EvalTest is an R Shiny application designed for evaluating diagnostic test performance. It aims to facilitate the application of statistical methods in diagnostic test evaluation by healthcare professionals.
The ‘EvalTest’ package provides a ‘Shiny’ application for evaluating diagnostic test performance using data from laboratory or diagnostic research. It supports both binary and continuous test variables. It allows users to compute and visualize:
Confusion matrix: for binary test results (or threshold categorized quantitative test results) and disease status.
Key performance indicators: sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), likelihood ratios (LR+ and LR-), accuracy, and Youden index.
Receiver Operating Characteristic (ROC) curve: determine optimal cut-off thresholds of quantitative tests, display ROC plot and area under curve (AUC) with confidence intervals.
Outputs and plot: The application provides interactive tables and plots that can be exported for reporting purposes.
You can install the development version of ‘EvalTest’ from GitHub like so:
devtools::install_github("NassimAyad87/EvalTest", dependencies = TRUE)Or from CRAN (after the package is published there):
install.packages(EvalTest)Launch the Shiny application using:
library(EvalTest)
run_app()This will open the application in your default web browser (or RStudio viewer pane) and follow these steps:
Before uploading your data, you should ensure that: the test variable is in one column (either qualitative or quantitative) and the reference variable (disease status) is in another column (binary: 1/0). There are no missing values in the selected columns.
Upload your data in Excel format (.xlsx).
Choose your variable test type (Qualitative or Quantitative).
Select the appropriate columns for test variable and reference variable (disease status).
Input disease prevalence value (between 0 and 1) of the study population.
Run the analysis and explore the results in the different tabs.
You can download the ROC plot and the results table for your report.
This package is licensed under the MIT License - see the LICENSE file for details.
To cite the ‘EvalTest’ package in publications, use this script:
citation("EvalTest")Or just cite as (after the package is published there):