According to a recent paper (open pdf here), one can specify both within- and between-subjects effects in a Bayes factor ANOVA. In the example they give (p. 28), this is specified in the following way:
bf = anovaBF(rt~a*d*p+s, data = dat, whichModels="withmain", whichRandom="s", iterations = 100000)
a = age , hence a between-subjects effect
d = distanceand
p = presentation as experimental manipulations and hence within-subjects effects. And
s = subject
I just want to double check: is it not necessary at all to specify which effects are between- and which are within-subjects?