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subpat

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This package is NOT VALIDATED, and should be reserved for exploratory analysis only.

subpat is a collection of shiny modules to create subpopulations and subgroups of clinical trial data. It was designed with CDISC ADaM data format in mind but supports any data format. It features two main applications, the Patient Listing Generator (PLG), and a TTE (time-to-event) analysis app.

Install

subpat is not available on CRAN. A development version can be installed by running

devtools::install_github("Novartis/subpat")

Patient Listing Generator (PLG)

PLG is designed for non-techincal users such as medical writers or clinicians to find specific patients and generate ad-hoc listings. It features an intuitive, graphical patient querying interface to find specific subjects from a clinical trial. The user can then use the created subpopulation to create ad-hoc (non-validated) listing to export. All of the components of the application can easily be reused in other Shiny applications due to the modular design.

TTE (time-to-event) analysis

The time-to-event (TTE) analysis application is a graphical and exploratory way for a statistician to analyze censored event data (such as survival times). This app uses the same subpopulation module as the PLG as well as a similarly designed subgroup creation interface. The subpopulations and subgroups are then used in the Kaplan Meier plots and Cox Proportional model modules. The variables are easily mapped to allow for data in any format.

Modules

It features modules for:

  • Subpopulation creation and editing
  • Subgroup creation and editing
  • Ad-hoc patient listings
  • Kaplan Meier survival plots and event table summary
  • Cox Proportional Hazard models

All of these modules are implemented with the {tidymodules} R package.

Usage

Patient Listing Generator (PLG)

subpat::runPlg()

TTE Analysis

subpat::runTTE()

Modules

subpat features many example Shiny applications to get you started using the modules. To see a list of examples, run

subpat::subpatExamples()
#> Example applications:
#> Call with index subpatExamples(2) or name subpatExamples('06_tte_simple')
#>   01_add-filter-example
#>   02_edit-population-example
#>   03_subpopulation-manager-example
#>   04_table-listing-example
#>   05_variable-selection-example
#>   06_tte_simple
#>   07_tte_mapping
#>   08_subgroup

All of the examples are found in inst/shiny-examples.

Vignettes

A more detailed introduction is found in the vignettes

PLG

vignette("plg", package = "subpat")

Modules Introduction

vignette("modules", package = "subpat")

TTE Module Integration

vignette("tte_integration.Rmd", package = "subpat")

Thanks

Special thanks to the SCC team at Novartis

Also thanks to Novartis for allowing this work to become an open-source project. It was started during my summer 2019 internship in Basel.

License

Copyright 2020 Novartis AG

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

  http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.