What is the one, best practice that defines a joint evaluation?
There is none! There is actually a menu of options, such as:
PURPOSE OF THE EVALUATION? Accountability, learning, coordination, policy/advocacy…
WHEN? Real time, mid-term, after (after action review), at end of a project (ex post), much later (impact)…
WHO EVALUATES? External (to agency and to program), external (to program, but not agency), peers…
and more… see Mapping options for joint evaluations.
What is important is that all stakeholders are clear about what kind of joint evaluation will be taking place, and the evaluation team should not start its data collection work until clarity is reached!
AIM Standing Team 
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