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Repeated measures designs or "Within-Subjects" designs are very important in live sciences and social sciences. Unfortunately, Mathematica's ANOVA package is not able to analyze those designs. It only handles "Between-Subjects" type of analyses.

During my whole research career I haven't been able to use Mathematica to analyze most of the studies I performed, which really is a pity.

In an e-mail exchange I had with WRI's Andy Ross in the beginning of this year he confirmed that I wasn't overlooking built-in functionality.

The question is: is any one aware of third party packages that handle these types of ANOVAs?

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I don't mean to sound like a jerk, but if you had your "whole research career" to build some tools for this in Mathematica why didn't you? Is the algorithm behind it that prohibitive? –  Mr.Wizard Jul 1 '12 at 6:32
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@Mr.Wizard have you read the linked article? It's sufficiently complex and error-prone that I preferred to use the other tools that I had readily available (Statistica in my case) instead of trying to come up with something myself. –  Sjoerd C. de Vries Jul 1 '12 at 6:58
    
Okay, just asking. It went over my head but that didn't surprise me. I guess it really is complex. :^) –  Mr.Wizard Jul 1 '12 at 7:00

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up vote 11 down vote accepted

Well, it's typical that just when you don't need it anymore (as I switched to a totally different discipline) the required functionality pops-up. I found that Vol. 13 (2011) of The Mathematica Journal contains an article about these types of designs, Computing Mixed-Design (Split-Plot) ANOVA. I thought it good to post it here, as I know many people would love to have this.

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