Submission: treedata.table

[uyedaj]

Submitting Author: Josef C Uyeda (@uyedaj)
Repository: https://github.com/uyedaj/treedata.table
Version submitted: 0.1.0
Editor: @jooolia
Reviewer 1: @Bisaloo
Reviewer 2: @karinorman
Archive: TBD
Version accepted: TBD

---

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

Package: treedata.table
Type: Package
Title: A Wrapper For data.table For Fast Manipulation Of Phylogenetic Trees Matched To Data
Version: 0.1.0
Authors@R: c(
    person("Josef Uyeda", email= "juyeda@vt.edu", role=c("aut", "cre")),
    person("Cristian Roman-Palacios", email= "cromanpa94@email.arizona.edu", role=c("aut")), 
    person("April Wright", email= "april.wright@southeastern.edu", role=c("aut"))
  )
Maintainer: Cristian Roman-Palacios <cromanpa94@email.arizona.edu>
Description: This package combines trait data and a phylogenetic tree (or trees) into a 
    single object of class treedata.table. The resulting object can be easily 
    manipulated to simultaneously change the trait- and tree-level sampling.
    Currently implemented functions allow users to use a data.table syntax when
    performing operations on the trait dataset within the treedata.table object.
License: MIT + file LICENSE
Depends:
  data.table, R (>= 2.10)
Imports:
  lazyeval, ape, geiger, utils
RoxygenNote: 6.1.1
Suggests: 
    knitr,
    rmarkdown,
    testthat
VignetteBuilder: knitr

Scope

• Please indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):

  • data retrieval
  • data extraction
  • database access
  • data munging
  • data deposition
  • workflow automation
  • version control
  • citation management and bibliometrics
  • scientific software wrappers
  • database software bindings
  • geospatial data
  • text analysis

• Explain how and why the package falls under these categories (briefly, 1-2 sentences):
  The package allows manipulation of data frames with data.table while maintaining a matched ordering to an ape phylogenetic tree. This allows rapid data munging without worrying about a
  mismatch with the tree order.

• Who is the target audience and what are scientific applications of this package?
  Researchers doing phylogenetic analyses.

• Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?
  treeplyr works similarly but is built on the package dplyr rather than data.table, which has some advantages to dplyr.

• 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.

Technical checks

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, Coveralls and/or CodeCov.

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:

JOSS Options

• 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:

MEE Options

• 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 (see MEE's Policy on Publishing Code)
• (Scope: Do consider MEE's Aims and Scope for your manuscript. We make no guarantee that your manuscript will be within MEE scope.)
• (Although not required, we strongly recommend having a full manuscript prepared when you submit here.)
• (Please do not submit your package separately to Methods in Ecology and Evolution)

Code of conduct

• I agree to abide by rOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

[maelle]

👋 @uyedaj! Thanks for your submission and sorry for the delay. I'll assign an editor to this submission shortly, who'll get started on the editor checks next week at the latest.

[jooolia]

Hi @uyedaj!
Thanks for the submission and for your work on this package. I will be your editor for this submission. I have done a few of the initial editor checks.

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 (updated 20 June 2020)
• Repository: The repository link resolves correctly (updated 20 June 2020)
• 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

• For the licence, the description says MIT, but the LICENCE file is not complete. This needs to be completed.
• I found the repository to be https://github.com/uyedaj/treedata.table, could you add the link at the top of the submission info so that it is easier to find the repo?
• Spell-checking: Looks good.
• Below are some automated checks performed on the package. Please address those without the tag reviewers.

goodpractice::gp output
── GP treedata.table

 It is good practice to

✖ write unit tests for all functions, and all package code in
 general. 34% of code lines are covered by test cases.

 R/as.treedata.table.R:40:NA
 R/as.treedata.table.R:43:NA
 R/as.treedata.table.R:44:NA
 R/as.treedata.table.R:49:NA
 R/as.treedata.table.R:55:NA
 ... and 151 more lines

• reviewers will determine if this appropriate amount of test coverage

• not use "Depends" in DESCRIPTION, as it can cause name clashes, and
  poor interaction with other packages. Use "Imports" instead.
  This can be argued if necessary. For more info see http://r-pkgs.had.co.nz/description.html

• add a "URL" field to DESCRIPTION. It helps users find information
  about your package online. If your package does not have a
  homepage, add an URL to GitHub, or the CRAN package package page. (Updated 20 June 2020)

• add a "BugReports" field to DESCRIPTION, and point it to a bug
  tracker. Many online code hosting services provide bug trackers for
  free, https://github.com, https://gitlab.com, etc. (Updated 20 June 2020)

• 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 '<-'. (Updated 20 June 2020)

  R/detectCharacterType.R:76:8
  R/detectCharacterType.R:104:8
  R/extractVector.R:31:10
  R/tdt_methods.R:16:5
  

• 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/as.treedata.table.R:1:1
  R/as.treedata.table.R:3:1
  R/as.treedata.table.R:4:1
  R/as.treedata.table.R:5:1
  R/as.treedata.table.R:11:1
  ... and 55 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. (Updated 20 June 2020)

  R/as.treedata.table.R:71:16
  R/as.treedata.table.R:118:8
  R/pull.treedata.table.R:20:18
  

• 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. (Updated 20 June 2020)

  R/as.treedata.table.R:59:38
  R/treedata.table.R:67:33
  R/treedata.table.R:69:47
  

• reviewers to consider and give feedback on
  ✖ fix this R CMD check WARNING: LaTeX errors when creating PDF
  version. This typically indicates Rd problems. LaTeX errors found:
  !pdfTeX error: pdflatex (file ts1-zi4r): Font ts1-zi4r at 600 not
  found ==> Fatal error occurred, no output PDF file produced!

• reviewers to consider and give feedback on
  R CMD check ERROR: Error: object 'head' not found whilst loading namespace 'treedata.table'

• avoid 'T' and 'F', as they are just variables which are set to the
  logicals 'TRUE' and 'FALSE' by default, but are not reserved words
  and hence can be overwritten by the user. Hence, one should always
  use 'TRUE' and 'FALSE' for the logicals. (Updated 20 June 2020)

  R/as.treedata.table.R:NA:NA
  R/as.treedata.table.R:NA:NA
  R/tdt_methods.R:NA:NA
  

─────────────────────────────────────────────────────────────

---

I will look for reviewers after these small issues have been addressed. Feel free to let me know if you have any questions.
Thanks! Julia

[wrightaprilm]

Hey team, I have some free time to tackle this tomorrow! I'll push these changes and post an update here then. Thanks @jooolia for getting back with us!

[wrightaprilm]

I think between my commit (7764ef2) and Scott's edit of the initial PR, we should have all these notes handled!

[jooolia]

Thanks @wrightaprilm! I will have a look tomorrow. Cheers, Julia

[noamross]

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[annakrystalli]

⚠️⚠️⚠️⚠️⚠️
In the interest of reducing load on reviewers and editors as we manage the
COVID-19 crisis, rOpenSci new submissions for software peer review are paused.

In this period new submissions will not be handled, nor new reviewers assigned.
Reviews and responses to reviews will be handled on a 'best effort' basis, but
no follow-up reminders will be sent.
Other rOpenSci community activities continue.

Please check back here again after 25 May when we will be announcing plans to slowly start back up.

We express our continued great
appreciation for the work of our authors and reviewers. Stay healthy and take
care of one other.

The rOpenSci Editorial Board
⚠️⚠️⚠️⚠️⚠️

[jooolia]

Hi @wrightaprilm and @uyedaj I will check the changes you made in March and get back to you. Then I will look for reviewers for the package. Thanks for your patience.
Cheers, Julia

[jooolia]

Hi @wrightaprilm and @uyedaj,
We are now looking for reviewers. Please add the rOpenSci review badge to your README.
You can do this with by adding to your README:
[![](https://badges.ropensci.org/367_status.svg)](https://github.com/ropensci/software-review/issues/367)

Thanks! Julia