Submission: mcbette

[richelbilderbeek]

Submitting Author: Richel Bilderbeek (@richelbilderbeek)
Repository: https://github.com/richelbilderbeek/mcbette
Version submitted: 1.8.2
Editor: @maelle
Reviewer 1: @vbaliga
Reviewer 2: @bjoelle
Archive: TBD
Version accepted: TBD

---

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

Package: mcbette
Title: Model Comparison Using 'babette'
Version: 1.8.2
Authors@R: c(
    person("Richel J.C.", "Bilderbeek", email = "richel@richelbilderbeek.nl", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1107-7049")))
Maintainer: Richel J.C. Bilderbeek <richel@richelbilderbeek.nl>
Description: 'BEAST2' (<http://www.beast2.org>) is a widely used
    Bayesian phylogenetic tool, that uses DNA/RNA/protein data
    and many model priors to create a posterior of jointly estimated 
    phylogenies and parameters.
    'mcbette' allows to do a Bayesian model comparison over some
    site and clock models, 
    using 'babette' (<https://www.github.com/ropensci/babette>).
License: GPL-3
LazyData: true
RoxygenNote: 7.0.2
VignetteBuilder: knitr
URL: https://github.com/richelbilderbeek/mcbette
BugReports: https://github.com/richelbilderbeek/mcbette/issues
Depends:
    babette,
    beautier (>= 2.3),
    beastier (>= 2.0.25),
    mauricer,
    tracerer
Imports:
    knitr,
    Rmpfr,
    testit
Suggests:
    ape,
    devtools,
    ggplot2,
    hunspell,
    lintr,
    nLTT,
    phangorn,
    rappdirs,
    rmarkdown,
    spelling,
    testthat (>= 2.1.0)
Language: en-US
Encoding: UTF-8
SystemRequirements: BEAST2 (http://www.beast2.org/)

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):

mcbette automates a model comparison using the tool 'BEAST2' with one of its packages.

⚠️ because mcbette is a wrapper for 'BEAST2' and because 'BEAST2' does not allow to do what mcbette does on Windows, this package does not work under the Windows operating system.

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

This package aims at scientists in the field of phylogenetics, as it allows to do a Bayesian model comparison of phylogenetic inference models. Or simpler: with mcbette you can pick the best model to build a phylogeny from a DNA sequence.

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

There is some overlap, as model comparison is an important topic in phylogenetics. Unique about mcbette is the way how it does so: it uses a novel 'BEAST2' package (called 'NS', shorthand of 'Nested Sampling') to directly estimate the marginal likelihood (a.k.a. the evidence) of an inference model. Because the technique of Nested Sampling is -in this field- novel, the 'BEAST2' package is novel and mcbette is novel.

• 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/.

I do intend to submit to JOSS, as it looks awesome! Because I did not expect this (for me, new) option, I am not prepared yet. I will await the acceptance of my submission first, than happily write this!

- [ ] The package is deposited in a long-term repository with the DOI: 

Not yet.

- (*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]

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 @richelbilderbeek for your submission! I'm now looking for reviewers.

In the meantime, I have a few comments/questions you can address:

• The link to BEAST2 in DESCRIPTION uses http, please replace it with https <https://www.beast2.org/> (I made a PR). If you used the http link in other packages, you can change it but that is obviously beyond the scope of my checks. 😉

• Have you thought about providing guidance/examples on other CI services e.g. GH actions, Circle CI?

• In the README I think the existence of two modes (online, and offline on Mac and Linux) could be made clearer.

• I made a PR for replacing usethis with remotes in the installation guidelines, which you've merged.

• In the README section about installation, please write how many dependencies in total are needed by the package (I had to install >30 packages) and that rJava and Rmpfr are among them (on e.g. Ubuntu, it means installing system dependencies before installing the R packages),
  to make it less of a surprise.

• In the FAQ, it says the other packages are not on CRAN, but they're on CRAN now, aren't they?

• Why is there no README.Rmd?

• Are your R packages listed somewhere on BEAST2 website?

• I note the JOSS paper.md isn't there yet.

goodpractice output

  ✖ not use "Depends" in DESCRIPTION, as it can cause name clashes, and
    poor interaction with other packages. Use "Imports" instead.
  ✖ not import packages as a whole, as this can cause name clashes between
    the imported packages. Instead, import only the specific functions you need.

What are the reasons for importing the whole packages?

  ✖ fix this R CMD check WARNING: LaTeX errors when creating PDF version.
    This typically indicates Rd problems. LaTeX errors found: ! LaTeX Error: File
    `ltxcmds.sty' not found. Type X to quit or <RETURN> to proceed, or enter new
    name. (Default extension: sty) ! Emergency stop. <read *> l.105
    \RequirePackage{ltxcmds}[2010/11/12] ^^M !  ==> Fatal error occurred, no output
    PDF file produced!

Maybe/probably just a setup thing?

---

Reviewers: @vbaliga @bjoelle
Due date: 2020-03-30

[maelle]

You can now add a review badge rodev::use_review_badge(360).

[maelle]

I forgot a question: why are there expectations in examples? Can't these cases & expectations live in tests?

[maelle]

Reviewer 1: @vbaliga (thanks for agreeing to review!). I'll add a deadline once the second reviewer is assigned.