R Observatory: Metrics for AMISforInfectiousDiseases version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

AMISforInfectiousDiseases

0.1.0Package record

Implement the AMIS Algorithm for Infectious Disease Models

0packages depend

2.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Simon SpencerCRAN page ↗GitHub ↗Issues ↗

Implements the Adaptive Multiple Importance Sampling (AMIS) algorithm, as described by Retkute et al. (2021, doi:10.1214/21-AOAS1486), to estimate key epidemiological parameters by combining outputs from a geostatistical model of infectious diseases (such as prevalence, incidence, or relative risk) with a disease transmission model. Utilising the resulting posterior distributions, the package enables forward projections at the local level.

Install

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

install.packages("AMISforInfectiousDiseases", 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("drsimonspencer/AMISforInfectiousDiseases-dev")

Development version from drsimonspencer/AMISforInfectiousDiseases-dev. 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-amisforinfectiousdiseases

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-AMISforInfectiousDiseases

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-AMISforInfectiousDiseases

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: 6.3 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-02

Show 1 earlier changeHide 1 earlier change

ERROR13 OK, 1 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.0

READMEYes · 463 wordsVignettesYes · 2 · staticNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 9 (1 internal)includes a package overview page
Examples that run: 100%1 run in a plain check
Exported functions with examples: 20%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 11%

Vignettes (2)

Fitting Ascariasis data HTML
Simulation study HTML

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #13,960 · ~8/day · ~244/mo

Releases R versions

Daily download trend is not available in this view yet.

29230 days

84190 days

2.9K1 year

Compare downloads with other packages →

Also on394 r2u32 autocran

How downloads are counted

Repository

drsimonspencer/amisforinfectiousdiseases-dev ↗Account: drsimonspencer

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2026-07-06 · Default branch at 0.1.1, ahead of CRAN 0.1.0 (checked 2026-10-21)

Responsiveness

not measured

How these are measured

PracticesBeta

2 development-tooling and community-health practices detected across 1 family in the upstream repository

Checks run against github.com/drsimonspencer/amisforinfectiousdiseases-dev on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing AMISforInfectiousDiseases adds 98 packages (55 with compiled code, 82 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.1

Imports (5)

Hmisc mclust mnormt Rcpp weights

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (6)

knitr ggplot2 patchwork rmarkdown sf viridis

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (7)

Simon Spencer

Author, Maintainer since 0.1.0 (2025)

Author

Author

Author

Author

Oxford Research Software Engineering

Copyright holder

University of Warwick

Copyright holder

Releases (1)

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.1.0Latest
record
2025-01-20 · current release
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-01-20
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1
Download size: 358 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("AMISforInfectiousDiseases")

Format

Spencer, S., Oxford Research Software Engineering, University of Warwick, Browning, R., Konzen, E., Lestang, T., & Retkute, R. (2025). AMISforInfectiousDiseases: Implement the AMIS Algorithm for Infectious Disease Models (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.AMISforInfectiousDiseases

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 AMISforInfectiousDiseases version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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