baRcodeR Submission

[yihanwu]

---

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

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• 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

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):

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

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.

Publication options

• 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.

[sckott]

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

Thanks for your submission @yihanwu !

Here's the output from goodpractice. You don't need to address these now, it's info for reviewers to use to get started.

── GP baRcodeR ─────────────

It is good practice to

  ✖ write unit tests for all functions, and all package code in general. 94% of code lines are covered by test cases.

    R/hidden_createPDF.R:272:NA
    R/hidden_createPDF.R:307:NA
    R/hidden_createPDF.R:308:NA
    R/hidden_createPDF.R:309:NA
    R/hidden_createPDF.R:310:NA
    ... and 14 more lines

  ✖ write short and simple functions. These functions have high cyclomatic complexity:custom_create_PDF (58).
  ✖ not use "Depends" in DESCRIPTION, as it can cause name clashes, and poor interaction with other packages. Use "Imports" instead.
  ✖ not import packages as a whole, as this can cause name clashes between the imported packages. Instead, import only the specific functions you need.
  ✖ avoid 'T' and 'F', as they are just variables which are set to the logicals 'TRUE' and 'FALSE' by default, but are not reserved words and hence can
    be overwritten by the user.  Hence, one should always use 'TRUE' and 'FALSE' for the logicals.

    R/hidden_createPDF.R:NA:NA
 ───────────────

Seeking reviewers now 🕐

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Reviewers:

• @raynamharris due date 2019-10-01
• @llrs due date 2019-10-01

[sckott]

reviewers are now assigned: @raynamharris & @llrs

[yihanwu]

Great! Thanks @sckott

[raynamharris]

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

• As the reviewer I confirm that there are no conflicts of interest for me to review this work (If you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

• A statement of need clearly stating problems the software is designed to solve and its target audience in README.
• Installation instructions: for the development version of package and any non-standard dependencies in README
• Vignette(s) demonstrating major functionality that runs successfully locally. The vingnette did not load.
• Function Documentation: for all exported functions in R help
• Examples for all exported functions in R Help that run successfully locally
• Community guidelines including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with URL, BugReports and Maintainer (which may be autogenerated via Authors@R).

Functionality

• Installation: Installation succeeds as documented.
• Functionality: Any functional claims of the software been confirmed.
• Performance: Any performance claims of the software been confirmed.
• Automated tests: Unit tests cover essential functions of the package
  and a reasonable range of inputs and conditions. All tests pass on the local machine. Did not perform automated tests
• Packaging guidelines: The package conforms to the rOpenSci packaging guidelines

Final approval (post-review)

• The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: 2 hours

• Should the author(s) deem it appropriate, I agree to be acknowledged as a package reviewer ("rev" role) in the package DESCRIPTION file.

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Review Comments

baRcodeR is an R package that reproducibly creates sample labels. It can be run from the RStudio console or from a GUI Addin. This is the first time I have ever used a GUI or Addin from within RStudio, and it worked very well after restarting R twice. I would recommend this package to my colleagues who do molecular work. Below is a list of minor comments and concerns.

• In the README, there is a "See also:" link to a similar package called zintr, but it is unclear why a user might want to refer to it or why they should chose one over the other or both. A brief elaboration would be helpful. Also, it would be useful to state that Zint is a barcode generator and library.
• I really like the graphical overview and the cheatsheet. These are both very useful. I also like that your cheatsheet is archived in FigShare with a DOI.
• Does this default layout only work with Uline products or is there an Avery alternative?
• In order for the baRcodeR GUI to appear in my Addins window, I had to restart RStudio. Perhaps add a note that you made need to restart R after successful installation of the package.
• The first time I clicked on baRcodeR GUI my R session was aborted. It worked the second time, so maybe add a comment to restart and retry. Also, this is the message that accompanied the first, unsuccessful launch of the GUI and the aborted R session.

baRcodeR:::make_labels()
Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3
Loading required package: shiny

• The Simple ID Code maker works great!
• When I click "Create Lable.csv" it appeared like nothing happened, but the file was indeed saved in my working directory. A real bonus would be a pop-up window or a message printed to the console that said something like "file save in your working directory", but a simple fix would be to clarify this in the README.
• When following the instructions in the "Using the RStudio addin" section, the text explaining the process comes after the example image, much like a figure legend. However, it would be much easier to follow along if the text was above the image instead of below it. Also, there is very little white space between the images and the text. Some level three headers (eg. Simple ID Codes with uniqID_maker and Hierarcical ID codes with uniqID_hier_maker could help distinguish the sections.)
• When I click "add level", I keep getting the error message Label Preview Input list has only one level. Did you forget a level or are you sure you are not looking for uniqIDMaker()? I was, however, successfully able to make a hierarchical labels despite the error message. Is there a way to prevent this error message from appearing?
• Why is the default font size 2.2 in the GUI? This seems a little small. Also, in the manual, the default size is 5.
• I installed the package with devtools::install_github("yihanwu/baRcodeR", build_vignettes = T, dependencies = T) when when I run 1vignette("Using-baRcodeR"), I get the warning message vignette ‘Using-baRcodeR’ not found.
• I was able to past the code from the GUI into the command line and regenerate the same pdf. Success!
• I'm not sure I understand the error correction description. The L,M,Q,H makes me think it goes form low quality to high quality, but this is conflicts with the 7%-30% damage description. What does damage mean? What do LMQ and H stand for? Please clarify.
• I noticed that this repo has been forked from another repo (nine2k/II-I-II-baRcodes-I-II-III)? Do those authors know that this is being submitted as a package? Will they be offered co-authorship?

Here is the session info from my workflow.

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

other attached packages:
[1] baRcodeR_0.1.4 qrcode_0.1.1   shiny_1.3.2   

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2        rstudioapi_0.10   knitr_1.24       
 [4] magrittr_1.5      xtable_1.8-4      R6_2.4.0         
 [7] rlang_0.4.0       stringr_1.4.0     tools_3.6.0      
[10] grid_3.6.0        DT_0.8            xfun_0.9         
[13] R.oo_1.22.0       miniUI_0.1.1.1    htmltools_0.3.6  
[16] crosstalk_1.0.0   yaml_2.2.0        digest_0.6.20    
[19] crayon_1.3.4      later_0.8.0       htmlwidgets_1.3  
[22] R.utils_2.9.0     promises_1.0.1    rsconnect_0.8.13 
[25] evaluate_0.14     mime_0.7          rmarkdown_1.15   
[28] stringi_1.4.3     compiler_3.6.0    R.methodsS3_1.7.1
[31] jsonlite_1.6      httpuv_1.5.1 

[sckott]

thanks so much for your review @raynamharris !

[yihanwu]

Thank you for the review @raynamharris!

[llrs]

Sorry for the delay. I plan to submit mine in a week or so. I already have most of it written but I want to check more the worflow.