sirfunctions

Project overview

The sirfunctions package contains key functions used by the Surveillance, Innovation, and Research (SIR) team within the Polio Eradication Branch (PEB) at the Centers for Disease Control and Prevention (CDC). It includes functions to download cleaned global polio data from the World Health Organization (WHO) Polio Information System (POLIS) and geographic files. In addition, the package contains functions to visualize important epidemiological trends and perform key performance indicators such as NPAFP rates, EV rates, and stool adequacy.

Nishant Kishore (PhD), was the original lead developer of the package, and I have since taken over maintenance and further development of it since February 2024. As an opensourced R package, there have been several contributors to the package, both within CDC and WHO. My key contributions include:

• Adding new functions to calculate additional key performance indicators and visualizations of maps.
• Adding analytical pipelines to perform desk reviews and KPI reporting.
• Improving existing visualizations and adding new plotting functions.
• Streamlining the package to improve code readability and deprecate rarely used functions.
• Overhauling documentation and vignettes to enhance user understanding while adhering to the tidyverse style guide.
• Ensuring compatibility with the latest R versions and dependencies.
• Allow outside collaborators to use functions that were previously availably only to CDC employees due to CDC-specific dependencies.
• Provide an R interface to access, download, and load data from Azure containers without the need for the Azure Storage Explorer application.
• Revising code to increase execution speed
• Create local caching system for downloading global polio data

The original goal of the package was to streamline and standardize the analysis of global polio surveillance data within CDC. With my contributions, the package has become more user-friendly and accessible to a wider audience, including outside collaborators. The sirfunctions package is now a comprehensive tool for polio surveillance data analysis, visualization, and reporting.

NOTE: Due to the sensitive nature of polio surveillance data, specific examples of visualizations and analyses created using the sirfunctions package cannot be shared publicly.

Technologies Used:

• Programming Languages: R
• Data Visualization: ggplot2, sf
• Data Manipulation: dplyr, tidyr, purrr, stringr
• Documentation: roxygen2, devtools, usethis
• Data access: AzureStor, AzureAuth, Microsoft365R