{"action":"created","issue":{"url":"https://api.github.com/repos/biocore/scikit-bio/issues/1532","repository_url":"https://api.github.com/repos/biocore/scikit-bio","labels_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1532/labels{/name}","comments_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1532/comments","events_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1532/events","html_url":"https://github.com/biocore/scikit-bio/pull/1532","id":257213708,"number":1532,"title":"Permdisp","user":{"login":"nreeve17","id":25165116,"avatar_url":"https://avatars0.githubusercontent.com/u/25165116?v=4","gravatar_id":"","url":"https://api.github.com/users/nreeve17","html_url":"https://github.com/nreeve17","followers_url":"https://api.github.com/users/nreeve17/followers","following_url":"https://api.github.com/users/nreeve17/following{/other_user}","gists_url":"https://api.github.com/users/nreeve17/gists{/gist_id}","starred_url":"https://api.github.com/users/nreeve17/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nreeve17/subscriptions","organizations_url":"https://api.github.com/users/nreeve17/orgs","repos_url":"https://api.github.com/users/nreeve17/repos","events_url":"https://api.github.com/users/nreeve17/events{/privacy}","received_events_url":"https://api.github.com/users/nreeve17/received_events","type":"User","site_admin":false},"labels":[{"id":176575058,"url":"https://api.github.com/repos/biocore/scikit-bio/labels/DO%20NOT%20MERGE","name":"DO NOT MERGE","color":"e11d21","default":false}],"state":"open","locked":false,"assignee":{"login":"gregcaporaso","id":192372,"avatar_url":"https://avatars2.githubusercontent.com/u/192372?v=4","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},"assignees":[{"login":"gregcaporaso","id":192372,"avatar_url":"https://avatars2.githubusercontent.com/u/192372?v=4","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}],"milestone":null,"comments":6,"created_at":"2017-09-12T23:27:58Z","updated_at":"2018-04-20T21:38:19Z","closed_at":null,"author_association":"NONE","pull_request":{"url":"https://api.github.com/repos/biocore/scikit-bio/pulls/1532","html_url":"https://github.com/biocore/scikit-bio/pull/1532","diff_url":"https://github.com/biocore/scikit-bio/pull/1532.diff","patch_url":"https://github.com/biocore/scikit-bio/pull/1532.patch"},"body":"Please complete the following checklist:\r\n\r\n* [x] I have read the guidelines in [CONTRIBUTING.md](https://github.com/biocore/scikit-bio/blob/master/CONTRIBUTING.md).\r\n\r\n* [x] I have documented all public-facing changes in [CHANGELOG.md](https://github.com/biocore/scikit-bio/blob/master/CHANGELOG.md).\r\n\r\n* [ ] **This pull request includes code, documentation, or other content derived from external source(s).** If this is the case, ensure the external source's license is compatible with scikit-bio's [license](https://github.com/biocore/scikit-bio/blob/master/COPYING.txt). Include the license in the `licenses` directory and add a comment in the code giving proper attribution. Ensure any other requirements set forth by the license and/or author are satisfied. **It is your responsibility to disclose code, documentation, or other content derived from external source(s).** If you have questions about whether something can be included in the project or how to give proper attribution, include those questions in your pull request and a reviewer will assist you.\r\n\r\n* [x] **This pull request does not include code, documentation, or other content derived from external source(s).**\r\n\r\n**Note:** [REVIEWING.md](https://github.com/biocore/scikit-bio/blob/master/REVIEWING.md) may also be helpful to see some of the things code reviewers will be verifying when reviewing your pull request.\r\n\r\nA part of this program uses the function hdmedians, which is under a GNU-GPL license. We have reached out to the author of hdmedians and asked if he could use a double license so that it could be compatible with scikit-bio. The author has yet to respond to our request. \r\n\r\nBenchmarking was done to compare the performance of the two test types that PERMDISP performs, median and centroid, against the performance of the analogous betadisper function in R, used by QIIME. Betadisper uses the median test by default and is what is used by QIIME.\r\n\r\nMatrix Size | Time (s) Median scikit-bio | Time (s) Centroid scikit-bio | Time (s) QIIME PERMDISP (median)\r\n-- | -- | -- | --\r\n10 | 4.8 | 2.93 | 3.3\r\n50 | 4.94 | 2.99 | 3.56\r\n100 | 5.21 | 3.1 | 3.43\r\n150 | 5.79 | 3.38 | 3.56\r\n200 | 7.73 | 3.66 | 3.67\r\n300 | 8.6 | 4.47 | 4.13\r\n500 | 15.4 | 7.22 | 5.79\r\n1000 | N/A | 26.9 | 12.72\r\n\r\n![image](https://user-images.githubusercontent.com/25165116/30499856-f7a04976-9a10-11e7-9fe5-f673bbe2d8af.png)\r\n![image](https://user-images.githubusercontent.com/25165116/30499874-02c33de0-9a11-11e7-8a3f-31fed09907ca.png)\r\n![image](https://user-images.githubusercontent.com/25165116/30499881-07a8fdfe-9a11-11e7-9534-bb1bab67716d.png)\r\n"},"comment":{"url":"https://api.github.com/repos/biocore/scikit-bio/issues/comments/383229599","html_url":"https://github.com/biocore/scikit-bio/pull/1532#issuecomment-383229599","issue_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1532","id":383229599,"user":{"login":"nreeve17","id":25165116,"avatar_url":"https://avatars0.githubusercontent.com/u/25165116?v=4","gravatar_id":"","url":"https://api.github.com/users/nreeve17","html_url":"https://github.com/nreeve17","followers_url":"https://api.github.com/users/nreeve17/followers","following_url":"https://api.github.com/users/nreeve17/following{/other_user}","gists_url":"https://api.github.com/users/nreeve17/gists{/gist_id}","starred_url":"https://api.github.com/users/nreeve17/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nreeve17/subscriptions","organizations_url":"https://api.github.com/users/nreeve17/orgs","repos_url":"https://api.github.com/users/nreeve17/repos","events_url":"https://api.github.com/users/nreeve17/events{/privacy}","received_events_url":"https://api.github.com/users/nreeve17/received_events","type":"User","site_admin":false},"created_at":"2018-04-20T21:38:18Z","updated_at":"2018-04-20T21:38:18Z","author_association":"NONE","body":"All of the comments have been addressed. We compiled a table to summarize the results between permdisp in skbio and betadisper used by R, with links to study ids in Qiita. \r\n\r\n# Spatial Median Comparisons\r\n**Data Set**|**Sample Size**|**metadata grouping**|**Number groups**|**Median F-val skbio**|**Median F-val betadisper**|**M p-val skbio**|**M p-val betadisper**|Qiita Study|PubMed\r\n:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:----:|:----:|\r\nMoving Pictures|33|BodySite|4|10.1956|10.4105|0.001|0.001|[550](https://qiita.ucsd.edu/study/description/550)|[21624126](https://www.ncbi.nlm.nih.gov/pubmed/21624126)\r\nMoving Pictures|33|Subject|2|0.0228117|0.02202|0.868|0.91|[550](https://qiita.ucsd.edu/study/description/550)|[21624126](https://www.ncbi.nlm.nih.gov/pubmed/21624126)\r\nKeyboard|77|sample\\_type|2|7.64607|7.64604|0.015|0.009|[232](https://qiita.ucsd.edu/study/description/232)|[20231444](https://www.ncbi.nlm.nih.gov/pubmed/20231444)\r\nSkin-forensic|17|sample\\_type|2|0.989882|0.9901|0.309|0.351|[393](https://qiita.ucsd.edu/study/description/393)|[20231444](https://www.ncbi.nlm.nih.gov/pubmed/20231444)\r\ndiet mammals converge|39|host\\_clade|6|30.0668|30.07818|0.989|0.001|[626](https://qiita.ucsd.edu/study/description/626)|[25974302](https://www.ncbi.nlm.nih.gov/pubmed/25974302)\r\ndiet mammals converge|39|host\\_family|22| 21.1988|21.19901| 0.521| 0.001|[626](https://qiita.ucsd.edu/study/description/626)|[25974302](https://www.ncbi.nlm.nih.gov/pubmed/25974302)\r\ndiet mammals converge|39|elevation|5|72.6057|72.61026|0.084|0.001|[626](https://qiita.ucsd.edu/study/description/626)|[25974302](https://www.ncbi.nlm.nih.gov/pubmed/25974302)\r\ndiet mammals converge|39|diet|3|1.39989|1.39994| 0.439|0.293|[626](https://qiita.ucsd.edu/study/description/626)|[25974302](https://www.ncbi.nlm.nih.gov/pubmed/25974302)\r\nnewborns|79|sex|2|2.2111|2.211|0.154|0.144|[395](https://qiita.ucsd.edu/study/description/395)|[20566857](https://www.ncbi.nlm.nih.gov/pubmed/20566857)\r\nnewborns|79|delivery\\_mode|3|10.8083|10.808|0.001|0.001|[395](https://qiita.ucsd.edu/study/description/395)|[20566857](https://www.ncbi.nlm.nih.gov/pubmed/20566857)\r\n\r\n# Centroid Comparisons\r\n**Data Set**|**Sample Size**|**metadata grouping**|**Number groups**|**Centroid F-val skbio**|**Cetroid F-val betadisper**|**M p-val skbio**|**M p-val betadisper**|Qiita Study|PubMed\r\n:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:-----:|:----:|:----:|\r\nMoving Pictures|33|BodySite|4|17.4242|17.72748|0.001|0.001|[550](https://qiita.ucsd.edu/study/description/550)|[21624126](https://www.ncbi.nlm.nih.gov/pubmed/21624126)\r\nMoving Pictures|33|Subject|2|0.0467885|0.04549|0.848|0.854|[550](https://qiita.ucsd.edu/study/description/550)|[21624126](https://www.ncbi.nlm.nih.gov/pubmed/21624126)\r\nKeyboard|77|sample\\_type|2|9.28355|9.28355|0.006|0.007|[232](https://qiita.ucsd.edu/study/description/232)|[20231444](https://www.ncbi.nlm.nih.gov/pubmed/20231444)\r\nSkin forensic|17|sample\\_type|2|1.40085|1.40085|0.329|0.266|[393](https://qiita.ucsd.edu/study/description/393)|[20231444](https://www.ncbi.nlm.nih.gov/pubmed/20231444)\r\ndiet mammals converge|39|host\\_clade|6|47.556|47.55598  |0.994|0.001|[626](https://qiita.ucsd.edu/study/description/626)|[25974302](https://www.ncbi.nlm.nih.gov/pubmed/25974302)\r\ndiet mammals converge|39|host\\_family|22|71.9981|71.99812|0.451|0.001|[626](https://qiita.ucsd.edu/study/description/626)|[25974302](https://www.ncbi.nlm.nih.gov/pubmed/25974302)\r\ndiet mammals converge|39|elevation|5|90.2223|90.2223|0.103|0.001|[626](https://qiita.ucsd.edu/study/description/626)|[25974302](https://www.ncbi.nlm.nih.gov/pubmed/25974302)\r\ndiet mammals converge|39|diet|3|2.08823|2.08823|0.405|0.135|[626](https://qiita.ucsd.edu/study/description/626)|[25974302](https://www.ncbi.nlm.nih.gov/pubmed/25974302)\r\nnewborns|79|sex|2|2.88853|2.88853|0.138|0.108|[395](https://qiita.ucsd.edu/study/description/395)|[20566857](https://www.ncbi.nlm.nih.gov/pubmed/20566857)|\r\nnewborns|79|delivery\\_mode|3|14.0445|14.04454|0.001|0.001|[395](https://qiita.ucsd.edu/study/description/395)|[20566857](https://www.ncbi.nlm.nih.gov/pubmed/20566857)\r\n"}}
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