EpiNova

0.1.0

Flexible Extended State-Space Epidemiological Models with Modern Inference

0packages depend

1.3Kdownloads / year

0.0%test coverage

12/13checks pass

Overview

About

Maintained by Subir HaitFirst published 2026-04-221 releasesCRAN page ↗GitHub ↗

An extended epidemiological modelling framework that goes beyond the classical SIR (Susceptible-Infectious-Recovered) model. Supports SEIR (Susceptible-Exposed-Infectious-Recovered), SEIRD (Susceptible-Exposed-Infectious-Recovered-Deceased), SVEIRD (Susceptible-Vaccinated-Exposed-Infectious-Recovered-Deceased), and age-stratified compartmental models with flexible intervention functions (spline-based, Gaussian process, or user-defined). Inference is available via maximum likelihood or sequential Monte Carlo (SMC, also known as particle filtering) with no external binary dependencies. Includes a dependency-free real-time effective reproduction number (Rt) estimator, spatial multi-patch models with gravity-model mobility, ensemble forecasting via Bayesian model averaging (BMA), and proper scoring rules including CRPS (Continuous Ranked Probability Score), coverage, and MAE (Mean Absolute Error) for forecast evaluation. Methods follow Anderson and May (1991, ISBN:9780198545996), Doucet, de Freitas, and Gordon (2001) doi:10.1007/978-1-4757-3437-9, Cori et al. (2013) doi:10.1093/aje/kwt133, and Gneiting and Raftery (2007) doi:10.1198/016214506000001437.

Install

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

install.packages("EpiNova", 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("causalfragility-lab/EpiNova")

Development version from causalfragility-lab/EpiNova. 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-epinova

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-EpiNova

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-EpiNova

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

Health

CRAN checks

1NOTE12OK

Failing flavors

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

Slowest check: 2.8 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.26

0.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-23
8 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 329 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 99%
Return-value docs: 96%
References docs: 0%

Downloads

1.3K

CRAN downloads in the past year

Rank #9,107 · ~4/day · ~112/mo

Releases R versions

Daily download trend is not available in this view yet.

23830 days

1.1K90 days

1.3K1 year

Compare downloads with other packages →

Also on34 r2u1 autocran

Repository

GitHub ↗ causalfragility-lab/epinova

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2026-04-21

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/causalfragility-lab/epinova on 2026-07-31.

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (6)

deSolve ggplot2 dplyr tidyrsplinesscales

LinkingTo (0)

none

Suggests (11)

DEoptimMASSnumDeriv rstan TMB EpiEstim knitr rmarkdown testthat ggpubr patchwork

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Subir Hait

Author, Maintainer

Authors (1)

Subir Hait

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
2026-04-22 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-04-22
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0.0
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →