Last updated on 2025-12-06 00:48:37 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.6 | 5.53 | 44.09 | 49.62 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.2.6 | 4.43 | 29.43 | 33.86 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.6 | 14.00 | 61.75 | 75.75 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.2.6 | 11.00 | 61.06 | 72.06 | OK | |
| r-devel-windows-x86_64 | 0.2.6 | 10.00 | 66.00 | 76.00 | OK | |
| r-patched-linux-x86_64 | 0.2.6 | 6.63 | 38.52 | 45.15 | OK | |
| r-release-linux-x86_64 | 0.2.6 | 4.91 | 40.62 | 45.53 | OK | |
| r-release-macos-arm64 | 0.2.6 | OK | ||||
| r-release-macos-x86_64 | 0.2.6 | 8.00 | 39.00 | 47.00 | OK | |
| r-release-windows-x86_64 | 0.2.6 | 11.00 | 64.00 | 75.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.6 | OK | ||||
| r-oldrel-macos-x86_64 | 0.2.6 | 6.00 | 34.00 | 40.00 | OK | |
| r-oldrel-windows-x86_64 | 0.2.6 | 12.00 | 79.00 | 91.00 | OK |
Version: 0.2.6
Check: examples
Result: ERROR
Running examples in ‘DanielBiostatistics10th-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Chapter08
> ### Title: Chapter 8: Analysis of Variance
> ### Aliases: Chapter08
>
> ### ** Examples
>
> library(DanielBiostatistics10th)
>
> # Example 8.2.1; Page 318 (10th ed), Page 280 (11th ed)
> head(EXA_C08_S02_01)
selenium type
1 26.72 VEN
2 28.58 VEN
3 29.71 VEN
4 26.95 VEN
5 10.97 VEN
6 21.97 VEN
> boxplot(selenium ~ type, data = EXA_C08_S02_01, main = 'Figure 8.2.7')
> (aov_d821 = aov(selenium ~ type, data = EXA_C08_S02_01))
Call:
aov(formula = selenium ~ type, data = EXA_C08_S02_01)
Terms:
type Residuals
Sum of Squares 21261.83 36747.23
Deg. of Freedom 3 140
Residual standard error: 16.20124
Estimated effects may be unbalanced
> # ?stats::aov # analysis-of-variance model
> anova(aov_d821)
Analysis of Variance Table
Response: selenium
Df Sum Sq Mean Sq F value Pr(>F)
type 3 21262 7087.3 27.001 7.684e-14 ***
Residuals 140 36747 262.5
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> # ?stats::anova # ANOVA table
>
> # Example 8.2.2; Page 325 (10th ed), Page 286 (11th ed)
> (tukey_d822 <- TukeyHSD(aov_d821, conf.level = 0.95)) # Figure 8.2.8
Tukey multiple comparisons of means
95% family-wise confidence level
Fit: aov(formula = selenium ~ type, data = EXA_C08_S02_01)
$type
diff lwr upr p adj
RRB-NRB -32.963297 -44.227468 -21.699125 0.0000000
SQU-NRB -18.800649 -31.151826 -6.449472 0.0006857
VEN-NRB -36.170840 -47.817763 -24.523916 0.0000000
SQU-RRB 14.162648 4.537925 23.787371 0.0011105
VEN-RRB -3.207543 -11.910101 5.495016 0.7732308
VEN-SQU -17.370190 -27.440173 -7.300208 0.0000881
> plot(tukey_d822)
>
> # Example 8.3.1; Page 339 (10th ed), Page 298 (11th ed)
> head(EXA_C08_S03_01)
time method ageGroup
1 7 A 1
2 8 A 2
3 9 A 3
4 10 A 4
5 11 A 5
6 9 B 1
> head(d831 <- within(EXA_C08_S03_01, expr = {
+ ageGroup = structure(ageGroup, levels = c('<20', '20s', '30s', '40s', '>50'), class = 'factor')
+ }))
time method ageGroup
1 7 A <20
2 8 A 20s
3 9 A 30s
4 10 A 40s
5 11 A >50
6 9 B <20
> (aov_831 = aov(time ~ method + ageGroup, data = d831))
Call:
aov(formula = time ~ method + ageGroup, data = d831)
Terms:
method ageGroup Residuals
Sum of Squares 18.533333 24.933333 3.466667
Deg. of Freedom 2 4 8
Residual standard error: 0.6582806
Estimated effects may be unbalanced
> anova(aov_831)
Analysis of Variance Table
Response: time
Df Sum Sq Mean Sq F value Pr(>F)
method 2 18.5333 9.2667 21.385 0.0006165 ***
ageGroup 4 24.9333 6.2333 14.385 0.0010017 **
Residuals 8 3.4667 0.4333
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
> # Example 8.4.1; Page 348 (10th ed), Page 307 (11th ed)
> head(EXA_C08_S04_01)
FUNC SUBJ TIME
1 80 1 1
2 95 2 1
3 65 3 1
4 50 4 1
5 60 5 1
6 70 6 1
> head(d841 <- within(EXA_C08_S04_01, expr = {
+ SUBJ = factor(SUBJ)
+ TIME = structure(TIME, levels = c('Baseline', '1-Mon', '3-Mon', '6-Mon'), class = 'factor')
+ }))
FUNC SUBJ TIME
1 80 1 Baseline
2 95 2 Baseline
3 65 3 Baseline
4 50 4 Baseline
5 60 5 Baseline
6 70 6 Baseline
> (aov_841 = aov(FUNC ~ SUBJ + TIME, data = d841))
Call:
aov(formula = FUNC ~ SUBJ + TIME, data = d841)
Terms:
SUBJ TIME Residuals
Sum of Squares 20237.500 2395.833 7404.167
Deg. of Freedom 17 3 51
Residual standard error: 12.04906
Estimated effects may be unbalanced
> anova(aov_841)
Analysis of Variance Table
Response: FUNC
Df Sum Sq Mean Sq F value Pr(>F)
SUBJ 17 20237.5 1190.44 8.1998 2.179e-09 ***
TIME 3 2395.8 798.61 5.5008 0.002371 **
Residuals 51 7404.2 145.18
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
> # Example 8.4.2; Page 352 (10th ed), Page 310 (11th ed)
> # (optional; out of the scope of this course)
> head(EXA_C08_S04_02)
subject treatment totalC1 totalC2 totalC3 totalC4
1 1 1 6 6 6 7
2 2 1 9 6 10 9
3 3 1 7 9 17 19
4 4 1 6 7 9 3
5 5 1 6 7 16 13
6 6 1 6 6 6 11
> names(EXA_C08_S04_02)[3:6] = c('baseline', '2wk', '4wk', '6wk')
> head(d842a <- within(EXA_C08_S04_02, expr = {
+ subject = factor(subject)
+ treatment = structure(treatment, levels = c('placebo', 'aloe_juice'), class = 'factor')
+ }))
subject treatment baseline 2wk 4wk 6wk
1 1 placebo 6 6 6 7
2 2 placebo 9 6 10 9
3 3 placebo 7 9 17 19
4 4 placebo 6 7 9 3
5 5 placebo 6 7 16 13
6 6 placebo 6 6 6 11
> head(d842b <- reshape2::melt(d842a, id.vars = c('subject', 'treatment'),
+ variable.name = 'time', value.name = 'OralScores'))
Error in loadNamespace(x) : there is no package called ‘reshape2’
Calls: head ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.6
Check: HTML version of manual
Result: NOTE
Skipping checking math rendering: package 'V8' unavailable
Flavor: r-devel-linux-x86_64-debian-gcc