{"action":"created","issue":{"url":"https://api.github.com/repos/adw96/DivNet/issues/13","repository_url":"https://api.github.com/repos/adw96/DivNet","labels_url":"https://api.github.com/repos/adw96/DivNet/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/adw96/DivNet/issues/13/comments","events_url":"https://api.github.com/repos/adw96/DivNet/issues/13/events","html_url":"https://github.com/adw96/DivNet/issues/13","id":348157619,"node_id":"MDU6SXNzdWUzNDgxNTc2MTk=","number":13,"title":"Relationship between Bray-Curtis distance and Shannon div estimates","user":{"login":"cyklee","id":19379839,"node_id":"MDQ6VXNlcjE5Mzc5ODM5","avatar_url":"https://avatars3.githubusercontent.com/u/19379839?v=4","gravatar_id":"","url":"https://api.github.com/users/cyklee","html_url":"https://github.com/cyklee","followers_url":"https://api.github.com/users/cyklee/followers","following_url":"https://api.github.com/users/cyklee/following{/other_user}","gists_url":"https://api.github.com/users/cyklee/gists{/gist_id}","starred_url":"https://api.github.com/users/cyklee/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cyklee/subscriptions","organizations_url":"https://api.github.com/users/cyklee/orgs","repos_url":"https://api.github.com/users/cyklee/repos","events_url":"https://api.github.com/users/cyklee/events{/privacy}","received_events_url":"https://api.github.com/users/cyklee/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":{"login":"adw96","id":17593682,"node_id":"MDQ6VXNlcjE3NTkzNjgy","avatar_url":"https://avatars3.githubusercontent.com/u/17593682?v=4","gravatar_id":"","url":"https://api.github.com/users/adw96","html_url":"https://github.com/adw96","followers_url":"https://api.github.com/users/adw96/followers","following_url":"https://api.github.com/users/adw96/following{/other_user}","gists_url":"https://api.github.com/users/adw96/gists{/gist_id}","starred_url":"https://api.github.com/users/adw96/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adw96/subscriptions","organizations_url":"https://api.github.com/users/adw96/orgs","repos_url":"https://api.github.com/users/adw96/repos","events_url":"https://api.github.com/users/adw96/events{/privacy}","received_events_url":"https://api.github.com/users/adw96/received_events","type":"User","site_admin":false},"assignees":[{"login":"adw96","id":17593682,"node_id":"MDQ6VXNlcjE3NTkzNjgy","avatar_url":"https://avatars3.githubusercontent.com/u/17593682?v=4","gravatar_id":"","url":"https://api.github.com/users/adw96","html_url":"https://github.com/adw96","followers_url":"https://api.github.com/users/adw96/followers","following_url":"https://api.github.com/users/adw96/following{/other_user}","gists_url":"https://api.github.com/users/adw96/gists{/gist_id}","starred_url":"https://api.github.com/users/adw96/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adw96/subscriptions","organizations_url":"https://api.github.com/users/adw96/orgs","repos_url":"https://api.github.com/users/adw96/repos","events_url":"https://api.github.com/users/adw96/events{/privacy}","received_events_url":"https://api.github.com/users/adw96/received_events","type":"User","site_admin":false}],"milestone":null,"comments":1,"created_at":"2018-08-07T03:53:34Z","updated_at":"2018-08-07T23:13:37Z","closed_at":"2018-08-07T18:18:21Z","author_association":"NONE","body":"Hi Amy,\r\n\r\nI hope this is an appropriate place to raise a question regarding the vignette.\r\n\r\nIn the DivNet vignette, it said:\r\n\r\n> For glassy and water samples, the estimated diversity is in the middle of the individual diversity estimates, while for altered samples the estimated diversity is lower. That's because the **water and glassy samples are much more similar to each other in terms of relative abundances than the altered samples**, as we can see from the distribution of Bray-Curtis distances between the samples\r\n\r\nHowever, in the estimates of Bray-Curtis distance plot below, glassy.water interaction showed the most distance, while altered.altered showed the least distance. Doesn't that indicate exactly the opposite to the statement above i.e. altered samples are quite similar to each other while glassy vs. water are quite different? Unless you meant glassy.glassy and water.water are quite similar, but those comparisons were not shown.\r\n\r\nIf possible, could you please clarify the relationship between similarity between samples (Bray-Curtis distance) and the resulting estimated Shannon diversity?\r\n\r\nThank you for all the hard work into DivNet and I am eager to implement it into my future projects!\r\n\r\nKevin"},"comment":{"url":"https://api.github.com/repos/adw96/DivNet/issues/comments/411232020","html_url":"https://github.com/adw96/DivNet/issues/13#issuecomment-411232020","issue_url":"https://api.github.com/repos/adw96/DivNet/issues/13","id":411232020,"node_id":"MDEyOklzc3VlQ29tbWVudDQxMTIzMjAyMA==","user":{"login":"cyklee","id":19379839,"node_id":"MDQ6VXNlcjE5Mzc5ODM5","avatar_url":"https://avatars3.githubusercontent.com/u/19379839?v=4","gravatar_id":"","url":"https://api.github.com/users/cyklee","html_url":"https://github.com/cyklee","followers_url":"https://api.github.com/users/cyklee/followers","following_url":"https://api.github.com/users/cyklee/following{/other_user}","gists_url":"https://api.github.com/users/cyklee/gists{/gist_id}","starred_url":"https://api.github.com/users/cyklee/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cyklee/subscriptions","organizations_url":"https://api.github.com/users/cyklee/orgs","repos_url":"https://api.github.com/users/cyklee/repos","events_url":"https://api.github.com/users/cyklee/events{/privacy}","received_events_url":"https://api.github.com/users/cyklee/received_events","type":"User","site_admin":false},"created_at":"2018-08-07T23:13:37Z","updated_at":"2018-08-07T23:13:37Z","author_association":"NONE","body":"Thanks for the speedy reply Amy. I think I'm getting tripped up by the wordings in the vignette example:\r\n\r\n> water and glassy samples are much more similar to each other in terms of relative abundances than the altered samples.\r\n\r\nDoes that mean either:\r\n\r\n1. `water.glassy` have lower BC distances compared to `water.altered` or `glassy.altered`.\r\n2. `water.water` & `glassy.glassy` have lower distribution of BC distances compared to `altered.altered`.\r\n\r\n... and as a result `water` and `glassy` have higher estimated Shannon diversity than `altered`?\r\n\r\nI'm pretty sure I'm misinterpreting it here but I can't see a better alternative interpretation. I'm trying to connect Figure 2 (Shannon diversity estimate) with Figure 3 (Estimate Bray-Curtis distance), so I have a better grasp on between group BC distance and how that would impact the estimated diversity when using DivNet.\r\n\r\nCheers,\r\n\r\nKevin"}}
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