R Observatory: Metrics for coarseDataTools version 0.7.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

coarseDataTools

0.7.2Package record

Analysis of Coarsely Observed Data

1packages depend

25.2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Nicholas G. ReichCRAN page ↗Website ↗

Functions to analyze coarse data. Specifically, it contains functions to (1) fit parametric accelerated failure time models to interval-censored survival time data, and (2) estimate the case-fatality ratio in scenarios with under-reporting. This package's development was motivated by applications to infectious disease: in particular, problems with estimating the incubation period and the case fatality ratio of a given disease. Sample data files are included in the package. See Reich et al. (2009) doi:10.1002/sim.3659, Reich et al. (2012) doi:10.1111/j.1541-0420.2011.01709.x, and Lessler et al. (2009) doi:10.1016/S1473-3099(09)70069-6.

Changes in 0.7.2

update cross-reference link for CRAN compatibility

From NEWS.md in the release

Install

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

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

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

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-coarsedatatools

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-coarseDataTools

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-coarseDataTools

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: 2.4 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.7.2

READMEYes · 163 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.7.2Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 17
Examples that run: 100%6 run in a plain check
Exported functions with examples: 33%
Documented parameters: 95%
Return-value docs: 100%
Help pages citing references: 6%

Vignettes (1)

Example for estimating the case fatality ratio HTML

How these are measured

Downloads

25.2K

CRAN downloads in the past year

Rank #2,061 · ~69/day · ~2.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.8K30 days

8.7K90 days

25.2K1 year

Compare downloads with other packages →

Also on180 r2u9 autocran71 c2d4u

How downloads are counted

Repository

nickreich/coarsedatatools ↗Account: nickreich

10Stars

6Forks

14Open issues

1Open PRs

6Releases

173Commits

8Commit identities

173 commits · Last activity 2025-04-11 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2024-09-24 · 92026-07-07 · 10

How these are measured

PracticesBeta

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

Checks run against github.com/nickreich/coarsedatatools on 2026-10-11.

Continuous integration (3)

GitHub ActionsR CMD check workflowTravis CI (config file)

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

Docs source (3)

pkgdown

GitHub Pages site last deployed 2025-04-11 · The repository has a site deploy workflow

pkgdown site last built 2025-04-11

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (2)

lintrLint workflow

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Installing coarseDataTools adds 6 packages (4 with compiled code, 3.7 MB of source tarballs). Heaviest: mcmc 1.5 MB, quantreg 903 KB, MCMCpack 718 KB.

Depends (1)

R >= 3.5.0

Imports (4)

MCMCpackgraphicsstatsmethods

LinkingTo (0)

none

Suggests (2)

markdown knitr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

4indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

EpiEstim

How these are counted

Code & Tests

Datasets

People & History

People (5)

Nicholas G. Reich

Author, Maintainer since 0.1 (2010)

Andrew Azman

Author · added in 3.0.2

Justin Lessler

Author · added in 2.13.1

Hugo Gruson

Contributor · added in 0.7.2

Zhian N. Kamvar

Contributor · added in 0.6-4

Releases (14)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
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R 4.5.0 released · 2025-04-11
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R 4.4.0 released · 2024-04-24
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R 4.3.0 released · 2023-04-21
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R 4.2.0 released · 2022-04-22
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R 4.1.0 released · 2021-05-18
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R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
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R 3.5.0 released · 2018-04-23
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R 3.4.0 released · 2017-04-21
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R 3.3.0 released · 2016-05-03
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R 3.2.0 released · 2015-04-16
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R 3.1.0 released · 2014-04-10
removedRemoved from CRAN
2013-08-05
3.0.2Latest
record
2013-08-04 · current release · diff ↗ ·
removed 1 export
pattern:.

added 9 exports
dic.fit.mcmc, dic.fit, EMforCFR, generate.coarse.data, get.obs.type, loglikhd, precision.simulation.coarse, precision.simulation.exact, precision.simulation
R
R 3.0.0 released · 2013-04-03

Show 19 earlier eventsHide 19 earlier events

R
R 2.15.0 released · 2012-03-30
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R 2.14.0 released · 2011-10-31
2.13.1
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2011-04-20 · diff ↗ ·
added 1 export
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R 2.13.0 released · 2011-04-13
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R 2.12.0 released · 2010-10-15
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2010-08-14 · diff ↗
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R 2.11.0 released · 2010-04-22
2.11.0
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2010-04-01 · diff ↗
0.7.2
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2025-04-11 · diff ↗
0.6-6
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2021-12-09 · diff ↗
0.6-5
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2019-12-06 · diff ↗
0.6-4
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2019-06-05 · diff ↗
0.6-3
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2016-03-12 · diff ↗
0.6-2
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2013-08-05 · diff ↗
0.5.1
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2012-10-29 · diff ↗
0.3
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2010-08-18 · diff ↗
0.2
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2010-05-05 · diff ↗
0.1
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2010-04-09
R
R 2.10.0 released · 2009-10-26

Package metadata

First published: 2010-04-01
Total releases: 14 / 16 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 2.3 KB / 4 files
Download size: 67 KB

Appears in task views

Epidemiology Survival Analysis

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("coarseDataTools")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 coarseDataTools version 0.7.2 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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