R Observatory: Metrics for survinger version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

survinger

0.1.1Package record

Design-Adjusted Inference for Pathogen Lineage Surveillance

0packages depend

2.5Kdownloads / year

91.3%test coverage

13/13flavors OK

Overview

About

Maintained by Cuiwei GaoCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 0.1.1

Fix test failure on M1 Mac (ARM64): Wilson CI is not centred on the point estimate by construction. Added floating-point tolerance to the CI-containment test (test-03-prevalence.R:63). Only the test was affected; no changes to estimation code.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("survinger", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("CuiweiG/survinger")

Development version from CuiweiG/survinger. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-survinger

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-survinger

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-survinger

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 5.9 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
WARNING12 OK, 1 WARNING2026-06-08
OK7 OK2026-04-06

Show 1 earlier changeHide 1 earlier change

ERROR1 OK, 2 ERROR2026-04-03

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.1

READMEYes · 666 wordsVignettesYes · 4 · dynamicNEWSYes · 100% structured · mentions 0.1.1Citation fileYes · software entry only

Help pages: 49 (17 internal)includes a package overview page
Examples that run: 100%31 run in a plain check
Exported functions with examples: 97%
Documented parameters: 99%
Return-value docs: 97%
Help pages citing references: 0%

Vignettes (4)

How these are measured

Downloads

2.5K

CRAN downloads in the past year

Rank #13,845 · ~7/day · ~208/mo

Releases R versions

Daily download trend is not available in this view yet.

31630 days

85690 days

2.5K1 year

Compare downloads with other packages →

Also on46 r2u6 autocran

How downloads are counted

Repository

cuiweig/survinger ↗Account: CuiweiG

1Stars

0Forks

0Open issues

0Open PRs

1Releases

64Commits

1Commit identities

biostatisticscranepidemiologypathogen-surveillancerr-packagesurvey-samplinghorvitz-thompson

64 commits · Last activity 2026-04-16 · 0% stars, 30d

Responsiveness

not measured

Stars over time

2026-04-27 · 12026-07-07 · 1

How these are measured

PracticesBeta

11 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/cuiweig/survinger on 2026-10-25.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Governance and community (3)

Code of conductContributing guideIssue templates

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-24 · The repository has a site deploy workflow

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Research and citation (1)

codemeta.json

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing survinger adds 28 packages (15 with compiled code, 17 MB of source tarballs). Heaviest: ggplot2 6.0 MB, isoband 1.5 MB, farver 1.2 MB.

Depends (1)

R >= 4.1.0

Imports (10)

checkmate cli dplyr generics ggplot2methodspurrr rlangstatstibble

LinkingTo (0)

none

Suggests (12)

MASSMatrixnloptr survey tidyr vctrs covr knitr rmarkdown scales testthat withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Cuiwei Gao

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.1.1Latest
record
2026-04-05 · current release · diff ↗
0.1.0
record
2026-04-02
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-04-02
Total releases: 2 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 12 KB / 1 file
Download size: 1.6 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("survinger")

The package provides a citation file, so citation() returns the authors' own entry.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for survinger version 0.1.1 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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