You can set the minimum size of the circles using different approaches. This answer deals with pack.radius:
If radius is specified, sets the pack layout’s radius accessor to the specified function and returns this pack layout.
First, we set a scale. You can see that the minimum value here is 20 (and the maximum is 50):
var sizeScale = d3.scaleSqrt() .range([20,50]);
Then, we use that scale in
Here is a demo using the same code you linked, from Mike Bostock: https://bl.ocks.org/anonymous/9590a06db119c7a67acdfd3c5b5f1e0a
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