EpiInvert

0.3.1

Variational Techniques in Epidemiology

0packages depend

3.1Kdownloads / year

51.9%test coverage

0/13checks pass

Overview

About

Maintained by Luis AlvarezFirst published 2022-05-186 releasesCRAN page ↗GitHub ↗

Using variational techniques we address some epidemiological problems as the incidence curve decomposition by inverting the renewal equation as described in Alvarez et al. (2021) doi:10.1073/pnas.2105112118 and Alvarez et al. (2022) doi:10.3390/biology11040540 or the estimation of the functional relationship between epidemiological indicators. We also propose a learning method for the short time forecast of the trend incidence curve as described in Morel et al. (2022) doi:10.1101/2022.11.05.22281904.

Install

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

install.packages("EpiInvert", 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("lalvarezmat/EpiInvert")

Development version from lalvarezmat/EpiInvert. 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-epiinvert

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-EpiInvert

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-EpiInvert

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

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 3.1 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.07

51.9%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-06-09
0 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
0 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-22
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
0 OK · 13 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 194 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 13%

Downloads

3.1K

CRAN downloads in the past year

Rank #12,619 · ~9/day · ~259/mo

Releases R versions

Daily download trend is not available in this view yet.

21430 days

80290 days

3.1K1 year

Compare downloads with other packages →

Also on448 r2u2 autocran

Repository

GitHub ↗ lalvarezmat/epiinvert

3Stars

0Forks

0Open issues

0Open PRs

0Releases

99Commits

1Contributors

99 commits · Last activity 2023-12-31 · 0% stars, 30d

Stars over time

2023-03-17 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/lalvarezmat/epiinvert on 2026-08-02.

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (1)

Rcpp

LinkingTo (1)

Rcpp

Suggests (7)

knitr ggplot2griddplyr testthat rmarkdown ggpubr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Luis Alvarez

Author, Maintainer

Authors (1)

Luis Alvarez

Author, Maintainer

Contributors (2)

Jean-David Morel

Contributor

Jean-Michel Morel

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.3.1Latest
2022-12-14 · current release · diff ↗
0.3.0
2022-12-08 · diff ↗
0.2.1
2022-10-16 · diff ↗
unarchivedReturned to CRAN
2022-10-16
archivedRemoved from CRAN
2022-08-24
issues were not corrected in time
0.2.0
2022-08-09 · diff ↗
0.1.1
2022-05-20 · diff ↗
0.1.0
2022-05-18
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-05-18
Total releases: 6 / 4 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.10
Bundled data: 1.6 MB / 6 files
Download size: 1.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Epidemiology

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