Quality Risk Assesment Clinical Trials

Quality Risk Assesment Clinical Trials

Publication

This repository contains part of the analysis code used for:

Koneswarakantha, B., Ménard, T. Statistical modeling for quality risk assessment of clinical trials: follow-up at the era of remote auditing (under-review) Therapeutic Innovation & Regulatory Science

Background - As investigator site audits have largely been conducted remotely during the COVID-19 pandemic, remote quality monitoring has gained some momentum. To further facilitate the conduct of remote Quality Assurance (QA) activities, we developed new quality indicators, building on a previously published statistical modelling methodology.
Methods - We modeled the risk of having an audit or inspection finding using historical audits and inspections data from 2011 - 2019. We used logistic regression to model finding risk for 4 clinical impact factor (CIF) categories: Safety Reporting, Data Integrity, Consent and Protecting Endpoints.
Results - Resulting Area Under the Receiver Operating Characteristic Curves were between 0.59 - 0.63 with calibrated predictive ranges of 25 - 43%. The combined and adjusted risk factors could be used to easily interpret risk estimates.
Conclusion - Continuous surveillance of the identified risk factors and resulting risk estimates could be used to complement remote QA strategies and help to manage audit targets and audit focus also in post-pandemic times.

Anonymization

We do not share any non-public data on clinical trials or company IT systems to this end the following steps have been performed.

repository does not contain any data only code output that describes and analyses the data
data preparation and features selection steps were removed
all internal IDs were removed
geographic locations were removed
all dates where removed except for start_date which was set to the first day of the corresponding year

Documentation and Code Output

website

Run Code

The repository does not contain any data, therefore code will only run if all data files are supplied.

Docker

This repository uses docker

Targets

targets is used as the execution manager. The workflow is specified in _targets.R and the _targets_r/ directory.

In order to implement changes to the workflow edit src/Rmd/00_workflow.Rmd and knit document from RStudio to refresh targets files.

Make changes to existing functions by adding browser() statements and executing tar_make(callr_function = NULL)

targets manages the rendering of the reports. The .Rmd templates can be found as src/Rmd/_{[0-9]}2_[a-z]+.Rmd. They begin with an underscore because like this they will be ignored by rmarkdown::render_site. targets creates .html files for each report into src/Rmd that will get picked up by rmarkdown::render_site and copied into docs. rmarkdown::render_site triggers only the rendering of 00_workflow.Rmd which triggers targets which then renders the reports.

Run all code and render website

Shell

docker compose build
docker compose up -d shell
docker container exec -it quality_risk_assesment_clinical_trials_shell_1 /bin/bash
R -e 'rmarkdown::render_site("src/Rmd")'
docker compose down

Rstudio

docker compose build
docker compose up -d rstudio

open http://localhost:8787/

enter user name and password as specified in docker-compose.yml

enter in R-Console

rmarkdown::render_site("src/Rmd")

enter in terminal

docker compose down

Introduction