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It doesn't help that you don't have a complete sentence. A missing subject
can cloud anyone's perception of how the language is used.. While this
style is common in API docs, just know that the comma rules should
technically follow a proper sentence structure.
Your comma placement with subject added:
{The shplee method} assigns numbers to actors and events, based on natural
groups called clusters.
Your alternate suggestion:
{The shplee method} assigns numbers, based on natural groups called
clusters, to actors and events.
Your alternate alternate suggestion:
{The shplee method} assigns numbers to actors and events. The numbers are
based on natural groups called clusters.
Your alternate suggestion works because the clause modifies "numbers"
instead of the "actors and events".
My preference is your alternate alternate suggestion, primarily for clarity
and plain language. The short sentences will aid translation or
interpretation by non-English speakers.
-Tony
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