Submission: workloopR

[vbaliga]

Submitting Author: Vikram B. Baliga (@vbaliga)
Repository: https://github.com/vbaliga/workloopR
Version submitted: 1.0.0
Editor: @lmullen
Reviewer 1: @jromanowska
Reviewer 2: @eebrown
Archive: TBD
Version accepted: TBD

---

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

Package: workloopR
Type: Package
Title: Analysis of Work Loops and Other Data from Muscle Physiology Experiments
Version: 1.0.0
Authors@R: c(
    person("Vikram B.", "Baliga",
        email = "vbaliga87@gmail.com",
        role = c("cre", "aut"),
        comment = c(ORCID = "0000-0002-9367-8974")),
    person("Shreeram", "Senthivasan",
        email = "shreeramsenthi@gmail.com",
        role = "aut",
        comment = c(ORCID = "0000-0002-7118-9547")))
Author: Vikram B. Baliga [cre, aut] (<https://orcid.org/0000-0002-9367-8974>),
    Shreeram Senthivasan [aut] (<https://orcid.org/0000-0002-7118-9547>)
Maintainer: Vikram B. Baliga <vbaliga87@gmail.com>
Description: Functions for the import, transformation, and analysis of data from muscle physiology experiments. The work loop technique is used to evaluate the mechanical work and power output of muscle. Josephson (1985) <https://jeb.biologists.org/content/114/1/493> modernized the technique for application in comparative biomechanics. Although our initial motivation was to provide functions to analyze work loop experiment data, as we developed the package we incorporated the ability to analyze data from experiments that are often complementary to work loops. There are currently three supported experiment types: work loops, simple twitches, and tetanus trials. Data can be imported directly from .ddf files or via an object constructor function. Through either method, data can then be cleaned or transformed via methods typically used in studies of muscle physiology. Data can then be analyzed to determine the timing and magnitude of force development and relaxation (for isometric trials) or the magnitude of work, net power, and instantaneous power among other things (for work loops). Although we do not provide plotting functions, all resultant objects are designed to be friendly to visualization via either base-R plotting or 'tidyverse' functions.
URL: https://github.com/vbaliga/workloopR
BugReports:https://github.com/vbaliga/workloopR/issues
Imports:
    pracma (>= 2.0.7),
    signal (>= 0.7-6)
Suggests:
    testthat (>= 2.1.1),
    knitr,
    rmarkdown
License: GPL (>= 3) + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1.9000
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
  • reproducibility
  • geospatial data
  • text analysis

• Explain how and why the package falls under these categories (briefly, 1-2 sentences):
  This package offers the ability to import data from specialized file formats (including .ddf) that contain data from muscle physiology experiments. Data can then be transformed, re-organized, and analyzed according to methods typically used in studies of muscle physiology.

• Who is the target audience and what are scientific applications of this package?
  Muscle physiologists or any other researchers interested in characterizing the properties of muscular tissue.

• Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?
  We know of no other packages in R that handle work loop and related data sets.

• 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.

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• 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.

[lmullen]

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)?

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Editor comments

@vbaliga Thank you for your submission. I am currently looking for suitable reviewers. The review will begin when we have both in place.

In the meantime, here are a few things that you can work on.

• Please run spelling::spell_check_package() in your package. I note a few genuine misspellings (and of course false positives).

Otherwise R CMD check looks very clean.

More TK.

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Reviewers: @jromanowska @eebrown
Due date: 2019-10-21

[vbaliga]

@lmullen Thank you for your feedback.

We used the spelling::spell_check_package() and took care of the misspellings throughout the package. The remaining items returned by that function are all proper nouns, specialized terms, and other false positives. We also fixed a few formatting issues in the package documentation. All changes are available now in the latest commit.

With respect to your editor checks, would you recommend that we deposit our package in a repository (e.g. figshare) after the review process? We are interested in submitting to JOSS and want to make sure we are taking the right steps. Please let me know if JOSS review is contingent on having the package in a repository.

Thanks!

[lmullen]

@vbaliga I generally think it is much easier to do the archival version of the package once the review is done. Doubtless the reviewers will make changes, and you can sync up the reviewed version, the CRAN version, and the figshare version if the package is accepted.

[vbaliga]

@lmullen Sounds good - thanks!

[shreeramsenthi]

Hi @lmullen, have there been any updates on finding potential reviewers? Thanks!

[lmullen]

@shreeramsenthi Yes, we are working on it. Please pardon the delay.

[shreeramsenthi]

@lmullen No problem at all. Thanks for the update!

[sckott]

@shreeramsenthi been helping out trying to find reviewers, no luck yet. Do any of the workloopR authors have suggestions for reviewers?

[sckott]

reviewers are @eebrown and @jromanowska - due date 2019-10-21

[vbaliga]

@sckott and @lmullen thank you!