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732A94 AdvancedRHT2024 Lab05

labratory assignment for masters course in r

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6 views

732A94 AdvancedRHT2024 Lab05

labratory assignment for masters course in r

Uploaded by

Uday Jain
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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732A94 Advanced R Programming

Computer lab 5

Krzysztof Bartoszek, Bayu Brahmantio, Simon Jorstedt, Duc Tran


(designed by Leif Jonsson, Måns Magnusson and Shashi Nagarajan)
(converted to LATEX by Arash Haratian)

3 October 2024 (A31)

Seminar date: 9 October 10:15 (A31)


Lab deadline: 13 October 23:59
Instructions

• Ideally this lab should be conducted by students two by two.


• The lab consists of writing a package that is version controlled on github.com or gitlab.liu.se.
• All students in the group should contribute equally much to the package. All group members
have to contribute to, understand and be able to explain all aspects of the work. In case some
member(s) of a group do not contribute equally this has to be reported and in this situation a formal
group work contract will be signed, stipulating the consequences for further unequal contributions.
• Other significant collaborations/discussions should be acknowledged in the solution.
• To copy other’s code is NOT allowed. Your solutions will be checked through URKUND.

• Copying solutions of others and from any online or offline resources is NOT allowed.
• Commit continously your addition and changes.
• Collaborations should be done using GitHub (ie you should commit using your own github account)
or using GitLab.

• In the lab some functions can be marked with an *. Students MUST do AT LEAST ONE
exercise marked with an * for each of the Labs 3 - 6 and Bonus. If only one exercise is marked with
an *, then it MUST be done.
• The deadline for the lab is on the lab’s title page.

• The lab should be turned in using an url to the repository containing the package on github/gitlab.liu.se
using LISAM. This should also include name, liu-id and, if applicable, github user names of the
students behind the project. In case of problems or if you do not have access to LISAM the url
may be emailed to baybr79@liu.se or marbr987@student.liu.se or araha147@student.liu.se
or krzysztof.bartoszek@liu.se.
• NO resubmissions will be allowed for the Bonus lab.
NO late submissions will be allowed for the Bonus lab.
• Inside your package you may not depend on any global variable (unless it is a standardR one, like
pi). Using them will result in an immediate failure of your code.If at any stage your code changes
any options, these changes have to be reverted before your code finishes.

• All notes raised by Travis/GitHub Actions/GitLab CI have to be taken care of or explicitly defended
in your submission.
• The seminars are there to discuss your solutions and obtain support with problems. Every group
has to present at least once during the seminars in order to pass the lab part.

1
LINKÖPING UNIVERSITY
STIMA
Department of Computer and Information Science Advanced R programming

Contents

1 A package connecting to a web API 3


1.1 Create a package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.1.1 Write the R code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.1.2 Write unit tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.1.3 Documentation and vignettes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2 * Create a Shiny application using your package . . . . . . . . . . . . . . . . . . . . . . . 4
1.3 Seminar and examination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.3.1 Examination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
LINKÖPING UNIVERSITY
STIMA
Department of Computer and Information Science Advanced R programming

Chapter 1

A package connecting to a web API

In this lab we will will create a package to connect to a web API using R. The purpose of this lab is to
start the work with a API package you will use and develop further during the course. You can choose
a connection to any API you find to have interesting data to analyze as well (you may use this data in
a machine learning project in the last lab). If the project is good enough you will be able to submit this
package to CRAN during the last week.
The API needs to be accepted by the teacher before you start. In the document
732A94 AdvancedRHT2017 Lab05 API projects.pdf you can find API:s suggestions to implement as an
R package.
Master students will also implement a simple Shiny application using the package to connect to the
API.

1.1 Create a package


Start out by creating your new package on GitHub with Travis / GitHub Actions or on gitlab.liu.se with
GitLab CI. You can choose the option you prefer. See lab 3 for details on how to set up a package.
Read about the package and discuss whcih functions you should have to access the data in the API.
There are often limits and configurations for a given API you need to access.
In genreal it is good to have as few functions as possible theat are exported in the package. But behind
these functions you may need to have more functionality not accessed by the users of your package.

1.1.1 Write the R code


Read about the package and discuss which functions you should have to access the data in the API.
There are often limits and configurations for a given API you need to access.
In general it is good to have as few functions as possible that are exported in the package. But behind
these functions you may need to have more functionality not accessed by the users of your package.

1.1.2 Write unit tests


Write a unit test suite for the functions in the package. Examples of test can be:
1. Downloading a big query
2. Testing the limits of the API configuration
3. Testing the inputs and outputs of your functions
4. Testing that the function allways return a given value for a specific set of inputs.
See chapter “Testing” in [3] or [2] for details.

1.1.3 Documentation and vignettes


Write a vignette that describes your package and how to use it with examples. For more information on
how to write a vignette and include them in your package see “Vignettes” in [3].
Document all public functions using roxygen2. See chapter “Object documentation” in [3] for details.
1.2 * Create a Shiny application using your package
Create a new repository on github for a Shiny application. Create a simple Shiny application that makes
it possible to interactively analyze data using your API package. At least one interactive widget should
be used. See “Lesson 6” in [1] for information on how to handle the situation of reactive programming
in Shiny when “slow” data is used.
It should be possible to run your shiny app out using the runGitHub() function.

1.3 Seminar and examination


During the seminar you will bring your own computer and demonstrate your package and what you found
difficult in the project.
We will present as many packages as possible during the seminar and you should

1. Show that the package can be built using R Studio and that all unit tests is passing.
2. Discuss why you implemented the functions as you did.
3. Give a short presentation of the testsuite.

4. Show your vignette/run the examples live.


5. * Present your Shiny application.

1.3.1 Examination
Turn in a the adress to your github or gitlab repo with the package using LISAM. To pass the lab you
need to:
1. Have the R package up on GitHub with a Travis CI, GitHub Actions, or GitLab CI pass/fail badge.
2. The test suites for the implemented function(s) should be included in the package.

3. The package should build without warnings (pass) on Travis CI, GitHub Actions, or GitLab CI.
4. All issues raised by Travis CI / GitHub Actions / GitLab CI should be taken care or justified why
they are not a problem or cannot be corrected. Be careful with namespace issues, these you HAVE
to take care of.

4
LINKÖPING UNIVERSITY
STIMA
Department of Computer and Information Science Advanced R programming

Bibliography

[1] R Studio. Shiny tutorial, 2016.

[2] Hadley Wickham. testthat: Get started with testing. The R Journal, 3(1):5–10, 2011.
[3] Hadley Wickham. R packages. ” O’Reilly Media, Inc.”, 2015.

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