Submission Group 10: canadacovidmetrics (R)

name: CanadaCovidMetrics about: Our package extracts covid data from OpenAPI, and formats the results in usable dataframes

Submitting Author Name: Adam Morphy Submitting Author Github Handle: !--author1-->@adammorphy<!--end-author1-- Other Package Authors Github handles: @Valli180, @LukeAC, @ming0701 Repository: https://github.com/UBC-MDS/canadacovidmetricsR Version submitted: v1.0.0 Submission type: Standard Editor: TBD Reviewers: Cuthbert Chow @cuthchow, Francisco Mejia @RamiroMejia, Margot Vore @voremargot, Thomas Siu @thomassiu

Archive: TBD Version accepted: TBD Language: en

Description

Package: canadacovidmetricsR
Title: What the Package Does (One Line, Title Case)
Version: 0.0.0.9000
Authors@R: 
    c(person(given = "Brandon",
           family = "Lam",
           role = c("aut", "cre"),
           email = "ming0701@student.ubc.ca"),
      person(given = "Adam",
           family = "Morphy",
           role = c("aut")),
      person(given = "Valli",
           family = "Akella",
           role = c("aut")),
      person(given = "Luke",
           family = "Collins",
           role = c("aut")))
Description: canadacovidmetricsR provides key metrics regarding COVID-19 situation in Canada across provinces using the [OpenCovid API](https://opencovid.ca/api/).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
Imports: 
    httr,
    jsonlite
Suggests: 
    testthat (>= 3.0.0)
Config/testthat/edition: 3

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.):
[x] 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):

Our package extracts covid data from an open API, and formats the results in usable data frames.
Who is the target audience and what are scientific applications of this package?

Our package is intended to speed up the process of communicating covid information in Canada, and therefore is targeted to science communicators, doctors, data scientists, and others who share covid data.
Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?

Existing packages use other APIs which do not update the data consistantly, and are not targeted to Canadian data (ex. John Hopkins University API). To our knowledge, no other package exists using OpenCovid API in the R ecosystem
(If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?
If you made a pre-submission inquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.
Explain reasons for any pkgcheck items which your package is unable to pass.
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)
(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

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

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

Briefly describe any working relationship you have (had) with the package authors.
[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
[ ] 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

[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: 1.5 Hours

[ ] 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

Hello Group 10 members,

Congratulations, you did a great job on your package.

I have the following comments about your package:

It would be relevant to show examples of all functions in Usage and Example in the README like you did in the python version of the package for get_deaths, get_recoveries get_vaccinations. You can also include a link to the vignettes to avoid including all the examples in this section
If you decided not to publish the package in CRAN, please remove the instructions install. packages("canadacovidmetricsR") in the README.
You can add exception handling for incorrect values in the argument date. When I run get_cases(loc = "BC", date = "2015-01-31"), I got this error:

No encoding supplied: defaulting to UTF-8.
Error in `colnames<-`(`*tmp*`, value = `*vtmp*`) : 
  attempt to set 'colnames' on an object with less than two dimensions

This can be confusing for the user.

When running the functions I get a warning message related to the encoding. It would be great if you can suppress this
In the vignettes the example of usage for the function get_deaths, returns an error. If I run get_deaths(loc = "BC", date = "2020-01-31"). The error is because there are no deaths on this date so it is a missing value in the query. You can add exemption handling for those dates with missing values or change the vignette example.
The Contributing Document is missing. The link in the README file is not working.

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

Briefly describe any working relationship you have (had) with the package authors.
[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
[ ] Installation instructions: for the development version of package and any non-standard dependencies in README
[ ] Vignette(s): demonstrating major functionality that runs successfully locally
[x] Function Documentation: for all exported functions
[] Examples: (that run successfully locally) for all exported functions
[ ] 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.
[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: 1hr

[ ] 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 you have a great concept for your package. Easily accessible data is very important to understand the dynamics of the pandemic. I really like how simple it is to use your functions and the simple outputs it gives you! The majority of your package is good but, as always, there is room for improvement. Here are some specific items that you may want to address.

install.packages("canadacovidmetricsR") did not work for me. I got an error that said your package was not avaliable for my version of R (4.1.1). I am unsure if this is just an error on my machine or if this is happening to others. I would suggest either debugging the issue or removing this as a download option from the readme. The devtool option worked great for the download.
The r code in the vignette doesn’t work correctly as many of the r code cells do not run when clicked. When looking at the markdown file, it appears that the r code cells have not been properly formatted so no code blocks are present. Formatting the markdown document would easily fix this issue.
The examples in the vignette error out. I think you meant for the year to be 2021 not 2020 in the examples.
If the user puts in a date prior to the start of the pandemic or a date that has yet to happen, it would be nice for a simple warning to pop up telling user that their entry is out of the valid date range. Currently the error message that pops up is not too clear as to the issue.
There is room to do more tests on the code as the code coverage is currently at 70%. It would be great if you are able to test more edge cases to make your package more robust against user error.
In the vignette, it may be nice to add in all the parameters of your function to each function explanation so if a user wants to play around with function, they can easily see what parameters they can add and delete.
Check that R formatting in consistent within your scripts and tests.

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

Briefly describe any working relationship you have (had) with the package authors.
[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
[ ] 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

[x] Installation: Installation succeeds as documented.
[x] Functionality: Any functional claims of the software been confirmed.
[ ] 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: 1 hours

[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 Group 10,

Once again congratulations on completing the R package! The package is very handy to use and it is with clear instructions on how to install and navigate. Here are some comments that you may consider to improve in the future:

Possibly to increase test coverage to cover necessary branches. Those marked in red in the codecov report could be considered. (See this.
In the vignette, it would be great if there are more examples on how to call the functions. For example, what are the key combinations of arguments that can be used? Also, providing a description that these functions return a data frame would be a great idea - as I thought it was a print statement initially =)
You may add additional checking on the input, especially on the locations. For example, if I use CANADA or 'bc' then it doesn't work.
The extraction always returns year 2000 when I use argument date. For example, get_cases(date = '2021-05-05') returns record of 2020-05-05.
Possibly to extend the functionality to accept multiple locations, for example, get_recoveries(loc = c("BC", "AB")).

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

Briefly describe any working relationship you have (had) with the package authors.
[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
[] 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).

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: 1 hour

[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 Group 10 members, great job on this R package. The package was a joy to use, and I just have several remarks for potential future improvement:

It may be prudent to write a broader range of tests, as the code coverage at the moment at 70%, and certain parts of the code may not work as intended but may not show up in the testing
It would be helpful to have more detailed explanations in the vignette of the package, to walk the user through more different variations and use cases for all the functions in the package
There are some warnings which appear when running the functions, even as shown in the examples, stating that 'No encoding supplied: defaulting to UTF-8.' Although it doesn't break any of the code, it may be beneficial to the package to address such issues to make usage more straightforward
The examples could highlight more of the function arguments, because the ones shown on the repository/vignette only show acquiring data for a single date, but not for a date range, which may be quite a common use case for the package
The error that is thrown for setting an invalid date, or for utilising a 'before' date which comes before an 'after' date, is not particularly helpful, and should ideally tell users what the correct date inputs should be.
For additional functionality, it may be good to allow users to specify a date window instead (e.g 10 days, 4 weeks), with either a single starting or ending date, to avoid having to calculate both date endpoints manually.

UBC-MDS / software-review-2022