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ISQ vs JCR
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Recall the original question.
"Question from a non-political scientist. How is ISQ viewed relative to JCR? Is there a clear ranking of these two journals? Thanks!"
So, the reader wants to know if there is a "clear ranking" based on perceptions of political scientists. So, one answer to that question would be to look at a survey of actual political scientists that asks this question. TRIPS project has done this for the past 10 years and in every survey ISQ > JCR. This is true across time and across countries. See top 10 from 2012 survey:
IO, ISQ, IS, FA, APSR, WP, EJIR, JCR, FP, RIS.
If you restrict it to just American responses, then JCR moves up to #7, ahead of EJIR, but is still behind ISQ, which is #2.
http://www.wm.edu/offices/itpir/_documents/trip/trip_around_the_world_2011.pdf