EpidigiR

0.1.2

Digital Epidemiological Analysis and Visualization Tools

0packages depend

1.6Kdownloads / year

40.6%test coverage

13/13checks pass

Overview

About

Maintained by Esther Atsabina WanjalaFirst published 2025-11-051 releasesCRAN page ↗

Integrates methods for epidemiological analysis, modeling, and visualization, including functions for summary statistics, SIR (Susceptible-Infectious-Recovered) modeling, DALY (Disability-Adjusted Life Years) estimation, age standardization, diagnostic test evaluation, NLP (Natural Language Processing) keyword extraction, clinical trial power analysis, survival analysis, SNP (Single Nucleotide Polymorphism) association, and machine learning methods such as logistic regression, k-means clustering, Random Forest, and Support Vector Machine (SVM). Includes datasets for prevalence estimation, SIR modeling, genomic analysis, clinical trials, DALY, diagnostic tests, and survival analysis. Methods are based on Gelman et al. (2013) doi:10.1201/b16018 and Wickham et al. (2019, ISBN:9781492052040>.

Install

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

install.packages("EpidigiR", 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-epidigir

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-EpidigiR

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-EpidigiR

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

Health

CRAN checks

13OK

Slowest check: 2.4 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.50

40.6%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

1.6K

CRAN downloads in the past year

Rank #21,334 · ~4/day · ~135/mo

Releases R versions

Daily download trend is not available in this view yet.

18330 days

56790 days

1.6K1 year

Compare downloads with other packages →

Also on49 r2u16 autocran

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (6)

deSolve sp tm glmnet caretsurvival

LinkingTo (0)

none

Suggests (8)

kernlab randomForeststatsknitr rmarkdown quarto usethis testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 649 (51%)Rd 413 (32%)Vignettes 214 (17%)

Code characteristics

Cyclomatic complexity: 20.0 median / 23 max
Test cases: 9 / 0.50 per code line

Test coverage

Line coverage

41%

Expression

44.8%

Tests / Examples

40.6% / 44% ex

Functions

3 3 exported

Complexity

17.7 avg / 23 max

Call network

3 nodes / 0 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

3 functions

Function	Cyclo	Coverage
epi_model exp	20	36%
epi_analyze exp	23	36%
epi_visualize exp	10	70%

Datasets

Bundled datasets · 10

Name	Class	Rows × Cols	Also ships in
clinical_data	data.frame	200 × 6	–
daly_data	data.frame	20 × 3	–
diagnostic_data	data.frame	10 × 5	–
epi_prevalence	data.frame	12 × 7	–
geno_data	data.frame	100 × 2	–
ml_data	data.frame	100 × 5	–
nlp_data	data.frame	100 × 2	–
sir_data	data.frame	50 × 4	–
survey_data	data.frame	20 × 3	–
survival_data	data.frame	100 × 3	–

People & History

People (1)

Maintainer (1)

Esther Atsabina Wanjala

Author, Maintainer

Authors (1)

Esther Atsabina Wanjala

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.2Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-11-05
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0.0
Bundled data: 11 KB / 10 files
Download size: 56 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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