{"action":"created","issue":{"url":"https://api.github.com/repos/biota/sourcetracker2/issues/48","repository_url":"https://api.github.com/repos/biota/sourcetracker2","labels_url":"https://api.github.com/repos/biota/sourcetracker2/issues/48/labels{/name}","comments_url":"https://api.github.com/repos/biota/sourcetracker2/issues/48/comments","events_url":"https://api.github.com/repos/biota/sourcetracker2/issues/48/events","html_url":"https://github.com/biota/sourcetracker2/issues/48","id":164178608,"number":48,"title":"resolve different default parameters","user":{"login":"gregcaporaso","id":192372,"avatar_url":"https://avatars.githubusercontent.com/u/192372?v=3","gravatar_id":"","url":"https://api.github.com/users/gregcaporaso","html_url":"https://github.com/gregcaporaso","followers_url":"https://api.github.com/users/gregcaporaso/followers","following_url":"https://api.github.com/users/gregcaporaso/following{/other_user}","gists_url":"https://api.github.com/users/gregcaporaso/gists{/gist_id}","starred_url":"https://api.github.com/users/gregcaporaso/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gregcaporaso/subscriptions","organizations_url":"https://api.github.com/users/gregcaporaso/orgs","repos_url":"https://api.github.com/users/gregcaporaso/repos","events_url":"https://api.github.com/users/gregcaporaso/events{/privacy}","received_events_url":"https://api.github.com/users/gregcaporaso/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":{"url":"https://api.github.com/repos/biota/sourcetracker2/milestones/1","html_url":"https://github.com/biota/sourcetracker2/milestones/2.0.2:%20draft%20public%20API","labels_url":"https://api.github.com/repos/biota/sourcetracker2/milestones/1/labels","id":1970791,"number":1,"title":"2.0.2: draft public API","description":"The second alpha release of SourceTracker 2.","creator":{"login":"gregcaporaso","id":192372,"avatar_url":"https://avatars.githubusercontent.com/u/192372?v=3","gravatar_id":"","url":"https://api.github.com/users/gregcaporaso","html_url":"https://github.com/gregcaporaso","followers_url":"https://api.github.com/users/gregcaporaso/followers","following_url":"https://api.github.com/users/gregcaporaso/following{/other_user}","gists_url":"https://api.github.com/users/gregcaporaso/gists{/gist_id}","starred_url":"https://api.github.com/users/gregcaporaso/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gregcaporaso/subscriptions","organizations_url":"https://api.github.com/users/gregcaporaso/orgs","repos_url":"https://api.github.com/users/gregcaporaso/repos","events_url":"https://api.github.com/users/gregcaporaso/events{/privacy}","received_events_url":"https://api.github.com/users/gregcaporaso/received_events","type":"User","site_admin":false},"open_issues":3,"closed_issues":11,"state":"open","created_at":"2016-08-29T21:20:58Z","updated_at":"2016-09-08T13:32:11Z","due_on":"2016-09-09T00:00:00Z","closed_at":null},"comments":0,"created_at":"2016-07-06T21:28:25Z","updated_at":"2016-09-08T13:32:11Z","closed_at":"2016-09-08T13:32:11Z","body":"We have three sets of default parameters floating around. The [CLI defaults for ST2](https://github.com/biota/sourcetracker2/blob/a7cbe058189832a75f44c07f9bce1371aa2eb3da/sourcetracker/_cli/gibbs.py#L3), the [CLI defaults for ST1,](https://github.com/danknights/sourcetracker/blob/a97d807f8a6931ea87b20db003bb535d300b6f1e/sourcetracker_for_qiime.r#L38) and another set that are introduced in the API documentation [here](https://github.com/biota/sourcetracker2/blob/a7cbe058189832a75f44c07f9bce1371aa2eb3da/sourcetracker/_sourcetracker.py#L943) (the \"API doc defaults\"). \r\n\r\nThe \"API doc defaults\" are orders of magnitude faster. In our upcoming parameter evaluation, we should decide on which of these we want to use under which circumstances (e.g., is there a fast setting and a more accurate setting?), and more clearly document that. We should also review the findings presented in [Henry et al](https://www.ncbi.nlm.nih.gov/pubmed/26921850) as that is relevant here. "},"comment":{"url":"https://api.github.com/repos/biota/sourcetracker2/issues/comments/245598008","html_url":"https://github.com/biota/sourcetracker2/issues/48#issuecomment-245598008","issue_url":"https://api.github.com/repos/biota/sourcetracker2/issues/48","id":245598008,"user":{"login":"gregcaporaso","id":192372,"avatar_url":"https://avatars.githubusercontent.com/u/192372?v=3","gravatar_id":"","url":"https://api.github.com/users/gregcaporaso","html_url":"https://github.com/gregcaporaso","followers_url":"https://api.github.com/users/gregcaporaso/followers","following_url":"https://api.github.com/users/gregcaporaso/following{/other_user}","gists_url":"https://api.github.com/users/gregcaporaso/gists{/gist_id}","starred_url":"https://api.github.com/users/gregcaporaso/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gregcaporaso/subscriptions","organizations_url":"https://api.github.com/users/gregcaporaso/orgs","repos_url":"https://api.github.com/users/gregcaporaso/repos","events_url":"https://api.github.com/users/gregcaporaso/events{/privacy}","received_events_url":"https://api.github.com/users/gregcaporaso/received_events","type":"User","site_admin":false},"created_at":"2016-09-08T13:32:11Z","updated_at":"2016-09-08T13:32:11Z","body":"The API and the CLI now have the same default parameters (#71). "}}
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