R Observatory: Metrics for surveil version 0.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

surveil

0.3.0Package record

Time Series Models for Disease Surveillance

0packages depend

3.6Kdownloads / year

53.9%test coverage

11/13flavors OK

Overview

About

Maintained by Connor DoneganCRAN page ↗GitHub ↗Website ↗

Fits time trend models for routine disease surveillance tasks and returns probability distributions for a variety of quantities of interest, including age-standardized rates, period and cumulative percent change, and measures of health inequality. The models are appropriate for count data such as disease incidence and mortality data, employing a Poisson or binomial likelihood and the first-difference (random-walk) prior for unknown risk. Optionally add a covariance matrix for multiple, correlated time series models. Inference is completed using Markov chain Monte Carlo via the Stan modeling language. References: Donegan, Hughes, and Lee (2022) doi:10.2196/34589; Stan Development Team (2021) https://mc-stan.org; Theil (1972, ISBN:0-444-10378-3).

Changes in 0.3.0

Example code in the documentation has been improved
The package vignettes have been re-written
The standardize function is now slightly easier to use: the standard population sizes provided by data(standard) can be passed to the standardize function without removing any unused age groups. Previously, it was necessary to subset the standard data before using standardize.

Another short illustration of cancer data analysis with surveil is provided here: <https://connordonegan.github.io/surveil-paper/>

From NEWS.md in the release

Install

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

install.packages("surveil", 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("ConnorDonegan/surveil")

Development version from ConnorDonegan/surveil. 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-surveil

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-surveil

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-surveil

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

2NOTE11OK

Check messages

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
All declared Imports should be used.

CRAN check page ↗

Slowest check: 14.6 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-07-29
ERROR10 OK, 2 NOTE, 1 ERROR2026-07-27
NOTE11 OK, 2 NOTE2026-06-09
ERROR10 OK, 2 NOTE, 1 ERROR2026-06-08
NOTE9 OK, 5 NOTE2026-04-22

Show 2 earlier changesHide 2 earlier changes

ERROR8 OK, 5 NOTE, 1 ERROR2026-04-18
NOTE9 OK, 5 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.0

READMEYes · 228 wordsVignettesYes · 4 · dynamicNEWSYes · 100% structured · mentions 0.3.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 16includes a package overview page
Examples that run: 100%11 run in a plain check
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 6%

Vignettes (4)

Age-standardized rates HTML
MCMC with surveil HTML
Measuring health inequality HTML
Using surveil for public health research HTML

How these are measured

Downloads

3.6K

CRAN downloads in the past year

Rank #12,622 · ~10/day · ~299/mo

Releases R versions

Daily download trend is not available in this view yet.

32530 days

89590 days

3.6K1 year

Compare downloads with other packages →

Also on361 r2u5 autocran

How downloads are counted

Repository

connordonegan/surveil ↗Account: ConnorDonegan

3Stars

1Forks

0Open issues

0Open PRs

4Releases

75Commits

3Commit identities

rstats-packager-statsrstanpublic-healthcancerhealth-equitybayesian-statistics

License file reads as GPL-3.0 · 75 commits · Last activity 2024-07-08 · +50% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 12

Stars over time

2021-12-15 · 22026-09-30 · 3

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/connordonegan/surveil on 2026-10-21.

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2024-07-08

pkgdown site last built 2024-07-08

Reproducibility and dev environment (1)

data-raw/

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

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Installing surveil adds 60 packages (29 with compiled code, 62 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

Depends (1)

R >= 3.5.0

Imports (13)

rstantoolsmethodsRcpp RcppParallel rstan tidybayes dplyr (>= 1.0.7)rlang tidyr ggplot2 gridExtra scales ggdist

LinkingTo (6)

BH Rcpp RcppEigen RcppParallel rstan StanHeaders (>= 2.26.0)

Suggests (3)

rmarkdown knitr testthat

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)

Connor Donegan

Author, Maintainer since 0.1.0 (2021)

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.3.0Latest
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2024-07-08 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
0.2.2
record
2023-10-03 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.2.1
record
2022-08-22 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.2.0
record
2022-04-03 · diff ↗
0.1.1
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2022-01-03 · diff ↗
0.1.0
record
2021-11-11
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-11-11
Total releases: 6 / 5 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Bundled data: 5.7 KB / 3 files
Download size: 626 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("surveil")

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

It points to 10.2196/34589.

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 surveil version 0.3.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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