RE (1): In this example , observations are irises. The measurement that can vary among different irises is its species, so it should be a predictor variable treated as a between-subjects factor. You seem to be saying that the example treats it as a within-subjects factor. Can you point to the place in the example where species is treated as a within-subjects factor?
RE (2): The link you provided doesn’t take me to another example. However, you might be referring to this example . In this example, the second sentence states that Group is a between-subjects factor, and it is treated as a between-subjects factor in the ANOVA table. Can you point me to the place in this example, or to another example, where a variable called Group is treated as a within-subjects factor?
RE your final question: The description of the first output argument of ranova states:
ranovatbl includes a term representing all differences across the within-subjects factors. This term has either the name of the within-subjects factor if specified while fitting the model, or the name Time if the name of the within-subjects factor is not specified while fitting the model or there are more than one within-subjects factors. ranovatbl also includes all interactions between the terms in the within-subject model and all between-subject model terms.
