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In an experiment, there are two kinds of variables. The independent variable is the variable that is believed to affect another variable. The dependent variable is the variable that is going to be impacted. Thus, the belief going into the experiment is that changing the independent variable will cause the dependent variable to change. In this case, you are going into the experiment with the expectation that time in the penitentiary will cause prisoners to be rehabilitated. This means that the dependent variable is clearly the rate of rehabilitation and the independent variable is something having to do with the stay in prison.
The dependent variable should probably be measured by the rate of rearrest. This can be taken as a measure of rehabilitation. A prisoner has been rehabilitated if they go back out into society and do not commit further crimes.
It is harder to know how to measure the independent variable. Of the factors that you mention in this question, specific skills learned is probably the best measure of the independent variable. There has to be some mechanism by which time in prison is causing rehabilitation. Learning skills would be a good way for this to happen.
Therefore, we will say that the independent variable is activities while in prison, measured by skills learned, and the dependent variable is rehabilitation, measured by rearrest rates.
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