epiverse

Meta-package for the Epiverse-TRACE R packages

https://github.com/epiverse-trace/epiverse

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
○
Academic publication links
○
Committers with academic emails
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (17.2%) to scientific vocabulary

Keywords

epiverse r r-package

Keywords from Contributors

colombia demographics

Last synced: 8 months ago · JSON representation ·

Repository

Meta-package for the Epiverse-TRACE R packages

Basic Info

Host: GitHub
Owner: epiverse-trace
License: other
Language: R
Default Branch: main
Homepage: https://epiverse-trace.github.io/epiverse/
Size: 8.26 MB

Statistics

Stars: 1
Watchers: 1
Forks: 0
Open Issues: 1
Releases: 0

Topics

epiverse r r-package

Created over 2 years ago · Last pushed 8 months ago

Metadata Files

Readme Changelog License Citation

README.Rmd

---
output: github_document
---








```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# {{ packagename }} 


[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/)
[![R-CMD-check](https://github.com/{{ gh_repo }}/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/{{ gh_repo }}/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/{{ gh_repo }}/branch/main/graph/badge.svg)](https://app.codecov.io/gh/{{ gh_repo }}?branch=main)
[![lifecycle-concept](https://raw.githubusercontent.com/reconverse/reconverse.github.io/master/images/badge-concept.svg)](https://www.reconverse.org/lifecycle.html#concept) 


{{ packagename }} is a meta-package to provide easy access to all Epiverse-TRACE packages.

If you are looking for information about the Epiverse-TRACE in general, please visit the [Epiverse-TRACE website](https://epiverse-trace.github.io/).

## Installation

You can install the development version of {{ packagename }} from
[GitHub](https://github.com/) with:

``` r
# install.packages("pak")
pak::pak("{{ gh_repo }}")
```

## Development

### Lifecycle

This package is currently a *concept*, as defined by the [RECON software
lifecycle](https://www.reconverse.org/lifecycle.html). This means that essential
features and mechanisms are still being developed, and the package is not ready
for use outside of the development team.


### Contributions

Contributions are welcome via [pull requests](https://github.com/{{ gh_repo }}/pulls).

### Code of Conduct

Please note that the {{ packagename }} project is released with a 
[Contributor Code of Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md).
By contributing to this project, you agree to abide by its terms.

Owner

Name: Epiverse-TRACE
Login: epiverse-trace
Kind: organization

Website: https://epiverse.org
Repositories: 17
Profile: https://github.com/epiverse-trace

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "epiverse" in publications use:'
type: software
license: MIT
title: 'epiverse: Meta-Package for the Epiverse-TRACE Project'
version: 0.0.1
abstract: A meta-package to provide easy access to all 'Epiverse-TRACE' packages released
  on CRAN. From a technical perspective, it is also where integration tests across
  packages are hosted, and where dependency scaffolding at the level of this ecosystem
  is investigated.
authors:
- family-names: Gruson
  given-names: Hugo
  email: hugo@data.org
  orcid: https://orcid.org/0000-0002-4094-1476
repository-code: https://github.com/epiverse-trace/epiverse
url: https://epiverse-trace.github.io/epiverse
contact:
- family-names: Gruson
  given-names: Hugo
  email: hugo@data.org
  orcid: https://orcid.org/0000-0002-4094-1476
keywords:
- epiverse
- r
- r-package
references:
- type: software
  title: cfr
  abstract: 'cfr: Estimate Disease Severity and Case Ascertainment'
  notes: Depends
  url: https://epiverse-trace.github.io/cfr/
  repository: https://CRAN.R-project.org/package=cfr
  authors:
  - family-names: Gupte
    given-names: Pratik R.
    email: pratik.gupte@lshtm.ac.uk
    orcid: https://orcid.org/0000-0001-5294-7819
  - family-names: Kucharski
    given-names: Adam
    email: adam.kucharski@lshtm.ac.uk
    orcid: https://orcid.org/0000-0001-8814-9421
  - family-names: Russell
    given-names: Tim
    email: timothy.russell@lshtm.ac.uk
    orcid: https://orcid.org/0000-0001-5610-6080
  year: '2025'
  doi: 10.32614/CRAN.package.cfr
- type: software
  title: cleanepi
  abstract: 'cleanepi: Clean and Standardize Epidemiological Data'
  notes: Depends
  url: https://epiverse-trace.github.io/cleanepi/
  repository: https://CRAN.R-project.org/package=cleanepi
  authors:
  - family-names: Mané
    given-names: Karim
    email: karim.mane@lshtm.ac.uk
    orcid: https://orcid.org/0000-0002-9892-2999
  - family-names: Degoot
    given-names: Abdoelnaser
    email: abdoelnaser-mahmood.degoot@lshtm.ac.uk
    orcid: https://orcid.org/0000-0001-8788-2496
  - family-names: Ahadzie
    given-names: Bankolé
    email: Bankole.Ahadzie@lshtm.ac.uk
  - family-names: Mohammed
    given-names: Nuredin
    email: Nuredin.Mohammed@lshtm.ac.uk
  - family-names: Bah
    given-names: Bubacarr
    email: Bubacarr.Bah1@lshtm.ac.uk
    orcid: https://orcid.org/0000-0003-3318-6668
  year: '2025'
  doi: 10.32614/CRAN.package.cleanepi
- type: software
  title: ColOpenData
  abstract: 'ColOpenData: Download Colombian Demographic, Climate and Geospatial Data'
  notes: Depends
  url: https://epiverse-trace.github.io/ColOpenData/
  repository: https://CRAN.R-project.org/package=ColOpenData
  authors:
  - family-names: Tavera-Cifuentes
    given-names: Maria Camila
    email: mc.tavera@uniandes.edu.co
    orcid: https://orcid.org/0009-0007-1610-4583
  - family-names: Otero
    given-names: Julian
    email: jd.otero10@uniandes.edu.co
    orcid: https://orcid.org/0009-0006-0429-7747
  year: '2025'
  doi: 10.32614/CRAN.package.ColOpenData
- type: software
  title: epiCo
  abstract: 'epiCo: Statistical and Viz Tools for Vector-Borne Diseases in Colombia'
  notes: Depends
  url: https://epiverse-trace.github.io/epiCo/
  repository: https://CRAN.R-project.org/package=epiCo
  authors:
  - family-names: Umaña
    given-names: Juan D.
    email: jd.umana10@uniandes.edu.co
    orcid: https://orcid.org/0000-0003-0316-6164
  - family-names: Montenegro-Torres
    given-names: Juan
    email: jf.montenegro@uniandes.edu.co
    orcid: https://orcid.org/0000-0003-2755-4743
  - family-names: Otero
    given-names: Julian
    email: jd.otero10@uniandes.edu.co
    orcid: https://orcid.org/0009-0006-0429-7747
  year: '2025'
  doi: 10.32614/CRAN.package.epiCo
- type: software
  title: epichains
  abstract: 'epichains: Simulating and Analysing Transmission Chain Statistics Using
    Branching Process Models'
  notes: Depends
  url: https://epiverse-trace.github.io/epichains/
  repository: https://CRAN.R-project.org/package=epichains
  authors:
  - family-names: Azam
    given-names: James M.
    email: james.azam@lshtm.ac.uk
    orcid: https://orcid.org/0000-0001-5782-7330
  - family-names: Funk
    given-names: Sebastian
    email: sebastian.funk@lshtm.ac.uk
    orcid: https://orcid.org/0000-0002-2842-3406
  - family-names: Finger
    given-names: Flavio
    email: flavio.finger@epicentre.msf.org
    orcid: https://orcid.org/0000-0002-8613-5170
  year: '2025'
  doi: 10.32614/CRAN.package.epichains
- type: software
  title: epiparameter
  abstract: 'epiparameter: Classes and Helper Functions for Working with Epidemiological
    Parameters'
  notes: Depends
  url: https://github.com/epiverse-trace/epiparameter/
  repository: https://CRAN.R-project.org/package=epiparameter
  authors:
  - family-names: Lambert
    given-names: Joshua W.
    email: joshua.lambert@lshtm.ac.uk
    orcid: https://orcid.org/0000-0001-5218-3046
  - family-names: Kucharski
    given-names: Adam
    email: adam.kucharski@lshtm.ac.uk
    orcid: https://orcid.org/0000-0001-8814-9421
  - family-names: Tamayo
    given-names: Carmen
    email: carmen.tamayo-cuartero@lshtm.ac.uk
    orcid: https://orcid.org/0000-0003-4184-2864
  year: '2025'
  doi: 10.32614/CRAN.package.epiparameter
- type: software
  title: finalsize
  abstract: 'finalsize: Calculate the Final Size of an Epidemic'
  notes: Depends
  url: https://epiverse-trace.github.io/finalsize/
  repository: https://CRAN.R-project.org/package=finalsize
  authors:
  - family-names: Gupte
    given-names: Pratik
    email: pratik.gupte@lshtm.ac.uk
    orcid: https://orcid.org/0000-0001-5294-7819
  - family-names: Van Leeuwen
    given-names: Edwin
    email: edwin.vanleeuwen@ukhsa.gov.uk
    orcid: https://orcid.org/0000-0002-2383-5305
  - family-names: Kucharski
    given-names: Adam
    email: adam.kucharski@lshtm.ac.uk
    orcid: https://orcid.org/0000-0001-8814-9421
  year: '2025'
  doi: 10.32614/CRAN.package.finalsize
- type: software
  title: linelist
  abstract: 'linelist: Tagging and Validating Epidemiological Data'
  notes: Depends
  url: https://epiverse-trace.github.io/linelist/
  repository: https://CRAN.R-project.org/package=linelist
  authors:
  - family-names: Gruson
    given-names: Hugo
    orcid: https://orcid.org/0000-0002-4094-1476
  - family-names: Jombart
    given-names: Thibaut
  year: '2025'
  doi: 10.32614/CRAN.package.linelist
- type: software
  title: simulist
  abstract: 'simulist: Simulate Disease Outbreak Line List and Contacts Data'
  notes: Depends
  url: https://epiverse-trace.github.io/simulist/
  repository: https://CRAN.R-project.org/package=simulist
  authors:
  - family-names: Lambert
    given-names: Joshua W.
    email: joshua.lambert@lshtm.ac.uk
    orcid: https://orcid.org/0000-0001-5218-3046
  - family-names: Tamayo
    given-names: Carmen
    email: carmen.tamayo-cuartero@lshtm.ac.uk
    orcid: https://orcid.org/0000-0003-4184-2864
  year: '2025'
  doi: 10.32614/CRAN.package.simulist
- type: software
  title: sivirep
  abstract: 'sivirep: Data Wrangling and Automated Reports from ''SIVIGILA'' Source'
  notes: Depends
  url: https://epiverse-trace.github.io/sivirep/
  repository: https://CRAN.R-project.org/package=sivirep
  authors:
  - family-names: Gómez-Millán
    given-names: Geraldine
    email: geralidine.gomez@javeriana.edu.co
    orcid: https://orcid.org/0009-0007-8701-0568
  - family-names: Cucunubá
    given-names: Zulma M.
    email: zulma.cucunuba@javeriana.edu.co
    orcid: https://orcid.org/0000-0002-8165-3198
  - family-names: Mendez-Romero
    given-names: Jennifer A.
    email: jenniferk2@hotmail.com
    orcid: https://orcid.org/0009-0001-6138-0225
  - family-names: Huguett-Aragón
    given-names: Claudia
    email: chuguett@hotmail.com
    orcid: https://orcid.org/0000-0002-9814-2386
  year: '2025'
  doi: 10.32614/CRAN.package.sivirep
- type: software
  title: superspreading
  abstract: 'superspreading: Understand Individual-Level Variation in Infectious Disease
    Transmission'
  notes: Depends
  url: https://epiverse-trace.github.io/superspreading/
  repository: https://CRAN.R-project.org/package=superspreading
  authors:
  - family-names: Lambert
    given-names: Joshua W.
    email: joshua.lambert@lshtm.ac.uk
    orcid: https://orcid.org/0000-0001-5218-3046
  - family-names: Kucharski
    given-names: Adam
    email: adam.kucharski@lshtm.ac.uk
    orcid: https://orcid.org/0000-0001-8814-9421
  - family-names: Adam
    given-names: Dillon C.
    email: dcadam@hku.hk
    orcid: https://orcid.org/0000-0002-7485-9905
  year: '2025'
  doi: 10.32614/CRAN.package.superspreading
- type: software
  title: vaccineff
  abstract: 'vaccineff: Estimate Vaccine Effectiveness Based on Different Study Designs'
  notes: Depends
  url: https://epiverse-trace.github.io/vaccineff/
  repository: https://CRAN.R-project.org/package=vaccineff
  authors:
  - family-names: Quevedo
    given-names: David Santiago
    email: ex-dsquevedo@javeriana.edu.co
    orcid: https://orcid.org/0000-0003-1583-4262
  - family-names: Cucunubá
    given-names: Zulma M.
    email: tracelacdev@gmail.com
    orcid: https://orcid.org/0000-0002-8165-3198
  year: '2025'
  doi: 10.32614/CRAN.package.vaccineff
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2025'
  doi: 10.32614/CRAN.package.knitr
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  url: https://pkgs.rstudio.com/rmarkdown/
  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Dervieux
    given-names: Christophe
    email: cderv@posit.co
    orcid: https://orcid.org/0000-0003-4474-2498
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@posit.co
  - family-names: Luraschi
    given-names: Javier
  - family-names: Ushey
    given-names: Kevin
    email: kevin@posit.co
  - family-names: Atkins
    given-names: Aron
    email: aron@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Chang
    given-names: Winston
    email: winston@posit.co
  - family-names: Iannone
    given-names: Richard
    email: rich@posit.co
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2025'
  doi: 10.32614/CRAN.package.rmarkdown
- type: software
  title: spelling
  abstract: 'spelling: Tools for Spell Checking in R'
  notes: Suggests
  url: https://ropensci.r-universe.dev/spelling
  repository: https://CRAN.R-project.org/package=spelling
  authors:
  - family-names: Ooms
    given-names: Jeroen
    email: jeroenooms@gmail.com
    orcid: https://orcid.org/0000-0002-4035-0289
  - family-names: Hester
    given-names: Jim
    email: james.hester@rstudio.com
  year: '2025'
  doi: 10.32614/CRAN.package.spelling
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.testthat
  version: '>= 3.0.0'

GitHub Events

Total

Issues event: 6
Delete event: 8
Issue comment event: 12
Push event: 34
Pull request review comment event: 4
Pull request review event: 10
Pull request event: 17
Create event: 8

Last Year

Issues event: 6
Delete event: 8
Issue comment event: 12
Push event: 34
Pull request review comment event: 4
Pull request review event: 10
Pull request event: 17
Create event: 8

Committers

Last synced: about 1 year ago

All Time

Total Commits: 21
Total Committers: 3
Avg Commits per committer: 7.0
Development Distribution Score (DDS): 0.19

Past Year

Commits: 12
Committers: 2
Avg Commits per committer: 6.0
Development Distribution Score (DDS): 0.083

Top Committers

Name	Email	Commits
Hugo Gruson	1****o	17
GitHub Action	a**n@g**m	3
Chris Hartgerink	c**s@l**g	1

Committer Domains (Top 20 + Academic)

libscie.org: 1 github.com: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time

Total issues: 3
Total pull requests: 3
Average time to close issues: 3 days
Average time to close pull requests: about 21 hours
Total issue authors: 2
Total pull request authors: 3
Average comments per issue: 0.0
Average comments per pull request: 0.0
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 1

Past Year

Issues: 2
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 1
Pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 0.0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 1

View more stats

Top Authors

Issue Authors

joshwlambert (3)
Bisaloo (1)

Pull Request Authors

joshwlambert (5)
Bisaloo (4)
chartgerink (2)
github-actions[bot] (2)

Top Labels

Issue Labels

Pull Request Labels

testing (4)

Dependencies

.github/workflows/R-CMD-check.yaml actions

actions/checkout v3 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/dependency-change.yaml actions

r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/pkgdown.yaml actions

JamesIves/github-pages-deploy-action 4.1.4 composite
actions/checkout v3 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/render_readme.yml actions

actions/checkout v3 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/test-coverage.yaml actions

actions/checkout v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/update-citation-cff.yaml actions

actions/checkout v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

DESCRIPTION cran

cfr * depends
finalsize * depends
linelist * depends
knitr * suggests
rmarkdown * suggests
spelling * suggests
testthat >= 3.0.0 suggests

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

epiverse

Science Score: 44.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies