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Input Data

NEST CoreDev

Source: vignettes/blueprint/input_data.Rmd
input_data.Rmd

Introduction

Reproducibility is paramount in the pharmaceutical industry. Accurate and consistent results are essential to ensure high-quality research and the safety of patients. By prioritizing reproducibility, researchers can validate their methods, confirm their findings, and contribute to the advancement of the field.

The teal.code package provides the qenv class that facilitates code reproducibility. Code is passed to a qenv object, where is evaluated in a specific environment. qenv also stores the code so that it can be retrieved on request.

The teal_data class, which serves as the primary data interface for teal applications, inherits this code tracking behavior from qenv.

Preparing data for a teal application

All teal applications run on data provided in a teal_data object. Data objects are stored and modified within the environment of the teal_data object and all R code used is tracked, which allows for the code to be evaluated and executed in the teal application, and reproduced outside the teal application. This includes data loading, preprocessing, filtering, transformations, and plotting, etc.

The teal_data object makes it easy for users to reproduce and validate the results of their analyses.

Learn more about the use of teal_data in the teal.data package vignettes.

Show R Code and Reporter

In both the teal.modules.clinical and teal.modules.general packages, you’ll find that most modules include a convenient Show R Code button. When this button is clicked, a modal window appears, revealing the R code responsible for generating the module’s output. This functionality is achieved by inspecting the teal_data object and retrieving code from it. With the Show R Code button, users can easily copy and independently run the code to reproduce the analysis presented in the teal module.

Show R Code
Show R Code

The Reporter feature also leverages the teal_data object in its operation. Much like the Show R Code mechanism, the code displayed in a Reporter Card is extracted from the teal_data object.

Reporter
Reporter

To learn more about the Reporter feature, please visit the teal.reporter documentation.

Overall, qenv from teal.code and its child class, teal_data, are powerful tools for ensuring code reproducibility and promoting high-quality research in the R programming language.