updated how the parameter penalty is converted to the shrinkage parameter used in cov_warton and corr_warton in synthetic likelihood calculation. in the previous version when shrinkage=’warton’, penalty=1 corresponded to using the sample covariance matrix without shrinkage and penalty=0 corresponded to maximum shrinkage. now the shrinkage parameter is calculated as 1-penalty so that penalty=0 corresponds to no shrinkage. this means that both penalised covariance matrix estimation methods (’warton’and ’glasso’) now return the sample covariance matrix when penalty=0 and a more shrunk or sparse solution when penalty increases.
Summary:
updated how the parameter
penalty
is converted to the shrinkage parameter used incov_warton
andcorr_warton
in synthetic likelihood calculation. in the previous version whenshrinkage=’warton’
,penalty=1
corresponded to using the sample covariance matrix without shrinkage andpenalty=0
corresponded to maximum shrinkage. now the shrinkage parameter is calculated as1-penalty
so thatpenalty=0
corresponds to no shrinkage. this means that both penalised covariance matrix estimation methods (’warton’
and’glasso’
) now return the sample covariance matrix whenpenalty=0
and a more shrunk or sparse solution whenpenalty
increases.Please make sure
If your contribution adds, removes or somehow changes the functional behavior of the package, please check that
make lint
,make docs
andmake test
and the proposed changes pass all unit tests (check step 6 of CONTRIBUTING.rst for details)
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