Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from https://github.com/ropensci/software-review/issues/338 below:

baRcodeR Submission · Issue #338 · ropensci/software-review · GitHub

Submitting Author: Yihan Wu (@yihanwu) and Robert Colautti (@ColauttiLab)
Repository: yihanwu/baRcodeR
Version submitted:0.1.4
Editor: @sckott
Reviewer 1: @raynamharris
Reviewer 2: @llrs
Archive: TBD
Version accepted: TBD

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

Package: baRcodeR
Title:  Label Creation for Tracking and Collecting Data from Biological Samples
Version: 0.1.4
Authors@R: 
    c(person(given = "Yihan", 
             family = "Wu", 
             role="aut", 
             email = "yihan.wu@queensu.ca", 
             comment = c(ORCID = "0000-0002-1202-4208")), 
      person(given = "Robert", 
             family = "Colautti", 
             email = "robert.colautti@queensu.ca", 
             role = c("aut", "cre"), 
             comment = c(ORCID = "0000-0003-4213-0711")))
Maintainer: Yihan Wu <yihan.wu@queensu.ca>
Description: Tools to generate unique identifier codes and printable barcoded 
    labels for the management of biological samples. The creation of unique ID 
    codes and printable PDF files can be initiated by standard commands, user 
    prompts, or through a GUI addin for R Studio. Biologically informative codes
    can be included for hierarchically structured sampling designs.
Depends:
    R (>= 3.4.0),
    qrcode
License: file LICENSE
Language: en-CA
Encoding: UTF-8
LazyData: true
Imports:
    DT (>= 0.3),
    grDevices,
    grid,
    miniUI (>= 0.1.1),
    shiny (>= 0.13),
    rstudioapi
Suggests: 
    testthat (>= 2.1.0),
    knitr,
    rmarkdown,
    covr,
    shinytest
RoxygenNote: 6.1.1
VignetteBuilder: knitr
URL: https://github.com/yihanwu/baRcodeR
BugReports: https://github.com/yihanwu/baRcodeR/issues

• 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):

Reproducibility: baRcodeR facilitates the creation of unique text identifier (ID) codes and scannable barcodes (linear and 2D) that can be printed onto customized sticker labels with consumer-grade printers to facilitate management, tracking, and data collection involving biological samples. Unique identifier codes and scannable barcode labels are produced via reproducible code which reduce transcription errors that arise with hand-written labels and manual entry of label codes. In contrast to commercial software, no proprietary hardware is required, labels can be generated automatically with biologically informative coding, and labels can be created from the command line.

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

baRcodeR is designed to minimize bookkeeping errors and to assist researchers who need to track, curate, or measure biological samples. It is particularly well-suited for large collaborative projects with complex sampling design and numerous samples shared among researchers. For example, a large biological research project may have subjects organized as population/treatment-by-family/line-by-time – that is, each subject sampled multiple times and representing a specific family group or genetic line from one or more nested experimental populations or treatments. The custom layout options in baRcodeR allow researchers to rapidly generate meaningful identifier codes that capture the hierarchical sampling structure, and then print customizable labels containing the ID codes as human-readable text with corresponding digital linear or 2D barcodes. The command-line interface also facilitates rapid re-creation of a set of generated identifiers with different sized labels or minor changes to identifier codes – for example, to label multiple tissue collection containers and then later to label test tubes for purified extracts, each with the same basic code with a new code corresponding to sample type.

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

  • zintr creates individual barcode image files but does not include functions for (i) automating the creation of biologically-relevant, unique ID codes or (ii) customizable layouts for printing multiple barcodes.
  • qrcode generates qrcodes and is a dependency for baRcodeR to generate 2D barcodes. However, qrcodes also does not include functions for (i) automating the creation of biologically-relevant, unique ID codes or (ii) customizable layouts for printing multiple barcodes.

• 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.

Presubmission inquiry #336, approved by editor @melvidoni

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.

• 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:

• 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:

• 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)

• I agree to abide by rOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4