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.

Version:	0.1.1
Depends:	R (≥ 4.1.0)
Imports:	checkmate (≥ 2.0.0), cli (≥ 3.0.0), dplyr (≥ 1.1.0), generics, ggplot2 (≥ 3.4.0), methods, purrr, rlang (≥ 1.0.0), stats, tibble
Suggests:	MASS, Matrix, nloptr (≥ 2.0.0), survey, tidyr, vctrs, covr, knitr, rmarkdown, scales, testthat (≥ 3.0.0), withr
Published:	2026-04-05
DOI:	10.32614/CRAN.package.survinger
Author:	Cuiwei Gao [aut, cre, cph]
Maintainer:	Cuiwei Gao <48gaocuiwei at gmail.com>
BugReports:	https://github.com/CuiweiG/survinger/issues
License:	MIT + file LICENSE
URL:	https://github.com/CuiweiG/survinger
NeedsCompilation:	no
Language:	en-US
Citation:	survinger citation info
Materials:	README, NEWS
CRAN checks:	survinger results

Documentation:

Reference manual:	survinger.html , survinger.pdf
Vignettes:	Optimizing Sequencing Resource Allocation (source, R code) Delay-Adjusted Nowcasting (source, R code) Real-World Case Study: European COVID-19 Genomic Surveillance (source, R code) Introduction to survinger (source, R code)

Downloads:

Package source:	survinger_0.1.1.tar.gz
Windows binaries:	r-devel: survinger_0.1.1.zip, r-release: not available, r-oldrel: not available
macOS binaries:	r-release (arm64): survinger_0.1.1.tgz, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available
Old sources:	survinger archive

Linking:

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