survinger

Design-Adjusted Inference for Pathogen Lineage Surveillance

v0.1.1 · Apr 5, 2026 · MIT + file LICENSE

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.

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CRAN Check Status

7 OK

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Flavor	Status	Time
r-devel-linux-x86_64-debian-gcc	OK	101.2s
r-devel-linux-x86_64-fedora-clang	OK	232.4s
r-devel-linux-x86_64-fedora-gcc	OK	250.8s
r-devel-macos-arm64	OK	44s
r-devel-windows-x86_64	OK	155s
r-release-linux-x86_64	OK	132.4s
r-release-macos-arm64	OK	37s

Check History

OK 7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 6, 2026

ERROR 1 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE Apr 3, 2026

ERROR r-devel-macos-arm64

tests

Running ‘testthat.R’ [6s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional te
...[truncated]...
 CI contains point estimate ───────────
  Expected `all(est$prevalence >= est$ci_lower)` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 159 ]
  Error:
  ! Test failures.
  Execution halted

ERROR r-release-macos-arm64

tests

Running ‘testthat.R’ [6s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional te
...[truncated]...
 CI contains point estimate ───────────
  Expected `all(est$prevalence >= est$ci_lower)` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 159 ]
  Error:
  ! Test failures.
  Execution halted

Dependency Network

Version History

updated 0.1.1 ← 0.1.0 diff Apr 5, 2026

new 0.1.0 Apr 2, 2026