Submission: phruta

[cromanpa94]

Date accepted: 2022-12-30
Submitting Author Name: Cristian Román-Palacios
Submitting Author Github Handle: @cromanpa94
Repository: https://github.com/cromanpa94/phruta
Version submitted: 0.1.0
Submission type: Standard
Editor: @annakrystalli
Reviewers: @raynamharris, @fboehm

Due date for @raynamharris: 2021-12-13

Due date for @fboehm: 2021-12-16
Archive: TBD
Version accepted: TBD

---

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

Package: phruta
Type: Package
Title: Phylogenetic Reconstruction and Time-dating
Version: 0.1.0
Authors@R: person("Cristian", "Roman Palacios", email = "cromanpa@g.ucla.edu",
                  role = c("aut", "cre"))
Description: The phruta R package is designed to simplify the basic 
            phylogenetic pipeline. Specifically, all code is run within 
            the same program and data from intermediate steps are saved in 
            independent folders. Furthrmore, all code is run within the 
            same environment which increases the reproducibility of your analysis. 
            phruta retrieves gene sequences, combines newly downloaded and local 
            gene sequences, and performs sequence alignments. 
Encoding: UTF-8
LazyData: true
biocViews: DECIPHER,
           Biostrings
Depends: R (>= 3.5.0)
Imports: 
    rgbif,
    pbapply,
    rentrez,
    taxize,
    ape,
    ips,
    geiger,
    methods,
    DECIPHER,
    Biostrings
RoxygenNote: 7.1.1
Suggests: 
    testthat (>= 3.0.0),
    covr,
    knitr,
    markdown,
    rmarkdown,
    spelling,
    utf8
VignetteBuilder: knitr
License: MIT + file LICENSE
Config/testthat/edition: 3
Language: en-US
Roxygen: list(markdown = TRUE)

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
  • data munging
  • data deposition
  • workflow automation
  • version control
  • citation management and bibliometrics
  • scientific software wrappers
  • field and lab reproducibility tools
  • database software bindings
  • geospatial data
  • text analysis

• Explain how and why the package falls under these categories (briefly, 1-2 sentences):
  phruta simplifies the phylogenetic pipeline in R, increases reproducibility, and helps organizing information used to infer molecular phylogenies. phruta retrieves sequences from genbank, curates the resulting files, perform multiple sequence alignment, and tree inference/dating.

• Who is the target audience and what are scientific applications of this package?
  Researchers, students, instructors, and analysts interesting in assembling phylogenies (and even time-calibrated phylogenies) for specific groups across the Tree of Life.

• Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?
  phylotaR retrieves orthologous clusters for particular clades. However, it has limited flexibility in terms of sampling outgroup taxa and (to my knowledge) does not perform any type of processing after retrieving the clusters.

• (If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?

• If you made a pre-submission inquiry, 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.

• I have read the guide for authors and rOpenSci packaging guide.

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, created with roxygen2.
• 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 intend for this package to go on Bioconductor?

• 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.

[noamross]

@ropensci-review-bot check package

[ropensci-review-bot]

Thanks, about to send the query.

[ropensci-review-bot]

Checks for phruta (v0.1.0)

git hash: 6356b12b

• ✔️ Package uses 'roxygen2'
• ✔️ Package has a 'contributing.md' file
• ✖️ Package does not have a 'CITATION' file
• ✖️ Package does not have a 'codemeta.json' file
• ✔️ All functions have examples
• ✖️ Package 'DESCRIPTION' does not have a URL field
• ✖️ Package 'DESCRIPTION' does not have a BugReports field
• ✔️ Package name is available
• ✖️ Continuous integration checks unavailable (no URL in 'DESCRIPTION')
• ✔️ Package coverage is 78.4%
• ✔️ R CMD check found no errors
• ✔️ R CMD check found no warnings

Important: All failing checks above must be addressed prior to proceeding

Package License: MIT + file LICENSE

---

1. Statistical Properties

This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.

Details of statistical properties (click to open)

The package has:

• code in R (100% in 9 files) and
• 1 authors
• 2 vignettes
• 1 internal data file
• 10 imported packages
• 40 exported functions (median 35 lines of code)
• no non-exported function in R (median 5 lines of code)

---

Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
The following terminology is used:

• loc = "Lines of Code"
• fn = "function"
• exp/not_exp = exported / not exported

The final measure (fn_call_network_size) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile.

measure	value	percentile	noteworthy
files_R	9	51.3
files_vignettes	3	90.8
files_tests	3	71.1
loc_R	311	29.5
loc_vignettes	115	56.3
loc_tests	172	48.4
num_vignettes	2	87.5
data_size_total	79882	82.2
data_size_median	79882	90.5
n_fns_r	40	40.8
n_fns_r_exported	40	83.0
n_fns_r_not_exported	0	0.0	TRUE
n_fns_per_file_r	3	38.6
num_params_per_fn	4	51.5
loc_per_fn_r	8	28.2
loc_per_fn_r_exp	35	70.3
loc_per_fn_r_not_exp	5	17.3
rel_whitespace_R	16	30.1
rel_whitespace_vignettes	92	87.4
rel_whitespace_tests	31	82.3
doclines_per_fn_exp	40	49.4
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	0	0.0	TRUE

---

1a. Network visualisation

Interactive network visualisation of calls between objects in package can be viewed by clicking here

---

2. goodpractice and other checks

Details of goodpractice and other checks (click to open)

---

3b. goodpractice results

R CMD check with rcmdcheck

R CMD check generated the following check_fails:

1. description_url
2. description_bugreports
3. no_import_package_as_a_whole

Test coverage with covr

Package coverage: 78.42

Cyclocomplexity with cyclocomp

No functions have cyclocomplexity >= 15

Static code analyses with lintr

lintr found the following 89 potential issues:

message	number of times
Avoid changing the working directory, or restore it in on.exit	3
Lines should not be more than 80 characters.	86

---

Package Versions

package	version
pkgstats	0.0.0.269
pkgcheck	0.0.1.373

---

Editor-in-Chief Instructions:

Processing may not proceed until the items marked with ✖️ have been resolved.

[mpadge]

@cromanpa94 Please excuse the delayed response. Most of the ROpenSci team were on vacation, and only now able to debug our new package check bot. Current Editor-in-Chief @noamross will respond asap.

[cromanpa94]

Hi @mpadge! No worries! I actually made some updates to the package earlier this month (currently on my dev branch). I will address these issues by the end of this week.

[mpadge]

@cromanpa94 To make editor @annakrystalli's job easier, can you run pkgcheck::pkgcheck() yourself once you've made appropriate changes and confirm the summary at the top (or result of summary() applied to check results) gives all ✔️ and no ✖️? It should also confirm, "This package may be submitted." Thanks!

[annakrystalli]

Thanks for the suggestion @mpadge ! And hello @cromanpa94 👋, I'll be your handling editor.

Let me know when you've resolved the issues in the initial checks and we'll take it from there.

P.S. Φρούτα (frouta in english characters) is also fruit in Greek! 😜

[cromanpa94]

@mpadge: Passing pkgcheck::pkgcheck() checks!! Thank you!

@annakrystalli: Hi there!! Looking forward to working with you! :) The latest version of the package is now live in the repo! Please let me know if there's anything else I should go over before we move on.

P.S. That's amazing!! I'm planning to add more details about the package's name later on! Φρούτα will certainly be there!

[annakrystalli]

@ropensci-review-bot check package

[ropensci-review-bot]

Thanks, about to send the query.