Comments (3)
Cause: This is due to incorrectly dropping logL and chi2 terms corresponding to 0-count (or "zero-frequency") outcomes when these should in fact be nonzero. In the chi2 case, the general term, N(p-f)^2/p, becomes N*p. In the logL within our "poisson picture", the general term N*f*log(p) - N*p becomes -N*p. In both cases these are nonzero even if f==0.
Fix: the hotfix deployed as Release 0.9.7.4 usually fixes this issue with a temporary patch that causes DataSet
-generation routines to not omit any probabilities.
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Update: a permanent fix that repairs the logL and chi2 functions will be merged into the main branches by pull request #64. We'll plan to close this issue once this appears in a release version of pyGSTi.
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As promised, closing this issue now that the version 0.98 release is out, which fixes this issue.
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