survinger: Design-Adjusted Inference for Pathogen Lineage Surveillance

Provides tools for optimizing sequencing resource allocation and estimating pathogen lineage prevalence under real-world genomic surveillance conditions. Implements constrained allocation optimization for limited sequencing capacity across multiple regions and sample sources. Includes Horvitz-Thompson and post-stratified estimators that account for unequal sequencing rates, delay-adjusted nowcasting for right-censored reporting data, and combined design-weighted delay-corrected inference with uncertainty propagation.

See also

Useful links:

• https://github.com/CuiweiG/survinger

• Report bugs at https://github.com/CuiweiG/survinger/issues

Author

Maintainer: Cuiwei Gao 48gaocuiwei@gmail.com [copyright holder]