SmokingHistoryGenerator

7.0.0

R Package for the Smoking History Generator

0packages depend

453downloads / year

63.1%test coverage

11/13checks pass

Overview

About

Maintained by John ClarkeFirst published 2026-06-132 releasesCRAN page ↗GitHub ↗

Efficient R interface to the Cancer Intervention and Surveillance Modeling Network (CISNET) Smoking History Generator microsimulation engine, which synthesizes individual smoking histories (initiation, cessation, intensity) and ages at death from calibrated initiation, cessation, cigarettes-per-day, and mortality tables. The wrapper exposes fixed-cohort and population data-frame simulation, multi-threaded segmentation, reproducible pseudo-random streams (L'Ecuyer RngStream MRG32k3a or Matsumoto--Nishimura Mersenne Twister), legacy CLI-style configuration files, and portable YAML configuration save/load with optional split smoking and mortality parameter bundles. Methods follow Jeon et al. (2012) doi:10.1111/j.1539-6924.2011.01775.x. Random number generators: Matsumoto and Nishimura (1998) doi:10.1145/272991.272995; L'Ecuyer (1999) doi:10.1287/opre.47.1.159; L'Ecuyer et al. (2002) doi:10.1287/opre.50.6.1073.358.

Install

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

install.packages("SmokingHistoryGenerator", 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("NCI-CISNET/shg-r")

Development version from NCI-CISNET/shg-r. 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-smokinghistorygenerator

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-SmokingHistoryGenerator

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-SmokingHistoryGenerator

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 2.7 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 5.35

63.1%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-07-11
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-13
6 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 813 wordsVignettesNopkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 9%

Downloads

453

CRAN downloads in the past year

Rank #22,991 · ~1/day · ~38/mo

Releases R versions

Daily download trend is not available in this view yet.

10530 days

45390 days

4531 year

Compare downloads with other packages →

Also on46 r2u

Repository

GitHub ↗ nci-cisnet/shg-r

0Stars

0Forks

0Open issues

0Open PRs

3Releases

538Commits

5Contributors

shg

License AGPL-3.0 · 538 commits · Last activity 2026-06-18

Releases over time

2025-02-17 · 12026-07-07 · 3

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/nci-cisnet/shg-r on 2026-08-02.

Continuous integration (1)

GitHub Actions

Research and citation (1)

CITATION.cff

Lint, format, editor (3)

lintrVS CodeRStudio project

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (3)

methodsRcpp yaml

LinkingTo (1)

Rcpp

Suggests (3)

testthat glue httr2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (7)

Maintainer (1)

John Clarke

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Contributors (3)

Pierre L'Ecuyer

Contributor, Copyright holder

Makoto Matsumoto

Contributor, Copyright holder

Takuji Nishimura

Contributor, Copyright holder

Pierre L'Ecuyer

Contributor, Copyright holder

Makoto Matsumoto

Contributor, Copyright holder

Takuji Nishimura

Contributor, Copyright holder

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

7.0.0Latest
2026-06-14 · current release · diff ↗
6.5.3-1.0.1
2026-06-13
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-13
Total releases: 2 / 1 yrs
License: GPL-3 OSI
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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