Data

Tools

Indexes

Applications

Experiments

Open Source Science

socialmixr

R package for deriving social mixing matrices from survey data.

https://github.com/epiforecasts/socialmixr

Science Score: 36.0%

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

  • ○
    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
    3 of 13 committers (23.1%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.7%) to scientific vocabulary

Keywords

r r-package

Keywords from Contributors

standardization epidemiology interpretability hacking outbreak-analysis stan animations mesh interactive gaussian-processes
Last synced: 6 months ago · JSON representation

Repository

R package for deriving social mixing matrices from survey data.

Basic Info
Statistics
  • Stars: 40
  • Watchers: 2
  • Forks: 13
  • Open Issues: 31
  • Releases: 6
Topics
r r-package
Created over 9 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---

# Social mixing matrices for infectious disease modelling in R


[![CRAN version](https://www.r-pkg.org/badges/version-ago/socialmixr)](https://cran.r-project.org/package=socialmixr)
[![R-CMD-check](https://github.com/epiforecasts/socialmixr/workflows/R-CMD-check/badge.svg)](https://github.com/epiforecasts/socialmixr/actions)
[![Codecov test coverage](https://codecov.io/gh/epiforecasts/socialmixr/graph/badge.svg)](https://app.codecov.io/gh/epiforecasts/socialmixr)


[socialmixr](https://github.com/epiforecasts/socialmixr) is an `R` package to derive social mixing matrices from survey data.

# Installation

The package can be installed using

```r
install.packages("socialmixr")
```

The current development version can be installed using the `remotes` package

```r
remotes::install_github("epiforecasts/socialmixr")
```

# Documentation

For information on how to use the socialmixr package, see the [introduction vignette](https://epiforecasts.io/socialmixr/articles/socialmixr.html).

## Contributors









All contributions to this project are gratefully acknowledged using the [`allcontributors` package](https://github.com/ropensci/allcontributors) following the [allcontributors](https://allcontributors.org) specification. Contributions of any kind are welcome!

### Code


sbfnk, 
Bisaloo, 
lwillem, 
alxsrobert, 
Degoot-AM, 
pearsonca, 
jarvisc1, 
jamesmbaazam, 
mariabnd, 
samclifford, 
TimTaylor



### Issue Authors


bastistician, 
BlackEdder, 
Pinzo1, 
florpi, 
cchauve, 
thutran, 
dlaydon, 
deusthindwa, 
krivit, 
linyang17, 
cliu822, 
NaomiWaterlow, 
aakhmetz, 
adamkucharski, 
chitrams, 
IsaacStopard



### Issue Contributors


vikkytom, 
njtierney, 
bahadzie, 
joshwlambert

Owner

  • Name: Epiforecasts
  • Login: epiforecasts
  • Kind: organization
  • Email: sebastian.funk@lshtm.ac.uk
  • Location: London

Researchers at the London School of Hygiene & Tropical Medicine doing research to forecast infectious diseases and perform real-time analyses.

GitHub Events

Total
  • Create event: 33
  • Release event: 1
  • Issues event: 37
  • Watch event: 1
  • Delete event: 29
  • Issue comment event: 51
  • Push event: 121
  • Pull request review comment event: 50
  • Pull request review event: 41
  • Pull request event: 42
  • Fork event: 1
Last Year
  • Create event: 33
  • Release event: 1
  • Issues event: 37
  • Watch event: 1
  • Delete event: 29
  • Issue comment event: 51
  • Push event: 121
  • Pull request review comment event: 50
  • Pull request review event: 41
  • Pull request event: 42
  • Fork event: 1

Committers

Last synced: 8 months ago

All Time
  • Total Commits: 571
  • Total Committers: 13
  • Avg Commits per committer: 43.923
  • Development Distribution Score (DDS): 0.229
Past Year
  • Commits: 42
  • Committers: 7
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.405
Top Committers
Name Email Commits
Sebastian Funk s****k@l****k 440
Hugo Gruson B****o 76
lwillem l****m@u****e 31
dependabot[bot] 4****] 10
alxsrobert a****3@g****m 4
github-actions[bot] 4****] 3
Maria 3****d 1
James Azam j****m@g****m 1
Chris u****9@g****m 1
Carl A. B. Pearson p****a 1
Abdoelnaser M Degoot d****t@a****a 1
Tim Taylor t****r@u****k 1
Sam Clifford s****d@l****k 1
Committer Domains (Top 20 + Academic)
lshtm.ac.uk: 2 ukhsa.gov.uk: 1 aims.ac.za: 1 uantwerpen.be: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 87
  • Total pull requests: 107
  • Average time to close issues: 4 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 26
  • Total pull request authors: 14
  • Average comments per issue: 1.41
  • Average comments per pull request: 0.91
  • Merged pull requests: 93
  • Bot issues: 0
  • Bot pull requests: 19
Past Year
  • Issues: 31
  • Pull requests: 39
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 21 days
  • Issue authors: 6
  • Pull request authors: 8
  • Average comments per issue: 0.9
  • Average comments per pull request: 0.26
  • Merged pull requests: 30
  • Bot issues: 0
  • Bot pull requests: 16
View more stats
Top Authors
Issue Authors
  • sbfnk (39)
  • Bisaloo (11)
  • lwillem (6)
  • njtierney (5)
  • jarvisc1 (2)
  • mariabnd (2)
  • BlackEdder (2)
  • Pinzo1 (1)
  • krivit (1)
  • bastistician (1)
  • aakhmetz (1)
  • Degoot-AM (1)
  • cliu822 (1)
  • TimTaylor (1)
  • adamkucharski (1)
Pull Request Authors
  • sbfnk (54)
  • Bisaloo (23)
  • dependabot[bot] (23)
  • lwillem (14)
  • github-actions[bot] (7)
  • njtierney (5)
  • Degoot-AM (2)
  • jamesmbaazam (2)
  • pearsonca (2)
  • alxsrobert (1)
  • mariabnd (1)
  • samclifford (1)
  • TimTaylor (1)
  • jarvisc1 (1)
Top Labels
Issue Labels
bug (7) help wanted (6) good first issue (3) enhancement (2) question (2) documentation (1)
Pull Request Labels
dependencies (23) documentation (7) github_actions (1)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 555 last-month
  • Total docker downloads: 41,971
  • Total dependent packages: 2
  • Total dependent repositories: 13
  • Total versions: 14
  • Total maintainers: 1
cran.r-project.org: socialmixr

Social Mixing Matrices for Infectious Disease Modelling

  • Versions: 14
  • Dependent Packages: 2
  • Dependent Repositories: 13
  • Downloads: 555 Last month
  • Docker Downloads: 41,971
Rankings
Docker downloads count: 0.6%
Forks count: 6.8%
Dependent repos count: 8.0%
Stargazers count: 9.0%
Average: 9.1%
Dependent packages count: 13.7%
Downloads: 16.5%
Maintainers (1)
sebastian.funk@lshtm.ac.uk
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • countrycode * imports
  • curl * imports
  • data.table * imports
  • fields * imports
  • grDevices * imports
  • httr * imports
  • jsonlite * imports
  • lubridate * imports
  • oai * imports
  • stringr * imports
  • wpp2017 * imports
  • xml2 * imports
  • ggplot2 * suggests
  • knitr * suggests
  • reshape2 * suggests
  • rmarkdown * suggests
  • roxyglobals >= 0.2.1 suggests
  • testthat * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/check-r-package v1 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
  • r-lib/actions/setup-r-dependencies v1 composite
.github/workflows/document.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 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
.github/workflows/pkgdown.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
  • r-lib/actions/setup-r-dependencies v1 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v1 composite
  • r-lib/actions/setup-r-dependencies v1 composite
.github/workflows/pr-commands.yaml actions
  • actions/checkout v4 composite
  • r-lib/actions/pr-fetch v2 composite
  • r-lib/actions/pr-push v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/render_readme.yaml actions
  • actions/checkout v4 composite
  • actions/upload-artifact v4 composite
  • peter-evans/create-pull-request v7 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/style.yaml actions
  • actions/cache v4 composite
  • actions/checkout v4 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite