submission - treestartr

[wrightaprilm]

Summary

• What does this package do? (explain in 50 words or less):
  This package helps users to build a reasonable starting phylogeny for phylogenetic analysis.
  In particular, this package allows researchers to add tips to a tree through either a graphical
  user interface, an automated system based on taxonomy, or by inputting a dataframe of taxa to
  be placed.

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

Package: treestartr
Type: Package
Title: Generate Starting Trees For Combined Molecular, Morphological and Stratigraphic Data
Version: 0.1.0
Authors@R: person("April", "Wright", role = c("aut", "cre"),
	email = "april.wright@selu.edu")
Description: Combine a list of taxa with a phylogeny to generate a starting tree for use in
    total evidence dating analyses.
URL: https://wrightaprilm.github.io/treeStartR/
BugReports: https://github.com/wrightaprilm/treeStartR/issues
License: MIT + file LICENSE
Depends:
	R (>= 3.0.0)
Imports:
	phytools (>= 0.6-4),
	ape
Suggests:
    knitr,
    testthat,
    covr,
    utils
VignetteBuilder: utils
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1

• URL for the package (the development repository, not a stylized html page):
  https://github.com/wrightaprilm/treeStartR

• 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.):

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

data munging, combining data sources for use with phylogenetic analysis programs (in particular RevBayes & Mr. Bayes)

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

As the complexity of phylogenetic models increases, it can be difficult to find starting phylogenetic trees for Bayesian MCMC that have computable likelihoods. Most programs start from a random addition tree, which, for large datasets, may not produce reasonable likelihoods. Most software allows users to input a starting tree. The starting tree is often gleaned from the literature. However, for people performing "total evidence" or "joint" phylogenetic analysis, there may not be a published tree with all the relevant taxa. This package allows users to easily create one. Fossil record taxa are commonly left off phylogenies, so I expect biologists and paleontologists working with fossils to be the chief users of this package.

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

Not to my knowledge.

• 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.

Emailed @sckott to discuss how to know if the package is ready, and if reviewers can help with a WARNING, but did not discuss specific scope questions.

Requirements

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

• [x ] 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.
• 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 (see MEE's Policy on Publishing Code)
  • (Scope: Do consider MEE's Aims and Scope for your manuscript. We make no gaurantee that your manuscript willl 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)

Detail

• Does R CMD check (or devtools::check()) succeed? Paste and describe any errors or warnings:
  I have two, and I'm unsure what they mean:

Undocumented code objects:
‘absent_list’ ‘ant_mrca_df’ ‘ant_taxa’ ‘ant_tree’ ‘mm’ ‘mol’
‘mrca_df’ ‘new_tree’ ‘tax_file’ ‘tax_list’ ‘tree’
Files in the 'vignettes' directory but no files in 'inst/doc':
‘vignette.Rmd’, ‘vignette.pdf’

• 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:

• 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:

Klaus Schliep - KlausVigo
David Bapst - dwbapst
Rachel Warnock - rachelwarnock

[sckott]

thanks for your submission @wrightaprilm !

Doing editor checks right now. On trying to install I get

➜  treeStartR git:(master) Rscript -e 'library(devtools); document(); install()'
Updating treestartr documentation
Loading treestartr
Error: 'ants' is not an exported object from 'namespace:treestartr'

can you fix? then i'll continue with editor checks

[wrightaprilm]

I misunderstood some stuff about data packaging. But I think it's working now!

[wrightaprilm]

Quick question - a user noted a (both run time and unit) test I should add for their use case, and I have added it. Should I push that now, or wait?

[sckott]

Yes, go ahead! Let me know when that's pushed

[wrightaprilm]

Alright, pushed.
Thanks!

[sckott]

thanks!, will have another look

[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 @wrightaprilm !

Here's the output from goodpractice. If you haven't used goodpractice it's an R package that checks a number of things with another package - most of which we agree with and want authors to follow. You don't need to address these now, it's info for reviewers to use to get started.

── GP treestartr ─────────
It is good practice to

  ✖ write unit tests for all functions, and all package code in general. 76% of code lines are covered by test cases.

    R/absent_tippR.R:15:NA
    R/absent_tippR.R:16:NA
    R/absent_tippR.R:19:NA
    R/absent_tippR.R:21:NA
    R/absent_tippR.R:22:NA
    ... and 28 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/taxon_testr.R:11:1
    R/tree_df.R:20:1

  ✖ 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/make_absent_df.R:14:23
    R/tree_df.R:24:21

  ✖ not import packages as a whole, as this can cause name clashes between the imported packages. Instead, import only the specific functions you need.
  ✖ fix this R CMD check NOTE: absent_tippr: no visible global function definition for ‘plot’ dataf_parsr: no visible global function definition for
    ‘read.csv’ test_dataf: no visible global function definition for ‘assert_that’ Undefined global functions or variables: assert_that plot read.csv Consider
    adding importFrom("graphics", "plot") importFrom("utils", "read.csv") to your NAMESPACE file.
  ✖ fix this R CMD check WARNING: Undocumented code objects: ‘absent_list’ ‘absent_tippr’ ‘dataf_parsr’ ‘genera_strippr’ ‘mrca_df’ ‘present_tippr’
    ‘rand_absent_tippr’ ‘text_placr’ ‘tree’ Undocumented data sets: ‘absent_list’ ‘mrca_df’ ‘tree’ All user-level objects in a package should have documentation
    entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
  ✖ fix this R CMD check WARNING: Data with usage in documentation object 'ants' but not in code: ants

Seeking reviewers now 🕐

---

Reviewers:

• @dwbapst due date 2018-08-27
• @rachelwarnock due ddate 2018-08-31