EpiEstim

A tool to estimate time varying instantaneous reproduction number during epidemics

https://github.com/mrc-ide/epiestim

Science Score: 67.0%

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

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 15 DOI reference(s) in README
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Academic publication links
Links to: plos.org, zenodo.org
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Committers with academic emails
6 of 16 committers (37.5%) from academic institutions
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Institutional organization owner
Organization mrc-ide has institutional domain (www.imperial.ac.uk)
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (12.2%) to scientific vocabulary

Keywords from Contributors

probability-distributions epidemiology epiverse parallel best-practices latex

Last synced: 6 months ago · JSON representation

Repository

A tool to estimate time varying instantaneous reproduction number during epidemics

Basic Info

Host: GitHub
Owner: mrc-ide
Language: R
Default Branch: main
Homepage: https://mrc-ide.github.io/EpiEstim
Size: 21.1 MB

Statistics

Stars: 99
Watchers: 15
Forks: 41
Open Issues: 48
Releases: 5

Created over 10 years ago · Last pushed 9 months ago

Metadata Files

Readme Changelog

EpiEstim

EpiEstim is a tool to estimate the time-varying instantaneous reproduction number during epidemics. To install the latest version, use: r install.packages('EpiEstim', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org'))

Vignettes

Please see https://mrc-ide.github.io/EpiEstim/ for vignettes with worked examples, FAQs and details about how EpiEstim can be used alongside some other R packages in an outbreak analysis workflow.

Cite our papers

Anne Cori, Neil M. Ferguson, Christophe Fraser, Simon Cauchemez, A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics, American Journal of Epidemiology, Volume 178, Issue 9, 1 November 2013, Pages 1505–1512.

console @article{Cori2013, author={Cori, A and Ferguson, NM and Fraser, C and Cauchemez, S}, year={2013}, title={{A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics}}, journal={Am. J. Epidemiol.}, doi={10.1093/aje/kwt133}, }

Thompson RN, Stockwin JE, van Gaalen RD, Polonsky JA, Kamvar ZN, Demarsh PA, et al. Improved inference of time-varying reproduction numbers during infectious disease outbreaks, Epidemics, Volume 29, 1 December 2019, 100356.

Nash RK, Nouvellet P, Cori A. Real-time estimation of the epidemic reproduction number: Scoping review of the applications and challenges, PLOS Digital Health, Volume 1, Issue 6, 27 June 2022, e0000052.

Bhatia S, Wardle J, Nash RK, Nouvellet P, Cori A. Extending EpiEstim to estimate the transmission advantage of pathogen variants in real-time: SARS-CoV-2 as a case-study, Epidemics, 21 June 2023, 100692.

Nash RK, Cori A, Nouvellet P. Estimating the epidemic reproduction number from temporally aggregated incidence data: a statistical modelling approach and software tool, PLOS Computational Biology, Volume 19, Issue 8, 28 August 2023, e1011439.

Brizzi A, O'Driscoll M, Dorigatti I., Refining Reproduction Number Estimates to Account for Unobserved Generations of Infection in Emerging Epidemics, Clinical Infectious Diseases, Volume 75, Issue 1, 1 July 2022, Pages e114–e121.

Citing this code resource

We kindly request that you cite this codebase as follows (BibTeX format):

console @misc{Cori2022, author={Cori, A and Kamvar, ZN and Stockwin, J and Jombart, T and Dahlqwist, E and FitzJohn, R and Thompson, R and Nash, RK and Wardle, J and Bhatia, S}, year={2022}, title={{EpiEstim v2.2-4: A tool to estimate time varying instantaneous reproduction number during epidemics}}, publisher={GitHub}, journal={GitHub repository}, howpublished = {\url{https://github.com/mrc-ide/EpiEstim}}, }

Owner

Name: MRC Centre for Global Infectious Disease Analysis
Login: mrc-ide
Kind: organization
Location: London, UK

Website: https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis
Repositories: 413
Profile: https://github.com/mrc-ide

MRC Centre hosted within the Department of Infectious Disease Epidemiology at Imperial College London

GitHub Events

Total

Issues event: 3
Watch event: 3
Delete event: 2
Issue comment event: 7
Push event: 11
Pull request review event: 2
Pull request event: 6
Fork event: 1
Create event: 4

Last Year

Issues event: 3
Watch event: 3
Delete event: 2
Issue comment event: 7
Push event: 11
Pull request review event: 2
Pull request event: 6
Fork event: 1
Create event: 4

Committers

Last synced: 10 months ago

All Time

Total Commits: 524
Total Committers: 16
Avg Commits per committer: 32.75
Development Distribution Score (DDS): 0.538

Past Year

Commits: 27
Committers: 3
Avg Commits per committer: 9.0
Development Distribution Score (DDS): 0.519

Top Committers

Name	Email	Commits
Anne Cori	a**i@i**k	242
rebeccanash	r**h@i**k	93
Zhian N. Kamvar	z**r@g**m	38
abriz97	a**i@l**t	36
Jake Stockwin	j**n@g**m	25
sangeeta	s**3@g**m	25
Hugo Gruson	B****o	22
Thibaut Jombart	t**t@g**m	16
Jack Wardle	j**9@i**k	13
Rich FitzJohn	r**n@i**k	5
Tim Pollington	t**n@g**m	3
Pietro Monticone	3****e	2
ElisabethDahlqwist	e**t@h**m	1
Ewout ter Hoeven	E**n@s**l	1
Anne Cori	a**i@W**l	1
Robin Thompson	r**n@l**k	1

Committer Domains (Top 20 + Academic)

imperial.ac.uk: 4 lmh.ox.ac.uk: 1 student.tudelft.nl: 1 live.it: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 65
Total pull requests: 52
Average time to close issues: 4 months
Average time to close pull requests: about 1 month
Total issue authors: 33
Total pull request authors: 14
Average comments per issue: 1.35
Average comments per pull request: 1.42
Merged pull requests: 46
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 3
Pull requests: 4
Average time to close issues: about 2 hours
Average time to close pull requests: about 2 months
Issue authors: 3
Pull request authors: 4
Average comments per issue: 1.67
Average comments per pull request: 0.75
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

annecori (11)
sangeetabhatia03 (9)
zkamvar (6)
thibautjombart (6)
robchallen (2)
abriz97 (2)
jstockwin (2)
pnouvellet (2)
adamkucharski (1)
steffilazerte (1)
tamas-ferenci (1)
BGalindo-Prieto (1)
arnold-c (1)
t-pollington (1)
seabbs (1)

Pull Request Authors

annecori (12)
zkamvar (8)
sangeetabhatia03 (7)
rebeccanash (5)
jstockwin (4)
Bisaloo (4)
richfitz (4)
pitmonticone (2)
j-wardle (2)
abriz97 (2)
thibautjombart (2)
seabbs (2)
EwoutH (1)
t-pollington (1)

Top Labels

Issue Labels

enhancement (6) bug (3) priority (1)

Pull Request Labels

enhancement (1)

Packages

Total packages: 1
Total downloads:
- cran 1,273 last-month
Total docker downloads: 21,770

Total dependent packages: 7
Total dependent repositories: 21
Total versions: 9
Total maintainers: 1

cran.r-project.org: EpiEstim

Estimate Time Varying Reproduction Numbers from Epidemic Curves

Homepage: https://github.com/mrc-ide/EpiEstim
Documentation: http://cran.r-project.org/web/packages/EpiEstim/EpiEstim.pdf
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
Latest release: 2.2-5
published 8 months ago

Versions: 9
Dependent Packages: 7
Dependent Repositories: 21
Downloads: 1,273 Last month
Docker Downloads: 21,770

Rankings

Docker downloads count: 0.6%

Forks count: 2.0%

Stargazers count: 4.2%

Average: 5.4%

Dependent repos count: 6.0%

Dependent packages count: 7.3%

Downloads: 12.4%

Maintainers (1)

a.cori@imperial.ac.uk

Last synced: 7 months ago

Dependencies

DESCRIPTION cran

R >= 2.10 depends
abind * imports
coarseDataTools >= 0.6 imports
coda * imports
fitdistrplus * imports
ggplot2 * imports
grDevices * imports
graphics * imports
gridExtra * imports
incidence >= 1.7.0 imports
reshape2 * imports
scales * imports
stats * imports
MCMCglmm * suggests
covr * suggests
dplyr * suggests
gghighlight * suggests
hrbrthemes * suggests
kableExtra * suggests
knitr * suggests
projections * suggests
readxl * suggests
rmarkdown * suggests
testthat * suggests
utils * suggests
vdiffr * suggests

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

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact main composite
r-lib/actions/setup-pandoc v1 composite
r-lib/actions/setup-r v1 composite

.github/workflows/pkgdown.yaml actions

actions/cache v2 composite
actions/checkout v2 composite
r-lib/actions/setup-pandoc v1 composite
r-lib/actions/setup-r v1 composite

.github/workflows/test-coverage.yaml actions

actions/cache v2 composite
actions/checkout v2 composite
r-lib/actions/setup-pandoc v1 composite
r-lib/actions/setup-r v1 composite

.github/workflows/lint-changed-files.yaml actions

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

EpiEstim

Science Score: 67.0%

Keywords from Contributors

Repository

Basic Info

Statistics

Metadata Files

README.md

EpiEstim

Vignettes

Cite our papers

Citing this code resource

Owner

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

Packages

cran.r-project.org: EpiEstim

Rankings

Maintainers (1)

Dependencies