Package: survinger
Title: Design-Adjusted Inference for Pathogen Lineage Surveillance
Version: 0.1.1
Authors@R: 
    person("Cuiwei", "Gao", , "48gaocuiwei@gmail.com",
           role = c("aut", "cre", "cph"))
Description: 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.
License: MIT + file LICENSE
URL: https://github.com/CuiweiG/survinger
BugReports: https://github.com/CuiweiG/survinger/issues
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
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
LazyData: true
RoxygenNote: 7.3.3
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2026-04-04 09:58:36 UTC; openclaw
Author: Cuiwei Gao [aut, cre, cph]
Maintainer: Cuiwei Gao <48gaocuiwei@gmail.com>
Repository: CRAN
Date/Publication: 2026-04-05 11:10:02 UTC
Built: R 4.5.2; ; 2026-04-08 02:02:12 UTC; unix
