treeio for parsing and exporting phylogenetic trees

[GuangchuangYu]

Summary

• What does this package do? (explain in 50 words or less):

Parsing and exporting phylogenetic trees with associated data.

• Paste the full DESCRIPTION file inside a code block below:

Package: treeio
Title: Base Classes and Functions for Phylogenetic Tree Input and Output
Version: 1.3.10
Authors@R: c(
    person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6485-8781")),
    person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com",   role = c("aut", "ths")),
    person("Casey", "Dunn",         email = "casey_dunn@brown.edu",    role = "ctb"),
    person("Bradley", "Jones",      email = "brj1@sfu.ca",             role = "ctb")
	  )
Description: Base classes and functions for parsing and exporting phylogenetic trees. 'treeio' supports parsing analysis findings from commonly used software packages, allows linking exteranl data to phylogeny and merging tree data obtained from different sources. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file.
Depends:
    R (>= 3.4.3)
Imports:
    ape,
    dplyr,
    jsonlite,
    magrittr,
    methods,
    rvcheck,
    tibble,
    tidytree (>= 0.1.6)
Suggests:
    ggplot2,
    ggtree,
    knitr,
    prettydoc,
    testthat,
    tidyr
VignetteBuilder: knitr
ByteCompile: true
License: Artistic-2.0
URL: https://guangchuangyu.github.io/treeio
BugReports: https://github.com/GuangchuangYu/treeio/issues
Encoding: UTF-8
LazyData: true
biocViews: Software, Annotation, Clustering, DataImport, DataRepresentation,
    Alignment, MultipleSequenceAlignment
RoxygenNote: 6.0.1

• URL for the package (the development repository, not a stylized html page):

https://github.com/GuangchuangYu/treeio

• Please indicate which category or categories from our package fit policies this package falls under *and why(? (e.g., data retrieval, reproducibility. If you are unsure, we suggest you make a pre-submission inquiry.):

data extraction

[e.g., "data extraction, because the package parses a scientific data file format"]

•   Who is the target audience and what are scientific applications of this package?  

Researchers doing ecology and evolution.

• Are there other R packages that accomplish the same thing? If so, how does
  yours differ or meet our criteria for best-in-category?

No.

•   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.

No.

Requirements

Confirm each of the following by checking the box. This package:

• does not violate the Terms of Service of any service it interacts with.
• has a CRAN and OSI accepted license.
• contains a README with instructions for installing the development version.
• includes documentation with examples for all functions.
• contains a vignette with examples of its essential functions and uses.
• has a test suite.
• has continuous integration, including reporting of test coverage, using services such as Travis CI, Coeveralls and/or CodeCov.
• I agree to abide by ROpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

Publication options

• Do you intend for this package to go on CRAN?
• Do you wish to automatically submit to the Journal of Open Source Software? If so:
  • The package has an obvious research application according to JOSS's definition.
  • The package contains a paper.md matching JOSS's requirements with a high-level description in the package root or in inst/.
  • The package is deposited in a long-term repository with the DOI:
  • (Do not submit your package separately to JOSS)
• Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:
  • The package is novel and will be of interest to the broad readership of the journal.
  • The manuscript describing the package is no longer than 3000 words.
  • You intend to archive the code for the package in a long-term repository which meets the requirements of the journal.
  • (Please do not submit your package separately to Methods in Ecology and Evolution)

Detail

• Does R CMD check (or devtools::check()) succeed? Paste and describe any errors or warnings:

• Does the package conform to rOpenSci packaging guidelines? Please describe any exceptions:

• If this is a resubmission following rejection, please explain the change in circumstances:

No.

• 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:

[sckott]

Hi @GuangchuangYu - Thanks very much for your submission. I'll report back with an editor check shortly

[sckott]

Editor checks:

• Fit: The package meets criteria for fit and overlap
• Automated tests: Package has a testing suite and is tested via Travis-CI or another CI service.
• License: The package has a CRAN or OSI accepted license
• Repository: The repository link resolves correctly
• Archive (JOSS only, may be post-review): The repository DOI resolves correctly
• Version (JOSS only, may be post-review): Does the release version given match the GitHub release (v1.0.0)?

---

Editor comments

Thanks for your submission @GuangchuangYu !!

• I do believe Artistic is a CRAN accepted license and a OSI accepted license, can you check that box?
• It looks like you have continuous integration with Bioconductor and Appveyor, so can check that box as well.
• I see you checked the submit to MEE box. This is our first one!
• You can put a ropensci review badge in your README

[![](https://badges.ropensci.org/179_status.svg)](https://github.com/ropensci/onboarding/issues/179)

• Goodpractice output for you and reviewers to consider:

It is good practice to

  ✖ write unit tests for all functions, and all package code
    in general. 7% of code lines are covered by test cases.

    R/AllGenerics.R:12:NA
    R/AllGenerics.R:26:NA
    R/ancestor.R:5:NA
    R/ancestor.R:6:NA
    R/ancestor.R:7:NA
    ... and 1326 more lines

  ✖ use '<-' for assignment instead of '='. '<-' is the
    standard, and R users and developers are used it and it is easier
    to read your code for them if you use '<-'.

    R/hyphy.R:205:18
    R/hyphy.R:207:18
    R/jtree.R:66:20
    R/jtree.R:68:21
    R/jtree.R:69:22
    ... and 50 more lines

  ✖ avoid long code lines, it is bad for readability. Also,
    many people prefer editor windows that are about 80 characters
    wide. Try make your lines shorter than 80 characters

    R/AllGenerics.R:26:1
    R/beast.R:136:1
    R/beast.R:199:1
    R/beast.R:206:1
    R/beast.R:239:1
    ... and 45 more lines

  ✖ avoid sapply(), it is not type safe. It might return a
    vector, or a list, depending on the input data. Consider using
    vapply() instead.

    R/beast.R:71:14
    R/beast.R:97:16
    R/beast.R:233:21
    R/beast.R:239:19
    R/beast.R:279:11
    ... and 16 more lines

  ✖ avoid 1:length(...), 1:nrow(...), 1:ncol(...),
    1:NROW(...) and 1:NCOL(...) expressions. They are error prone and
    result 1:0 if the expression on the right hand side is zero. Use
    seq_len() or seq_along() instead.

    R/method-groupOTU.R:61:19
    R/write-beast.R:88:25
    R/write-beast.R:160:15
    tests/testthat/test-nhx.R:75:25

During check:

* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘CONTRIBUTORS.md’

Seeking reviewers now 🕐

---

Reviewers: @uyedaj @fmichonneau
Due date: 2018-02-06

[GuangchuangYu]

thanks @sckott !

I have checked all the boxes you mentioned and add ropensci badge on README.md.

[GuangchuangYu]

current goodpractice output

It is good practice to

  ✖ write unit tests for all functions, and all package code
    in general. 71% of code lines are covered by test cases.

    R/beast.R:23:NA
    R/beast.R:24:NA
    R/beast.R:25:NA
    R/beast.R:26:NA
    R/beast.R:81:NA
    ... and 411 more lines