What is stated clearly by Laura in the film & diary, and by Albert, Cooper, and Doc Hayward within the series, but the only evidence is Leland confessing to murder in insane Bob rants and rape isn't brought up. Then later after Leland dies, Harry can't believe that Bob exists, and then Cooper says "Is it any easier to believe that a father would rape and murder his own daughter?" 

Maddy was murdered right in front of us, as that sequence went on it was not clear, but we were let on to see that Bob was indeed sexually abusing /as Leland was dancing. That is what I saw,