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
.
teal
applicationAll 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.
{dot teal_data_dot_diagram, echo=FALSE}
digraph G {
teal_data [label = "teal_data"];
node [shape=box];
teal_modules [label = "teal modules analysis R code"];
library [label = "R library() calls"];
filter_states [label = "filter states R code"];
data [label = "data preprocessing R code"];
teal_modules -> teal_data;
library -> teal_data;
edge [dir="back"];
teal_data -> filter_states;
teal_data -> data;
}
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.
{width=50%}
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.
{width=50%}
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.
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