_plot-basics/mixed-model-4.svg
• afex_plot-basics/multiple-geoms-work-1.svg
• afex_plot-basics/multiple-geoms-work-2.svg
• afex_plot-basics/one-way-within.svg
• afex_plot-basics/plot-first-for-afex-plot-works-1.svg
• afex_plot-basics/plot-first-for-afex-plot-works-2.svg
• afex_plot-basics/plot-first-for-afex-plot-works-3.svg
• afex_plot-basics/plot-first-for-afex-plot-works-4.svg
• afex_plot-basics/two-way.svg
• afex_plot-basics/x-trace-panel.svg
• afex_plot-bugs/afex-plot-binomial-glm-with-factor-2.svg
• afex_plot-bugs/afex-plot-dv-y-works.svg
• afex_plot-bugs/afex-plot-lmm-type-2.svg
• afex_plot-bugs/afex-plot-mermod-objects-with-missing-data.svg
• afex_plot-default-support/afex-plots-binomial-glm-1.svg
• afex_plot-default-support/afex-plots-binomial-glm-2.svg
• afex_plot-default-support/afex-plots-lm-model-2.svg
• afex_plot-default-support/afex-plots-nlme-2.svg
• afex_plot-default-support/afex-plots-nlme-3.svg
• afex_plot-default-support/afex-plots-nlme-4.svg
• afex_plot-default-support/afex-plots-nlme-5.svg
• afex_plot-default-support/afex-plots-poisson-glm-1.svg
• afex_plot-default-support/afex-plots-poisson-glm-2.svg
• afex_plot-vignette/afex-plot-glmmtmb-1.svg
• afex_plot-vignette/afex-plot-glmmtmb-2.svg
• afex_plot-vignette/afex-plot-glmmtmb-3.svg
>
> proc.time()
user system elapsed
53.14 1.31 54.40