Submission: pictureperrrfect (R)

Submitting Author: Kangbo Lu (@KangboLu)
Other Authors: Chad Neald (@ChadNeald), Debananda Sarkar (@debanandasarkar), Dustin Burnham (@dusty736)
Repository: https://github.com/UBC-MDS/pictureperrrfect
Version submitted: 0.3.0 Editor: Tiffany Timbers (@ttimbers ) Reviewers: TBD

Archive: TBD Version accepted: TBD

Paste the full DESCRIPTION file inside a code block below:

Package: pictureperrrfect
Title: Pictureperrrfect
Version: 0.0.0.9000
Authors@R: c(
    person("Chad", "Neald", email = "chad_neald@hotmail.com", role = "cre"),
    person("Dustin", "Burnham", role = "aut"),
    person("Debananda", "Sarkar", role = "aut"),
    person("Kangbo", "Lu", role = "aut"))
Description: A fun R utility package to make your pictures perfect! The package enables users to process, manipulate, and gather data about their images.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
Imports: 
    magrittr,
    stats,
    imager,
    tidyverse,
    dplyr,
    reticulate,
    abind,
    devtools,
    knitr
Suggests: 
    testthat (>= 3.0.0),
    covr,
    here
URL: https://github.com/UBC-MDS/pictureperrrfect
BugReports: https://github.com/UBC-MDS/pictureperrrfect/issues
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
- [x] data extraction
- [x] 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):
The package pictureperrrfect is an image utility package intended to manipulate images through a variety of functions. The intention is that a user with little to no experience can quickly call a function to alter, compress, or print out statistics for an image.
Who is the target audience and what are scientific applications of this package?
Data scientists and casual programmers want to apply image processing functions to images. The scientific application of our package is to help speed up the image processing process with a simple call to our functions.
Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?
Image processing is very popular in the R ecosystem so we are aware that we are not reinventing the wheel with our package, but we hope to gain a deeper understanding of the inner workings of an image package. Specifically, the “imager” library has functions that rotate, flip an image, or filter which covers 3 of our 4 functions.
(If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?
Yes. Our package complies with the "guidance around _Ethics, Data Privacy and Human Subjects Research".
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.

[x] I have read the guide for authors and rOpenSci packaging guide.

This package:

[x] does not violate the Terms of Service of any service it interacts with.
[x] has a CRAN and OSI accepted license.
[x] contains a README with instructions for installing the development version.
[x] includes documentation with examples for all functions, created with roxygen2.
[x] contains a vignette with examples of its essential functions and uses.
[x] has a test suite.
[x] 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 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](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/journal-resources/policy-on-publishing-code.html)) - (*Scope: Do consider MEE's [Aims and Scope](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/aims-and-scope/read-full-aims-and-scope.html) 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

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

Assigning @AnitaLi-0371 & @fei-chang as reviewers.

Package Review

[x] 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:

[x] A statement of need clearly stating problems the software is designed to solve and its target audience in README
[x] Installation instructions: for the development version of package and any non-standard dependencies in README
[x] Vignette(s) demonstrating major functionality that runs successfully locally
[x] Function Documentation: for all exported functions
[x] Examples (that run successfully locally) for all exported functions
[x] Community guidelines including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with URL, BugReports and Maintainer (which may be autogenerated via Authors@R).

For packages co-submitting to JOSS

[ ] The package has an obvious research application according to JOSS's definition

The package contains a paper.md matching JOSS's requirements with:

[ ] A short summary describing the high-level functionality of the software

[ ] Authors: A list of authors with their affiliations

[ ] A statement of need clearly stating problems the software is designed to solve and its target audience.

[ ] References: with DOIs for all those that have one (e.g. papers, datasets, software).

Functionality

[x] Installation: Installation succeeds as documented.
[x] Functionality: Any functional claims of the software been confirmed.
[x] Performance: Any performance claims of the software been confirmed.
[x] 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.
[x] Packaging guidelines: The package conforms to the rOpenSci packaging guidelines

Estimated hours spent reviewing: 3

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

Review Comments

Hi Chad, Debananda, Dustin and Kangbo,

Great work on this package! This package is pretty useful for handling pictures and I really appreciate the clean and nice documentations on functions and usages for this package. Also, all functions described in the documentation are well-implemented. By testing both automatically and manually, all functions could run without reporting bugs. Below are just a few suggestions that you may consider to make this package even better:

Functionality

The function rotation_perrrfect runs very slow. In particular, when I tested on images of size greater than 1000x1000, the run-times are considerably long. Compared to another image-helping R package magick which also supports the rotation method of pictures, the run-time of the rotation_perrrfectis about 7-8 times slower. Therefore it would be good to find some ways to reduce the run-time of this function.
Allowing the input n_rot to be 4 may be a little redundant in function rotation_perrrfect. As rotating 360 degree will produce no change at all and simply return the original image, but the function still takes a long time to run when the image size is big and the n_rot is set to 4.
In function filter_perrrfect, it may be a good idea to have a flexible fliter_size depending on the input size of the image. Currently, when users enter large-size images with the default function call, the blurring effect is very weak and the users may be confused and think that the function is not working. Making the fliter_size flexible will make this function more user-friendly.

Documentation

By running goodpractice::gp(), I found that in many files there are long code lines. Long code lines can be bad for readability and it may be a good idea to reduce the lines shorter than 80 characters.
By running spell_check_files, I noticed that there are a few typos in the README file. For example, in "Features" section, the sentence "The package pictureperrrfect is an image untility package..." should be "utiility". And in Function 4 there is a typo in the sentence "a user can specifiy...".

Thank you for the work you've done to make this great package and it is my great pleasure to write this review for it. Let me know if there are any questions.

Best,

Fei

Package Review

[x] As the reviewer I confirm that there are no conflicts of interest for me to review this work.

Documentation

The package includes all the following forms of documentation:

[x] A statement of need clearly stating problems the software is designed to solve and its target audience in README
[x] Installation instructions: for the development version of package and any non-standard dependencies in README
[x] Vignette(s) demonstrating major functionality that runs successfully locally
[x] Function Documentation: for all exported functions
[x] Examples (that run successfully locally) for all exported functions
[x] Community guidelines including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with URL, BugReports and Maintainer (which may be autogenerated via Authors@R).

For packages co-submitting to JOSS

[ ] The package has an obvious research application according to JOSS's definition

The package contains a paper.md matching JOSS's requirements with:

[ ] A short summary describing the high-level functionality of the software

[ ] Authors: A list of authors with their affiliations

[ ] A statement of need clearly stating problems the software is designed to solve and its target audience.

[ ] References: with DOIs for all those that have one (e.g. papers, datasets, software).

Functionality

[x] Installation: Installation succeeds as documented.
[x] Functionality: Any functional claims of the software been confirmed.
[x] Performance: Any performance claims of the software been confirmed.
[x] 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.
[x] Packaging guidelines: The package conforms to the rOpenSci packaging guidelines

Estimated hours spent reviewing: 2hrs

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

Review Comments

I think this is a very helpful package to modify pictures or get basic information from them. In general, you have very well documented functions and examples. All the values are clearly defined. The functions run smoothly without any issues. There are only a few minor things that you may want to adjust.

Functionality

The function get_property_perrrfect has a list with values and have mean and median stored for each channel. Personally, I would prefer having a mean and median properly indexed (i.e. a sublist with values' name) so that users do not need to remember which value is which.
For the function get_property_perrrfect, under the Features section, it says the function "will include a plotted histogram of values for each channel". I think this would be a very beneficial feature, however, I do not see any examples of color histogram. I also checked the codes for get_property_perrrfect, and it does not seem to have any codes for histogram (or it is written in another function that I may miss).

Documentation

Feature description need to be consistent with functions. If there are examples of color histogram, I think it is necessary to show them in the webpage or under Usage, as they are some of the important output from the function get_property_perrrfect.

Overall I found this package is easy to use and well documented!

Anita

UBC-MDS / software-review-2021