Reproducibility

NEST coreDev

2022-04-22

Reproducibility is an important feature when it comes to data analysis for the following reasons:

• Enables users to reproduce the outputs at any moment in a simple R console outside of a reactive shiny app.
• Provides transparency where it helps users and others understand what happened during the analysis.

This is where the chunks concept of theteal.code package comes into play. It provides a mechanism to develop reproducible shiny/teal modules. The teal package complements the chunks concept by providing a server and an interface to retrieve the reproducible code via a Show R code button.

Note that there is a public shinymeta R package from RStudio that offers similar functionality. However, currently, shinymeta can not be easily integrated into teal modules and hence we recommend using chunks for teal based apps.

Reproducibility in teal

Teal applications can be designed and set up such that for every output displayed, the associated R code can be requested via the Show R code button. In order to develop a teal application with reproducible outputs the app developer needs to take this into account when implementing the app.

The reproducible code displayed for outputs in teal is always made from three parts:

1. Header which includes information such as:

• directory path
• server name
• R version
• date
• libPaths()
• packages’ versions.

2. Preprocessing Code: refers to the code which precedes the teal app initialization, this includes:

• Data imports
• Data transformation
• Checking data reproducibility

3. Teal Module Analysis Code which includes:

• Filtering and encodings
• Data analysis/visualization

The header is created by teal, the preprocessing code must be supplied by the app developer and the analysis code is provided by the teal modules.

Chunks

The code chunks were introduced to allow the development of reproducible shiny/teal modules. A reproducible module includes a “Show R Code” button which can display the code needed to reproduce the outputs of the module. Inside the modal, which pops up after clicking the button, you should see:

1. The code loading the necessary libraries - by teal::get_code
2. The code used for loading and filtering data sets - by teal::FilteredData
3. The code used for merging multiple data sets - by teal.transform::data_merge_srv
4. The code generating the outputs - by code chunks

The code chunks were especially designed for the code leading from an input data set to the outputs. To get more information about the concept of chunks, please refer to article basic chunks.