{"action":"created","issue":{"url":"https://api.github.com/repos/ropensci/onboarding/issues/212","repository_url":"https://api.github.com/repos/ropensci/onboarding","labels_url":"https://api.github.com/repos/ropensci/onboarding/issues/212/labels{/name}","comments_url":"https://api.github.com/repos/ropensci/onboarding/issues/212/comments","events_url":"https://api.github.com/repos/ropensci/onboarding/issues/212/events","html_url":"https://github.com/ropensci/onboarding/issues/212","id":317081822,"node_id":"MDU6SXNzdWUzMTcwODE4MjI=","number":212,"title":"Submission: phylogram","user":{"login":"shaunpwilkinson","id":10361217,"node_id":"MDQ6VXNlcjEwMzYxMjE3","avatar_url":"https://avatars0.githubusercontent.com/u/10361217?v=4","gravatar_id":"","url":"https://api.github.com/users/shaunpwilkinson","html_url":"https://github.com/shaunpwilkinson","followers_url":"https://api.github.com/users/shaunpwilkinson/followers","following_url":"https://api.github.com/users/shaunpwilkinson/following{/other_user}","gists_url":"https://api.github.com/users/shaunpwilkinson/gists{/gist_id}","starred_url":"https://api.github.com/users/shaunpwilkinson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/shaunpwilkinson/subscriptions","organizations_url":"https://api.github.com/users/shaunpwilkinson/orgs","repos_url":"https://api.github.com/users/shaunpwilkinson/repos","events_url":"https://api.github.com/users/shaunpwilkinson/events{/privacy}","received_events_url":"https://api.github.com/users/shaunpwilkinson/received_events","type":"User","site_admin":false},"labels":[{"id":204814757,"node_id":"MDU6TGFiZWwyMDQ4MTQ3NTc=","url":"https://api.github.com/repos/ropensci/onboarding/labels/6/approved","name":"6/approved","color":"F9886C","default":false},{"id":185501572,"node_id":"MDU6TGFiZWwxODU1MDE1NzI=","url":"https://api.github.com/repos/ropensci/onboarding/labels/package","name":"package","color":"fbca04","default":false},{"id":799683666,"node_id":"MDU6TGFiZWw3OTk2ODM2NjY=","url":"https://api.github.com/repos/ropensci/onboarding/labels/topic:phylogenetics","name":"topic:phylogenetics","color":"e99695","default":false}],"state":"open","locked":false,"assignee":{"login":"sckott","id":577668,"node_id":"MDQ6VXNlcjU3NzY2OA==","avatar_url":"https://avatars1.githubusercontent.com/u/577668?v=4","gravatar_id":"","url":"https://api.github.com/users/sckott","html_url":"https://github.com/sckott","followers_url":"https://api.github.com/users/sckott/followers","following_url":"https://api.github.com/users/sckott/following{/other_user}","gists_url":"https://api.github.com/users/sckott/gists{/gist_id}","starred_url":"https://api.github.com/users/sckott/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sckott/subscriptions","organizations_url":"https://api.github.com/users/sckott/orgs","repos_url":"https://api.github.com/users/sckott/repos","events_url":"https://api.github.com/users/sckott/events{/privacy}","received_events_url":"https://api.github.com/users/sckott/received_events","type":"User","site_admin":false},"assignees":[{"login":"sckott","id":577668,"node_id":"MDQ6VXNlcjU3NzY2OA==","avatar_url":"https://avatars1.githubusercontent.com/u/577668?v=4","gravatar_id":"","url":"https://api.github.com/users/sckott","html_url":"https://github.com/sckott","followers_url":"https://api.github.com/users/sckott/followers","following_url":"https://api.github.com/users/sckott/following{/other_user}","gists_url":"https://api.github.com/users/sckott/gists{/gist_id}","starred_url":"https://api.github.com/users/sckott/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sckott/subscriptions","organizations_url":"https://api.github.com/users/sckott/orgs","repos_url":"https://api.github.com/users/sckott/repos","events_url":"https://api.github.com/users/sckott/events{/privacy}","received_events_url":"https://api.github.com/users/sckott/received_events","type":"User","site_admin":false}],"milestone":null,"comments":25,"created_at":"2018-04-24T06:06:32Z","updated_at":"2018-06-12T22:15:13Z","closed_at":null,"author_association":"NONE","body":"### Summary\r\n\r\n-   What does this package do? (explain in 50 words or less):\r\n\r\nThe phylogram R package is a tool for for developing  phylogenetic trees as deeply-nested lists known as \"dendrogram\" objects. It provides functions for importing and exporting trees in  parenthetic text format, as well as several tools for command-line tree manipulation and conversion between \"dendrogram\" and \"phylo\" class objects.\r\n\r\n-   Paste the full DESCRIPTION file inside a code block below:\r\n\r\n```\r\nPackage: phylogram\r\nType: Package\r\nTitle: Dendrograms for Evolutionary Analysis\r\nVersion: 2.0.1.9000\r\nAuthors@R: person(\"Shaun\", \"Wilkinson\", role = c(\"aut\", \"cre\"),\r\n                     email = \"shaunpwilkinson@gmail.com\")\r\nAuthor: Shaun Wilkinson [aut, cre]\r\nMaintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>\r\nDescription: Contains functions for importing and exporting 'dendrogram' \r\n    objects in parenthetic text format, as well as several \r\n    functions for command-line tree manipulation.\r\nLicense: GPL-3\r\nLazyData: TRUE\r\nURL: http://github.com/shaunpwilkinson/phylogram\r\nBugReports: http://github.com/shaunpwilkinson/phylogram/issues\r\nEncoding: UTF-8\r\nDepends:\r\n    R (>= 3.0.0),\r\n    methods,\r\n    stats\r\nImports:\r\n    ape (>= 4.0),\r\nSuggests:\r\n    knitr,\r\n    rmarkdown,\r\n    testthat\r\nRoxygenNote: 6.0.1\r\nVignetteBuilder: knitr\r\n```\r\n\r\n-   URL for the package (the development repository, not a stylized html page):\r\n\r\nhttps://github.com/shaunpwilkinson/phylogram\r\n\r\n- Please indicate which category or categories from our [package fit policies](https://github.com/ropensci/onboarding/blob/master/policies.md#package-fit) this package falls under ***and why**(? (e.g., data retrieval, reproducibility. If you are unsure, we suggest you make a pre-submission inquiry.):\r\n\r\n[e.g., \"data extraction, because the package parses a scientific data file format\"]\r\n\r\nData extraction, the package contains a text parser for trees in the Newick parenthetic text format, and functions for converting between dendrogram and phylo object types.\r\n\r\n-   Who is the target audience and what are scientific applications of this package?  \r\n\r\nBiologists and bioinformaticists wishing to access the many analytical and tree-visualization functions available for dendrogram objects in R. \r\n\r\n-   Are there other R packages that accomplish the same thing? If so, how does\r\nyours differ or meet [our criteria for best-in-category](https://github.com/ropensci/onboarding/blob/master/policies.md#overlap)?\r\n\r\nThere are other packages that can parse Newick strings to create phylo objects (e.g. ape, ggtree) but none that we are aware of that enable two-way conversion between phylo and dendrogram objects.\r\n\r\n-   If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.\r\n\r\n### Requirements\r\n\r\nConfirm each of the following by checking the box.  This package:\r\n\r\n- [x] does not violate the Terms of Service of any service it interacts with. \r\n- [x] has a CRAN and OSI accepted license.\r\n- [x] contains a README with instructions for installing the development version. \r\n- [x] includes documentation with examples for all functions.\r\n- [x] contains a vignette with examples of its essential functions and uses.\r\n- [x] has a test suite.\r\n- [x] has continuous integration, including reporting of test coverage, using services such as Travis CI, Coveralls and/or CodeCov.\r\n- [x] I agree to abide by [ROpenSci's Code of Conduct](https://github.com/ropensci/onboarding/blob/master/policies.md#code-of-conduct) during the review process and in maintaining my package should it be accepted.\r\n\r\n#### Publication options\r\n\r\n- [x] Do you intend for this package to go on CRAN?  \r\n- [x] Do you wish to automatically submit to the [Journal of Open Source Software](http://joss.theoj.org/)? If so:\r\n    - [x] The package has an **obvious research application** according to [JOSS's definition](http://joss.theoj.org/about#submission_requirements).\r\n    - [x] The package contains a `paper.md` matching [JOSS's requirements](http://joss.theoj.org/about#paper_structure) with a high-level description in the package root or in `inst/`.\r\n    - [x] The package is deposited in a long-term repository with the DOI: 10.5281/zenodo.1227670\r\n    - (*Do not submit your package separately to JOSS*)\r\n- [ ] Do you wish to submit an Applications Article about your package to [Methods in Ecology and Evolution](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/)? If so:\r\n    - [ ] The package is novel and will be of interest to the broad readership of the journal. \r\n    - [ ] The manuscript describing the package is no longer than 3000 words.\r\n    - [ ] You intend to archive the code for the package in a long-term repository which meets the requirements of the journal (see [MEE's Policy on Publishing Code](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/journal-resources/policy-on-publishing-code.html))\r\n    - (*Scope: Do consider MEE's [Aims and Scope](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/aims-and-scope/read-full-aims-and-scope.html) for your manuscript. We make no gaurantee that your manuscript willl be within MEE scope.*)\r\n    - (*Although not required, we strongly recommend having a full manuscript prepared when you submit here.*)\r\n    - (*Please do not submit your package separately to Methods in Ecology and Evolution*)\r\n\r\n### Detail\r\n\r\n- [x] Does `R CMD check` (or `devtools::check()`) succeed?  Paste and describe any errors or warnings:\r\n\r\nNo errors or warnings.\r\n\r\n- [x] Does the package conform to [rOpenSci packaging guidelines](https://github.com/ropensci/onboarding/blob/master/packaging_guide.md)? Please describe any exceptions:\r\n\r\n- If this is a resubmission following rejection, please explain the change in circumstances:\r\n\r\n- If possible, please provide recommendations of reviewers - those with experience with similar packages and/or likely users of your package - and their GitHub user names:\r\n\r\nTal Galili (talgalili)\r\nZuguang Gu (jokergoo)\r\nMichael Krabbe Borregaard (mkborregaard)\r\nGuangchuang Yu (GuangchuangYu)\r\n\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/ropensci/onboarding/issues/comments/396751964","html_url":"https://github.com/ropensci/onboarding/issues/212#issuecomment-396751964","issue_url":"https://api.github.com/repos/ropensci/onboarding/issues/212","id":396751964,"node_id":"MDEyOklzc3VlQ29tbWVudDM5Njc1MTk2NA==","user":{"login":"sckott","id":577668,"node_id":"MDQ6VXNlcjU3NzY2OA==","avatar_url":"https://avatars1.githubusercontent.com/u/577668?v=4","gravatar_id":"","url":"https://api.github.com/users/sckott","html_url":"https://github.com/sckott","followers_url":"https://api.github.com/users/sckott/followers","following_url":"https://api.github.com/users/sckott/following{/other_user}","gists_url":"https://api.github.com/users/sckott/gists{/gist_id}","starred_url":"https://api.github.com/users/sckott/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sckott/subscriptions","organizations_url":"https://api.github.com/users/sckott/orgs","repos_url":"https://api.github.com/users/sckott/repos","events_url":"https://api.github.com/users/sckott/events{/privacy}","received_events_url":"https://api.github.com/users/sckott/received_events","type":"User","site_admin":false},"created_at":"2018-06-12T22:15:13Z","updated_at":"2018-06-12T22:15:13Z","author_association":"MEMBER","body":"Nah, seems good as is. \r\n\r\n----\r\n\r\nApproved!  Thanks again for your submission @shaunpwilkinson  \r\n\r\n* Please transfer the package  to `ropensci`- I've invited you to a team within our ropensci organization. After you accept you should be able to move it. You'll be made admin once you do.* Make sure to \r\n* Make sure to \r\n    * add rOpenSci footer to README\r\n`[![ropensci_footer](https://ropensci.org/public_images/ropensci_footer.png)](https://ropensci.org)`\r\n    * Change any needed links, such those for CI badges\r\n    * Travis CI should update to the new location automatically - you may have to update other CI systems manually\r\n* In a new `.github` folder in the root of the pkg, add a `CONTRIBUTING.md` file, an issue template file, and a PR template file, see https://github.com/ropensci/dotgithubfiles/ for examples, you can copy them directly and edit as you wish\r\n* We're starting to roll out software metadata files to all ropensci pkgs via the Codemeta initiative, see  https://github.com/ropensci/codemetar/#codemetar  for how to include it in your pkg, after installing the pkg - should be easy as running `codemetar::write_codemeta()` in the root of your pkg\r\n* For the MEE paper, go ahead now and submit your manuscript to MEE if you haven't already. They tell me there's an option to say the software has been reviewed by ropensci in their submission template\r\n* For JOSS:\r\n    * After you transfer the repo, i'll add a Zenodo webhoook to your repo. After that, generate a new release associated with a git tag in your repo. This doesn't mean you have to submit to CRAN with that git tag/release, its just to get a Zenodo DOI - and you can put a zenodo badge in your readme, then after each git tag it will generate a new Zenodo release\r\n    * Then submit your `paper.md` to JOSS at http://joss.theoj.org/papers/new\r\n\r\n---\r\n\r\n* Are you interested in doing a blog post for our blog https://ropensci.org/blog/ ?  either a short-form intro to it (https://ropensci.org/technotes/) or long-form post with more narrative about its development (https://ropensci.org/blog/). If so, we'll have our community manager @stefaniebutland get in touch with you on that"}}
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