{"action":"created","issue":{"url":"https://api.github.com/repos/openjournals/joss-reviews/issues/634","repository_url":"https://api.github.com/repos/openjournals/joss-reviews","labels_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/634/labels{/name}","comments_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/634/comments","events_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/634/events","html_url":"https://github.com/openjournals/joss-reviews/issues/634","id":306229487,"node_id":"MDU6SXNzdWUzMDYyMjk0ODc=","number":634,"title":"[REVIEW]: genieR: An R package for inference of demographic history of phylogenies","user":{"login":"whedon","id":18508068,"node_id":"MDQ6VXNlcjE4NTA4MDY4","avatar_url":"https://avatars3.githubusercontent.com/u/18508068?v=4","gravatar_id":"","url":"https://api.github.com/users/whedon","html_url":"https://github.com/whedon","followers_url":"https://api.github.com/users/whedon/followers","following_url":"https://api.github.com/users/whedon/following{/other_user}","gists_url":"https://api.github.com/users/whedon/gists{/gist_id}","starred_url":"https://api.github.com/users/whedon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/whedon/subscriptions","organizations_url":"https://api.github.com/users/whedon/orgs","repos_url":"https://api.github.com/users/whedon/repos","events_url":"https://api.github.com/users/whedon/events{/privacy}","received_events_url":"https://api.github.com/users/whedon/received_events","type":"User","site_admin":false},"labels":[{"id":330465313,"node_id":"MDU6TGFiZWwzMzA0NjUzMTM=","url":"https://api.github.com/repos/openjournals/joss-reviews/labels/review","name":"review","color":"fbca04","default":false}],"state":"open","locked":false,"assignee":{"login":"george-githinji","id":12426355,"node_id":"MDQ6VXNlcjEyNDI2MzU1","avatar_url":"https://avatars3.githubusercontent.com/u/12426355?v=4","gravatar_id":"","url":"https://api.github.com/users/george-githinji","html_url":"https://github.com/george-githinji","followers_url":"https://api.github.com/users/george-githinji/followers","following_url":"https://api.github.com/users/george-githinji/following{/other_user}","gists_url":"https://api.github.com/users/george-githinji/gists{/gist_id}","starred_url":"https://api.github.com/users/george-githinji/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/george-githinji/subscriptions","organizations_url":"https://api.github.com/users/george-githinji/orgs","repos_url":"https://api.github.com/users/george-githinji/repos","events_url":"https://api.github.com/users/george-githinji/events{/privacy}","received_events_url":"https://api.github.com/users/george-githinji/received_events","type":"User","site_admin":false},"assignees":[{"login":"george-githinji","id":12426355,"node_id":"MDQ6VXNlcjEyNDI2MzU1","avatar_url":"https://avatars3.githubusercontent.com/u/12426355?v=4","gravatar_id":"","url":"https://api.github.com/users/george-githinji","html_url":"https://github.com/george-githinji","followers_url":"https://api.github.com/users/george-githinji/followers","following_url":"https://api.github.com/users/george-githinji/following{/other_user}","gists_url":"https://api.github.com/users/george-githinji/gists{/gist_id}","starred_url":"https://api.github.com/users/george-githinji/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/george-githinji/subscriptions","organizations_url":"https://api.github.com/users/george-githinji/orgs","repos_url":"https://api.github.com/users/george-githinji/repos","events_url":"https://api.github.com/users/george-githinji/events{/privacy}","received_events_url":"https://api.github.com/users/george-githinji/received_events","type":"User","site_admin":false}],"milestone":null,"comments":9,"created_at":"2018-03-18T10:42:28Z","updated_at":"2018-07-08T16:39:04Z","closed_at":null,"author_association":"COLLABORATOR","body":"**Submitting author:** @xiangfstats (<a href=\"http://orcid.org/0000-0003-3644-7114\">Fei Xiang</a>)\r\n**Repository:** <a href=\"https://github.com/xiangfstats/GenieR\" target =\"_blank\">https://github.com/xiangfstats/GenieR</a>\r\n**Version:** v1.0.0\r\n**Editor:** @biorelated\r\n**Reviewer:** @pboesu\r\n**Archive:** Pending\r\n\r\n## Status\r\n\r\n[![status](http://joss.theoj.org/papers/a0b1e6b2abfc2abade8cf11043be7bc6/status.svg)](http://joss.theoj.org/papers/a0b1e6b2abfc2abade8cf11043be7bc6)\r\n\r\nStatus badge code:\r\n\r\n```\r\nHTML: <a href=\"http://joss.theoj.org/papers/a0b1e6b2abfc2abade8cf11043be7bc6\"><img src=\"http://joss.theoj.org/papers/a0b1e6b2abfc2abade8cf11043be7bc6/status.svg\"></a>\r\nMarkdown: [![status](http://joss.theoj.org/papers/a0b1e6b2abfc2abade8cf11043be7bc6/status.svg)](http://joss.theoj.org/papers/a0b1e6b2abfc2abade8cf11043be7bc6)\r\n```\r\n**Reviewers and authors**:\r\n\r\nPlease avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the <a href=\"https://github.com/xiangfstats/GenieR\" target=\"_blank\">target repository</a> and link to those issues (especially acceptance-blockers) in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)\r\n\r\n## Reviewer instructions & questions\r\n\r\n@pboesu, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:\r\n1. Make sure you're logged in to your GitHub account\r\n2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations\r\n\r\nThe reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @biorelated know.\r\n\r\n  ### Conflict of interest\r\n\r\n- [x] As the reviewer I confirm that I have read the [JOSS conflict of interest policy](https://github.com/openjournals/joss/blob/master/COI.md) and that there are no conflicts of interest for me to review this work.\r\n\r\n### Code of Conduct\r\n\r\n- [x] I confirm that I read and will adhere to the [JOSS code of conduct](https://joss.theoj.org/about#code_of_conduct).\r\n\r\n### General checks\r\n\r\n- [x] **Repository:** Is the source code for this software available at the <a target=\"_blank\" href=\"https://github.com/xiangfstats/GenieR\">repository url</a>?\r\n- [x] **License:** Does the repository contain a plain-text LICENSE file with the contents of an [OSI approved](https://opensource.org/licenses/alphabetical) software license?\r\n- [ ] **Version:** Does the release version given match the GitHub release (v1.0.0)?\r\n  ⚠️ **TODO:** No github release exists. DESCRIPTION file lists version as 0.1.0. Please harmonize version numbering and create github release.\r\n- [x] **Authorship:** Has the submitting author (@xiangfstats) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?\r\n\r\n### Functionality\r\n\r\n- [ ] **Installation:** Does installation proceed as outlined in the documentation?\r\nInstallation works as described on the reviewers machine (Windows 10, R 3.4.2, Rtools 3.5)\r\n⚠️ **Suggestion:** It might be worth pointing out (for the benefit of Windows users - not sure what the target audience is likely using) that a C++ compiler / Rtools installation is necessary. See PR.\r\n- [x] **Functionality:** Have the functional claims of the software been confirmed?\r\n- [x] **Performance:** If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)\r\n\r\n### Documentation\r\n\r\n- [x] **A statement of need:** Do the authors clearly state what problems the software is designed to solve and who the target audience is?\r\n- [ ] **Installation instructions:** Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.\r\n- [x] **Example usage:** Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).\r\n- [ ] **Functionality documentation:** Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?\r\n- [ ] **Automated tests:** Are there automated tests or manual steps described so that the function of the software can be verified?\r\n⚠️ **Suggestion:** Automated tests are provided covering input checking. All of these appear to be 'negative tests' i.e. based on `expect_error()`. I'd suggest that the authors also implement tests that check the code provides correct output when provided with correct inputs.\r\n- [x] **Community guidelines:** Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support\r\n\r\n### Software paper\r\n\r\n- [x] **Authors:** Does the `paper.md` file include a list of authors with their affiliations?\r\n- [x] **A statement of need:** Do the authors clearly state what problems the software is designed to solve and who the target audience is?\r\n- [ ] **References:** Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/openjournals/joss-reviews/issues/comments/403299934","html_url":"https://github.com/openjournals/joss-reviews/issues/634#issuecomment-403299934","issue_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/634","id":403299934,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMzI5OTkzNA==","user":{"login":"george-githinji","id":12426355,"node_id":"MDQ6VXNlcjEyNDI2MzU1","avatar_url":"https://avatars3.githubusercontent.com/u/12426355?v=4","gravatar_id":"","url":"https://api.github.com/users/george-githinji","html_url":"https://github.com/george-githinji","followers_url":"https://api.github.com/users/george-githinji/followers","following_url":"https://api.github.com/users/george-githinji/following{/other_user}","gists_url":"https://api.github.com/users/george-githinji/gists{/gist_id}","starred_url":"https://api.github.com/users/george-githinji/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/george-githinji/subscriptions","organizations_url":"https://api.github.com/users/george-githinji/orgs","repos_url":"https://api.github.com/users/george-githinji/repos","events_url":"https://api.github.com/users/george-githinji/events{/privacy}","received_events_url":"https://api.github.com/users/george-githinji/received_events","type":"User","site_admin":false},"created_at":"2018-07-08T16:39:04Z","updated_at":"2018-07-08T16:39:04Z","author_association":"COLLABORATOR","body":"Dear @pboesu Please review the improvements made by @xiangfstats. Kindly let me know if you need some assistance or if you are not in a position to. Thank you. "}}
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