pathviewR: Tools to import, clean, and visualize animal movement data in R

[vbaliga]

Submitting Author: Name (@vbaliga)
Repository: https://github.com/vbaliga/pathviewr
Version submitted: v0.9.4 (ropensci/pathviewr@6e04870)
Editor: @maelle
Reviewers: @asbonnetlebrun, @marcosci

Due date for @asbonnetlebrun: 2020-12-05

Due date for @marcosci: 2020-12-21
Archive: TBD
Version accepted: TBD

---

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

Package: pathviewr
Title: Wrangle, Analyze, and Visualize Animal Movement Data
Version: 0.9.4
Authors@R: 
    c(person(given = "Melissa S.", 
             family = "Armstrong",
             role = "aut",
             email = "melissa.armstrong@gmail.com",
             comment = c(ORCID = "0000-0002-3059-0094")),
      person(given = "Vikram B.",
             family = "Baliga", 
             role = c("aut", "cre"),
             email = "vbaliga87@gmail.com",
             comment = c(ORCID = "0000-0002-9367-8974")),
      person(given = "Eric R.", 
             family = "Press",
             role = "aut",
             email = "epress12@gmail.com",
             comment = c(ORCID = "0000-0002-1944-3755"))
      )
Description: Tools to import, clean, and visualize 
    animal movement data from motion capture systems such as Optitrack's 
    Motive, the Straw Lab's Flydra, or from other sources. We provide 
    functions to remove artifacts, standardize tunnel position and tunnel 
    axes, select a region of interest, isolate specific trajectories, fill
    gaps in trajectory data, and calculate 3D and per-axis velocity. For 
    experiments of visual guidance, we also provide functions that use 
    animal position to estimate perception of visual stimuli. 
License: GPL-3
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1.9000
Imports: 
    R.matlab,
    data.table (>= 1.12.2),
    magrittr (>= 1.5),
    dplyr (>= 1.0.0),
    stringr (>= 1.4.0),
    tibble (>= 3.0.1),
    tidyr (>= 1.1.0),
    fANCOVA,
    purrr (>= 0.3.3),
    ggplot2 (>= 3.3.0),
    tidyselect (>= 1.1.0),
    cowplot
Suggests: 
    knitr,
    rmarkdown,
    testthat,
    covr
VignetteBuilder: knitr
URL: https://github.com/vbaliga/pathviewr
BugReports: https://github.com/vbaliga/pathviewr/issues

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):
  pathviewR provides tools to extract data from motion capture software such as Optitrack's Motive and the Straw Lab's Flydra (among other sources). Tools to wrangle and clean data sets to isolate specific trajectories of animal movement are offered, along with the capability to use automated workflows for processing data from high throughput laboratory experiments.

• Who is the target audience and what are scientific applications of this package?
  Users of motion capture software, including researchers who study animal and/or object motion in a laboratory setting, especially for analyses of visual guidance of behavior.

• 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 are not aware of any other R (or otherwise open source) packages that import & wrangle data from Optitrack's Motive or the Straw Lab's Flydra. Although there are other R packages that handle animal movement trajectory data, these packages tend to be geared towards analyses of large-scale, geospatial movement data (e.g. trajectories or various R packages in the AniMove software suite). In contrast, pathviewR specifically targets tracking of animals (or other subjects) in laboratory settings (e.g. in a flight tunnel) and offers tools to estimate visual perceptions as subjects move in relation to their surroundings.

• (If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?
  pathviewR, although not specifically geared towards collecting data from human subjects, is in compliance with rOpenSci's policy.

• 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.

• 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 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.

[maelle]

Thanks @vbaliga and co-authors for your submission! I have a few minor comments/questions below, and will now start looking for reviewers.

Editor checks:

• Documentation: The package has sufficient documentation available online (README, pkgdown docs) to allow for an assessment of functionality and scope without installing the package.
• 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

---

Editor comments

• In https://vbaliga.github.io/pathviewR/articles/data-import-cleaning.html#data-from-other-sources-1 I would expect to read whether you'd welcome additions of further data import functions, and how an user should request/contribute such a function.

• Why is the CITATION TBD, why not add a citation of the manual for now?

• Why do you use so many continuous integration services, since GitHub Actions would handle all operating systems?

---

Reviewers:
Due date:

[maelle]

Please add this badge to the package README

[![](https://badges.ropensci.org/409_status.svg)](https://github.com/ropensci/software-review/issues/409)

[vbaliga]

Hi @maelle,

Thank you for looking over pathviewR and providing us with feedback. My co-authors (@scienceisfiction and @epress12) and I worked together earlier today to address each of your comments, and a few changes to our repo have been made in ropensci/pathviewr@688c198. Here is our reply to each of your specific comments:

In https://vbaliga.github.io/pathviewR/articles/data-import-cleaning.html#data-from-other-sources-1 I would expect to read whether you'd welcome additions of further data import functions, and how an user should request/contribute such a function.

Thanks for pointing this out. We very much welcome users to reach out to us regarding further import functions. We created an Issue template in our repository to allow users to request further import functions, and a link to our Issues templates is now provided in the section of the vignette that you specified.

Why is the CITATION TBD, why not add a citation of the manual for now?

Thanks for catching this! We have now added a citation of the Manual of this package. It appears both as a CITATION file within /inst as well as in the Citation section of our readme.

Why do you use so many continuous integration services, since GitHub Actions would handle all operating systems?

Please forgive our ignorance. We use Travis CI because I had the impression that it was emphasized in the rOpenSci devguide and because of my familiarity with it in authoring a previous rOpenSci package (ropensci/workloopR). We added GitHub Actions because we were interested in seeing what it had to offer. Admittedly, we are less familiar with GitHub Actions' breadth of coverage (moreover, it is a newer service, right?). Would you advise we use only GitHub Actions? Or is it okay that we continue using both Travis CI and GitHub Actions?

Please add this badge to the package README

The badge has been added. Thanks again for considering our package!

Best regards,
Vikram
🐢

[maelle]

👋 @vbaliga, @scienceisfiction and @epress12! Thanks for your work!

• Regarding the issue template, awesome! Would you also welcome people to contribute functions and if so what would be the process? Maybe that could be a question in the template?

• Regarding continuous integration yes that's hard to keep up. In https://devguide.ropensci.org/ci.html#whichci we've now put GitHub Actions first which is admittedly not a very obvious way to recommend it. We recommend it over Travis now because it has all operating systems, and because Travis is changing its pricing. E.g. https://www.jeffgeerling.com/blog/2020/travis-cis-new-pricing-plan-threw-wrench-my-open-source-works And since GitHub Actions has support for Windows, you can do without Appveyor. Hard to tell what we'll all be using in a few years 😅

I've found a reviewer that I'll assign soon, and am still looking for the second reviewer.

[maelle]

Thanks a lot @asbonnetlebrun for agreeing to review! Your review is due on 2020-12-09.

Please find links to our reviewer guide and review template.

[vbaliga]

Hi @maelle,

Thanks very much for your advice. We've expanded our issue template to welcome people to contribute functions and added a question to the template accordingly (see ropensci/pathviewr@7c4c32d). We have also now shifted to using GitHub Actions exclusively for CI using the "standard" check across Mac/Win/Linux and revised our method of updating Codecov through Actions as well (see ropensci/pathviewr@f3a787b).

Thanks again!
Vikram
🐢

[maelle]

Thanks a lot @marcosci for agreeing to review! Your review is due on 2020-12-21.

Please find links to our reviewer guide and review template.

[maelle]

With this, now both reviewers @asbonnetlebrun and @marcosci are assigned. 😸

[stefaniebutland]

Hi @asbonnetlebrun. I'm rOpenSci's Community Manager. If you would like to join our Slack group, please email me at stefanie@ropensci.org; I was not able to find your email address.