How to run 2x2 mixed anova with unequal sample size in R?

Question

I am trying to run 2x2 mixed ANOVA with unequal sample size using R. The data was collected from 30 individuals with two different conditions (i.e., 2 levels of within factor), and they were allocated by k-means clustering analysis (i.e., # of group 1 = 11, # of group 2 = 19). Here is a sample of my code and the output:

summary(aov(JH ~ Box+Group+Box:Group+Error(P/Box), data = d3))

Error: P
          Df Sum Sq Mean Sq F value Pr(>F)
Group      1  0.027 0.02715    1.56   0.22
Box:Group  1  0.001 0.00078    0.04   0.83
Residuals 27  0.470 0.01741               

Error: P:Box
          Df   Sum Sq  Mean Sq F value Pr(>F)
Box        1 0.000000 1.00e-07    0.00   0.97
Group      1 0.000022 2.17e-05    0.24   0.63
Box:Group  1 0.000032 3.24e-05    0.35   0.56
Residuals 27 0.002488 9.21e-05

Unlike the output when I ran 2x2 mixed ANOVA with equal sample sizes using another dataset (the output attached below), I had another interaction effect under Error: P.

summary(aov(HipLoadingK ~ Box*Sex+Error(P/Box), data = TW))

Error: P
          Df  Sum Sq  Mean Sq F value  Pr(>F)   
Sex        1 0.02578 0.025779   8.038 0.00841 **
Residuals 28 0.08980 0.003207                   
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Error: P:Box
          Df   Sum Sq  Mean Sq F value Pr(>F)  
Box        1 0.003454 0.003454   4.271 0.0481 *
Box:Sex    1 0.000066 0.000066   0.082 0.7765  
Residuals 28 0.022645 0.000809

Is this result fine as long as I interpret appropriate results for each between/within main effects and interaction effect? Or should I edit my code to get the correct outputs? If so, please let me know what should be added or edited in my code.

two parts to your question, the interpretation part about whether it's ok, that belongs to cross-validated. the coding part, your output looks really weird I don't understand you are trying to do here without a reproducible example — StupidWolf
@StupidWolf Thank you for your considering my question. I just found out my allocation code caused the error. After fixing the code, it worked! — Youngmin Chun

Youngmin Chun Youngmin Chun · Accepted Answer · 2020-11-15T00:32:49

When I change the dataset from a short format to a long format, I accidentally put the different order of group name for each participant. For instance, P01 was group A in X condition, but his or her group was B in Y condition. After I fixed the code, it worked well.

How to run 2x2 mixed anova with unequal sample size in R?

1 Answers