o2geosocial

o2geosocial infers probabilistic transmission trees of infectious diseases by integrating epidemiological surveillance data such as age group, location, onset date, and genotype to reconstruct transmission chains when full genetic sequences are unavailable.

Key Features:

• Integration of Multiple Data Types: Combines age group, location, onset date, and genotype from surveillance datasets to inform transmission inference.
• Transmission Tree Reconstruction: Employs a simple transmission process model to reconstruct transmission trees and clusters cases by genotype into separate trees without computing genetic distances.
• Probabilistic Inference: Estimates importation status and likely infector–infectee relationships using statistical inference to produce probabilistic transmission trees.
• Visualization and Summarization: Provides functions to summarize and visualize inferred cluster size distributions and transmission clusters.

Scientific Applications:

• Identify High-Risk Regions: Analyze reconstructed transmission trees to detect regions where importations have repeatedly produced large outbreaks.
• Assess Transmission Dynamics: Quantify individual secondary transmissions and identify features associated with high-transmission events.
• Inform Public Health Interventions: Provide evidence on at-risk areas and populations to guide targeted interventions and resource allocation.

Methodology:

Builds upon the R package outbreaker2 to extend inference to datasets lacking comprehensive genetic sequences; integrates age group, onset date, location, and genotype data; uses a transmission process model that does not rely on genetic distance and clusters cases by genotype into separate trees; infers importation statuses and transmission links probabilistically.