restez -- submission (original) (raw)

Summary

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

The restez package downloads all or sections of GenBank and creates a local SQLite copy of the database for querying. The package comes with a series of useful functions for querying the database and is designed to work with rentrez.

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

Package: restez
Type: Package
Title: Create and Query a Local Copy of GenBank in R
Version: 0.0.0
Authors@R: person("Dom", "Bennett", role = c("aut", "cre"), email = "dominic.john.bennett@gmail.com")
Maintainer: D.J. Bennett <dominic.john.bennett@gmail.com>
Description: Download large sections of GenBank and generate a local SQL-based
    database. A user can then query this database using restez functions or
    through rentrez wrappers.
URL: https://github.com/AntonelliLab/restez#readme
BugReports: https://github.com/AntonelliLab/restez/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends:
    R (>= 3.3.0)
Imports:
    utils,
    rentrez,
    RSQLite,
    DBI,
    R.utils,
    downloader,
    RCurl,
    cli,
    crayon
Suggests:
    testthat,
    knitr,
    rmarkdown
RoxygenNote: 6.0.1
VignetteBuilder: knitr

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

https://github.com/AntonelliLab/restez

• 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 retrieval, for users that wish to retrieve lots of sequence information and find NCBI's Entrez too slow.

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

Researchers wishing to perform any form of analysis with DNA sequence data. For my own purposes, I will use the package to retrieve large amounts of sequence data for phylogenetic analysis.

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

Hajk-Georg Drost's Biomartr is similar and is in fact the inspiration for restez. It only allows users to download genome specific data, however, not GenBank sequences. From the ecologcial sciences perspective, genome data is just not nearly taxonomically representative enough yet for any questions concerning biodiversity.

• 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.

NA

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, 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.

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  • (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:
• 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:

I imagine the rentrez and biomartr developers to be good reviewers: dwinter and HajkD