sivirep: A package for strengthening epidemiological surveillance and report generation—Use case in Colombia

This paper presents sivirep, an open-source R package created to streamline epidemiological surveillance and reporting in public health. sivirep is part of the Epiverse TRACE-LAC initiative, which aims to strengthen the infrastructure and epidemic response to infectious diseases in Latin America and the Caribbean. This package automates the downloading, preprocessing, and preparation of data from Colombia’s epidemiological surveillance and reporting system, “SIVIGILA”. sivirep also provides a customizable R Markdown template for subsequent analysis and automatic generation of epidemiological reports. sivirep was developed in Spanish to improve the engagement of local users, but can be used worldwide, keeping both potential global uses aligned with local needs. This tool also can facilitate teaching and learning on SIVIGILA data source for students and researchers from various fields.