{"action":"created","issue":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/976","repository_url":"https://api.github.com/repos/markovmodel/PyEMMA","labels_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/976/labels{/name}","comments_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/976/comments","events_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/976/events","html_url":"https://github.com/markovmodel/PyEMMA/pull/976","id":185124199,"number":976,"title":"Koopman","user":{"login":"fnueske","id":11500718,"avatar_url":"https://avatars.githubusercontent.com/u/11500718?v=3","gravatar_id":"","url":"https://api.github.com/users/fnueske","html_url":"https://github.com/fnueske","followers_url":"https://api.github.com/users/fnueske/followers","following_url":"https://api.github.com/users/fnueske/following{/other_user}","gists_url":"https://api.github.com/users/fnueske/gists{/gist_id}","starred_url":"https://api.github.com/users/fnueske/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fnueske/subscriptions","organizations_url":"https://api.github.com/users/fnueske/orgs","repos_url":"https://api.github.com/users/fnueske/repos","events_url":"https://api.github.com/users/fnueske/events{/privacy}","received_events_url":"https://api.github.com/users/fnueske/received_events","type":"User","site_admin":false},"labels":[{"id":358818370,"url":"https://api.github.com/repos/markovmodel/PyEMMA/labels/on-hold","name":"on-hold","color":"d93f0b","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2016-10-25T13:53:35Z","updated_at":"2016-11-14T15:04:10Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/pulls/976","html_url":"https://github.com/markovmodel/PyEMMA/pull/976","diff_url":"https://github.com/markovmodel/PyEMMA/pull/976.diff","patch_url":"https://github.com/markovmodel/PyEMMA/pull/976.patch"},"body":"@fabian-paul and I have drafted a first version of the koopman module. It includes two new transformers, Koopman and EquilibriumKoopman, which realize the non-reversible and reversible (incl. re-weighting) estimation, respectively. There is a single api-function koopman which allows the user to select non-reversible or reversible estimation through the \"eq\"-flag. If reversible estimation is selected, the non-reversible result is also available as a property \"non_equilibrium_estimator\". The re-weighting factors for all data points can be accessed as well. The reversible estimator also has new properties \"mean_pc\", \"cov_pc\", \"cos_tau_pc\", which contain the equilibrium means, covariances and correlations, w.r.t. the decorrelated basis set (as described in our paper.)\nWe have provided some simple tests, I have also tested the module against 1d-data and reproduced the analysis of Trypsin-Benzamidine. Please don't mind the docstrings right now, these are still the (copied) TICA docstrings, we will replace them soon. For the moment I think it is important that ( @franknoe , @marscher )\n\n1) we discuss if the structure of the module is okay like that.\n2) we agree on a way that variational is used. At the moment I'm using direct imports everywhere.\n3) PRs 42 and 43  in variational are merged. At least 43  fixes some important errors.\n"},"comment":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/comments/260358330","html_url":"https://github.com/markovmodel/PyEMMA/pull/976#issuecomment-260358330","issue_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/976","id":260358330,"user":{"login":"fnueske","id":11500718,"avatar_url":"https://avatars.githubusercontent.com/u/11500718?v=3","gravatar_id":"","url":"https://api.github.com/users/fnueske","html_url":"https://github.com/fnueske","followers_url":"https://api.github.com/users/fnueske/followers","following_url":"https://api.github.com/users/fnueske/following{/other_user}","gists_url":"https://api.github.com/users/fnueske/gists{/gist_id}","starred_url":"https://api.github.com/users/fnueske/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fnueske/subscriptions","organizations_url":"https://api.github.com/users/fnueske/orgs","repos_url":"https://api.github.com/users/fnueske/repos","events_url":"https://api.github.com/users/fnueske/events{/privacy}","received_events_url":"https://api.github.com/users/fnueske/received_events","type":"User","site_admin":false},"created_at":"2016-11-14T15:04:10Z","updated_at":"2016-11-14T15:04:10Z","body":"@franknoe , what do you mean by this? The branch is public as part of the pyemma repo."}}
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