Submission group 28: CovidTrackerR

[Davidwang11]

Submitting Author:

• Cuthbert Chow (@cuthchow)
• Tianwei Wang (@Davidwang11)
• Siqi Tao (@SiqiTao)
• Jessie Wong (@jessie14)

Package Name: CovidTrackerR One-Line Description of Package: CovidTrackerR provides basic data cleaning, wrangling and plotting of Covid tracking data in Canada. Repository Link: https://github.com/UBC-MDS/Group28-CovidTracker-R Version submitted:
Editor: TBD
Reviewer 1: Aldo de Almeida Saltao Barros Reviewer 2: Morgan Rosenberg Reviewer 3: Affrin Sultana Reviewer 4: Katia Aristova Archive: TBD
Version accepted: TBD

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

Package: CovidTrackerR
Title: Tracking covid data in Canada
Version: 0.0.0.9000
Authors@R: 
    person("Cuthbert", "Chow", , "first.last@example.com", role = c("aut", "cre"))
    person("Tianwei", "Wang", , "first.last@example.com", role = c("aut", "cre"))
    person("Siqi", "Tao", , "first.last@example.com", role = c("aut", "cre"))
    person("Jessie", "Wong", , "first.last@example.com", role = c("aut", "cre"))
Description: Provides basic data cleaning, wrangling and plotting of Covid tracking data in Canada.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
Suggests: 
    testthat (>= 3.0.0)
Config/testthat/edition: 3
Imports: 
    lubridate,
    geojsonio,
    stringr,
    dplyr,
    broom,
    plotly,
    httr,
    mapproj
Depends: 
    tidyverse

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
  • [ ] 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 is designed for the easy retrieval and analysis of data pertaining to Covid trends in Canada, including information about cases, vaccinations, testing, and mortality. The package serves as a wrapper for the opencovid.ca API, and provides additional helper functions for visualising the data, either as a time series or in the form of a map, and summary information during a time period.

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

Any people who have basic R knowledge and care about the covid-related information in Canada.

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

There are several R packages, which have some overlapping functionality as our package, but none which perform all the data acquisition, analysis, and graphing tasks which CovidTracker encompasses. The packages designed for covid data retrieval also do not use the same data source as CovidTracker and do not provide the same level of granularity.

• (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](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.

[aldojasb]

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
• [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.
• [ ] 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: 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.

---

Review Comments

1. The test file is very well designed, my only suggestion here is to put more tests (asserts) for the function getcoviddata.
2. The functions in R are working pretty well, I would only suggest tidier output for the function calculate_stat_summary. A table output would be great here.
3. Similar packages session is also good. My only suggestion here is to explain a little bit better the benefits and drawbacks of the other packages and compare how your package is better than those ones.
4. the Usage and Examples is pretty good. My only suggestion here is to cut off the code part and insert only the code for the function and the outcome, removing the other R's outputs like "Loading required package: tidyverse", etc.
5. The functions in R are working pretty well, I would only suggest adding a new input for the plot_timeseries in which you can select the period that you want in the plot. e.g from july-2020 to dez-2020.

[morganrosenberg50]

Package Review

• 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
• [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

• [ ] 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.
• [x] Packaging guidelines: The package conforms to the rOpenSci packaging guidelines.

Estimated hours spent reviewing: 2 hr

• [ ] 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

• Overall, same comments from the review of your Python package - a really interesting and useful function
• I think it may be interesting to specify how the other COVID packages you list are either complimentary or distinct from your package. For example, I notice that one of the packages you link to reports on daily data - in the future if someone wants to contribute to your package to add this functionality, it may be useful for them to first investigate this package.
• I quite like the simplicity and effectiveness of your plot_geographical's visualization. It seems to plot absolute values. For the next version, it may be useful to either switch to per capita values or or give the user the option between the two. Given the extreme differences in population between provinces, the current approach could be misleading.
• I was unable to run the package as I seemed to have problems installing the the units package (dependency of sf package) and the sf package through the installation instructions. When I install manually, I get the following message:

There are binary versions available but the source versions are later: binary source needs_compilation units 0.7-2 0.8-0 TRUE sf 1.0-5 1.0-6 TRUE

However, I'm still unable to install these binary versions - this may be a problem with my machine, however, I would advise testing on a MacBook M1 chip machine (if you already have, this is definitely a me problem, and when I figure it out I'll aim to circle back!).

Based on: https://devguide.ropensci.org/reviewtemplate.html

[Affrin101]

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

• [x] Community guidelines: including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with URL, Bug Reports 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: 1.5 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

• Well done Group 28 on developing such a simple yet comprehensive package to track Covid related data. I can see its usefulness right away especially during times like these.
• Installation guide was simple and easy to follow and could be done successfully without any hiccups.
• The example code in README was very helpful for me to check the functionality of your package. However, the example code in README and vignette have different arguments being passed. It would be great if you keep both the example sections in Vignette and in the README file consistent. Ex: get_covid_data() has a date parameter in the vignette but not in the README.
• The function codes are well written and well documented, comments above each check make it really easy to understand the functionality of that piece of code.
• Great job on test cases/ exception handling in each function. There are sufficient tests for each function. All possible edge cases have been covered.
• I could not find the contact details of the authors of the package. I think this would be nice to add the contributors and contributing and license section to the Readme with the name of all the authors mentioned. Also, on the website, I could only find the name of one author.
• Really liked the idea of plotting the covid cases on a geographical map/choropleth maps.

[katerinkus]

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:

• [ ] 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).

Functionality

• [x] Installation: Installation succeeds as documented.
• [ ] 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: 1.5h

• [ ] 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

This is a helpful and versatile package and I can easily see how it could be further expanded. It could have hospitalization counts and death counts and other info.

• The purpose of the package is clear and concise but I was not sure about the intended audience.
• The vignettes were are helpful and descriptive.
• I was not 100% sure what the count column represented in calculate_stat_summary() function. I am guessing it is the total number of records. If so, I am not sure if it is useful in this context.
• I would have preferred the data to be sorted in descending order (new to old). At first, I was not sure that it worked correctly but then I saw that the cases started from 2020, hence the super low numbers.
• I found it a bit tedious having to reformat dates for the plot_timeseries() function. My first instinct was to use the same format as in the output of get_covid_data(): 25-09-2020. However, the package asked me to restructure the date to this format: YYYY-MM-DD. The resulting plot looked difficult to read and it is unclear what year it is for. Perhaps, it may be a better idea to use some other format. I also was not sure what was meant by: trendlines and smoothing options as I only found start and end options.
• The package passed check() and test() without errors. I got a few depreciation warnings but nothing significant.