pathviewR: Tools to import, clean, and visualize animal movement data in R · Issue #409 · ropensci/software-review (original) (raw)

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.

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