Pro-rata will work out the cost for the member between the start date and the first payment date. For example if you have setup your membership plans to only ask for a payment on the 1st and they sign up on the 3th they will have a whole month for free before making a payment. Pro-rata will work out the cost for this time and request a payment.
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Step 1:
Go to the settings cog within the top right hand corner. 

Step 2:

Then to membership plans

Step 3:

Now click the membership plan you would like to turn pro-rata on/off for.

Step 4:

Press the payments tab and in here you can turn pro-rata on / off for this plan.

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