[External] Possible bug

with(CO2, table(Treatment, Plant))

Plant
Treatment    Qn1 Qn2 Qn3 Qc1 Qc3 Qc2 Mn3 Mn2 Mn1 Mc2 Mc3 Mc1
  nonchilled   7   7   7   0   0   0   7   7   7   0   0   0
  chilled      0   0   0   7   7   7   0   0   0   7   7   7

Plants are nested within Treatments.
Hence when Plant is first, it picks up the effect of Treatment.

You can see that in the sums of squares and degrees of freedom from both ANOVA tables.

summary(aov(CO2$uptake~CO2$Treatment*CO2$Plant))

Df Sum Sq Mean Sq F value   Pr(>F)    
CO2$Treatment  1    988   988.1  14.685 0.000269 ***
CO2$Plant     10   3874   387.4   5.757 2.66e-06 ***
Residuals     72   4845    67.3                     
---
Signif. codes:  0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1

summary(aov(CO2$uptake~CO2$Plant*CO2$Treatment))

Df Sum Sq Mean Sq F value   Pr(>F)    
CO2$Plant   11   4862   442.0   6.569 1.84e-07 ***
Residuals   72   4845    67.3                     
---
Signif. codes:  0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1

On Mar 17, 2022, at 10:17, konrad via R-help <r-help at r-project.org> wrote:

summary(aov(CO2$uptake~CO2$Plant*CO2$Treatment))'