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epiCo

R package for statistical and spatiotemporal modeling of epidemiological data for vector-borne diseases in Colombia

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

Science Score: 67.0%

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Keywords

colombia decision-support demographics epiverse outbreak-analysis r r-package sdg-3 spatio-temporal-analysis vector-borne-diseases

Keywords from Contributors

interpretability standardization hack
Last synced: 6 months ago · JSON representation ·

Repository

R package for statistical and spatiotemporal modeling of epidemiological data for vector-borne diseases in Colombia

Basic Info
Statistics
  • Stars: 14
  • Watchers: 3
  • Forks: 2
  • Open Issues: 10
  • Releases: 2
Topics
colombia decision-support demographics epiverse outbreak-analysis r r-package sdg-3 spatio-temporal-analysis vector-borne-diseases
Created over 3 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog License Citation

README.md

epiCo

epiCo provides statistical and visualization tools for the analysis of demographic indicators, and spatio-temporal behavior and characterization of outbreaks of vector-borne diseases (VBDs) in Colombia.

License: MIT R-CMD-check Codecov test coverage lifecycle-maturing DOI <!-- badges: end -->

Installation

You can install the stable version of epiCo from CRAN with:

r install.packages("epiCo")

You can also install the development version of epiCo from GitHub with:

``` r

install.packages("remotes")

remotes::install_github("epiverse-trace/epiCo") ```

Motivation

When reviewing the current epidemiological bulletins published by the local Secretariats of Health in Colombia, we identified an opportunity to create a tool to: - Include spatial and demographic risk assessments into their routine epidemiological reports to better identify population groups for potential interventions. - Facilitate the understanding of the different epidemiological profiles within a region in Colombia regarding the onset, duration, magnitude, and frequency of the outbreaks. - Strengthen the transparency of the methods used for the outbreak analysis. - Provide more informative context by performing spatial correlation analysis.

The package allows for interoperable analyses of linelist data from SIVIGILA (accessible using the Epiverse-TRACE package sivirep) with spatial and demographic data (accessible using the Epiverse-TRACE package ColOpenData).

epiCo can be used to perform the following main tasks at the municipality, departmental, or national level:

  1. To identify demographic vulnerabilities from linelist data and the socioeconomic census, including risk assessment based on age, gender, occupation, and ethnicity.
  2. To assess hot-spot analyses (as Local Moran's index) based on real travel distances in Colombia estimated from Bravo-Vega C., Santos-Vega M., & Cordovez J.M. (2022).
  3. To generate automated outbreak characterization (onset, duration, magnitude, and frequency) using traditional methods as the endemic channel and poisson tests for unusual behavior.
  4. Future features will include correlation analyses between categorical socioeconomic data, climate time series and epidemiological data, nowcasting assessment, underreport estimation, and short-term forecasting.

All features are performed automatically from epidemiological, demographic, spatial, and socioeconomic data published by Colombian institutions, but methods can also be customized as well as input data, so hypothetical information can be tested within the package.

Modules

epiCo contains three modules documented in the following vignettes:

  1. Demographic analyses with epiCo
  2. Building an Endemic Channel with epiCo
  3. Spatiotemporal analyses with epiCo

Development

Lifecycle

This package is currently a maturing product, as defined by the RECON software lifecycle. This means that essential features and mechanisms are functional, documented, and tested. However, the package is open to receive code reviews and is being socialized with expert users.

Contributions

Contributions are welcome via pull requests.

Contributors to the project include:

We acknowledge the contribution of collaborators in Universidad de los Andes, Pontificia Universidad Javeriana, Instituto Nacional de Salud de Colombia, Secretaría de Salud del Tolima, and Epimodelac Course attendees who provided insightful feedback for the package.

Code of Conduct

Please note that the epiCo project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Funding

This work is part of the TRACE-LAC research project funded by the International Research Centre (IDRC) Ottawa, Canada.[109848-001-].

Owner

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

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 "epiCo" in publications use:'
type: software
license: MIT
title: 'epiCo: Statistical and Viz Tools for Vector-Borne Diseases in Colombia'
version: 1.0.0
doi: 10.32614/CRAN.package.epiCo
abstract: Provides statistical and visualization tools for the analysis of demographic
  indicators, and spatio-temporal behavior and characterization of outbreaks of vector-borne
  diseases (VBDs) in Colombia. It implements travel times estimated in Bravo-Vega
  C., Santos-Vega M., & Cordovez J.M. (2022), and the endemic channel method (Bortman,
  M. (1999) <https://iris.paho.org/handle/10665.2/8562>).
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
repository: https://CRAN.R-project.org/package=epiCo
repository-code: https://github.com/epiverse-trace/epiCo
url: https://epiverse-trace.github.io/epiCo/
contact:
- family-names: Umaña
  given-names: Juan D.
  email: jd.umana10@uniandes.edu.co
  orcid: https://orcid.org/0000-0003-0316-6164
keywords:
- colombia
- decision-support
- demographics
- epiverse
- outbreak-analysis
- r
- r-package
- spatio-temporal-analysis
- vector-borne-diseases
references:
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2024'
  version: '>= 4.0.0'
- type: software
  title: dplyr
  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Imports
  url: https://dplyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=dplyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: François
    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
  - family-names: Henry
    given-names: Lionel
  - family-names: Müller
    given-names: Kirill
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
    orcid: https://orcid.org/0000-0003-4777-038X
  year: '2024'
  doi: 10.32614/CRAN.package.dplyr
- type: software
  title: ggplot2
  abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
  notes: Imports
  url: https://ggplot2.tidyverse.org
  repository: https://CRAN.R-project.org/package=ggplot2
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Chang
    given-names: Winston
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Henry
    given-names: Lionel
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Takahashi
    given-names: Kohske
  - family-names: Wilke
    given-names: Claus
    orcid: https://orcid.org/0000-0002-7470-9261
  - family-names: Woo
    given-names: Kara
    orcid: https://orcid.org/0000-0002-5125-4188
  - family-names: Yutani
    given-names: Hiroaki
    orcid: https://orcid.org/0000-0002-3385-7233
  - family-names: Dunnington
    given-names: Dewey
    orcid: https://orcid.org/0000-0002-9415-4582
  - family-names: Brand
    given-names: Teun
    name-particle: van den
    orcid: https://orcid.org/0000-0002-9335-7468
  year: '2024'
  doi: 10.32614/CRAN.package.ggplot2
- type: software
  title: ggraph
  abstract: 'ggraph: An Implementation of Grammar of Graphics for Graphs and Networks'
  notes: Imports
  url: https://ggraph.data-imaginist.com
  repository: https://CRAN.R-project.org/package=ggraph
  authors:
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomasp85@gmail.com
    orcid: https://orcid.org/0000-0002-5147-4711
  year: '2024'
  doi: 10.32614/CRAN.package.ggraph
- type: software
  title: grDevices
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2024'
- type: software
  title: igraph
  abstract: 'igraph: Network Analysis and Visualization'
  notes: Imports
  url: https://r.igraph.org/
  repository: https://CRAN.R-project.org/package=igraph
  authors:
  - family-names: Csárdi
    given-names: Gábor
    email: csardi.gabor@gmail.com
    orcid: https://orcid.org/0000-0001-7098-9676
  - family-names: Nepusz
    given-names: Tamás
    email: ntamas@gmail.com
    orcid: https://orcid.org/0000-0002-1451-338X
  - family-names: Traag
    given-names: Vincent
    orcid: https://orcid.org/0000-0003-3170-3879
  - family-names: Horvát
    given-names: Szabolcs
    email: szhorvat@gmail.com
    orcid: https://orcid.org/0000-0002-3100-523X
  - family-names: Zanini
    given-names: Fabio
    email: fabio.zanini@unsw.edu.au
    orcid: https://orcid.org/0000-0001-7097-8539
  - family-names: Noom
    given-names: Daniel
  - family-names: Müller
    given-names: Kirill
    email: kirill@cynkra.com
    orcid: https://orcid.org/0000-0002-1416-3412
  year: '2024'
  doi: 10.32614/CRAN.package.igraph
- type: software
  title: incidence
  abstract: 'incidence: Compute, Handle, Plot and Model Incidence of Dated Events'
  notes: Imports
  url: https://www.repidemicsconsortium.org/incidence/
  repository: https://CRAN.R-project.org/package=incidence
  authors:
  - family-names: Jombart
    given-names: Thibaut
    email: thibautjombart@gmail.com
  - family-names: Kamvar
    given-names: Zhian N.
    email: zkamvar@gmail.com
    orcid: https://orcid.org/0000-0003-1458-7108
  - family-names: FitzJohn
    given-names: Rich
    email: rich.fitzjohn@gmail.com
  year: '2024'
  doi: 10.32614/CRAN.package.incidence
- type: software
  title: leaflet
  abstract: 'leaflet: Create Interactive Web Maps with the JavaScript ''Leaflet''
    Library'
  notes: Imports
  url: https://rstudio.github.io/leaflet/
  repository: https://CRAN.R-project.org/package=leaflet
  authors:
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Schloerke
    given-names: Barret
    email: barret@posit.co
    orcid: https://orcid.org/0000-0001-9986-114X
  - family-names: Karambelkar
    given-names: Bhaskar
  - family-names: Xie
    given-names: Yihui
  year: '2024'
  doi: 10.32614/CRAN.package.leaflet
- type: software
  title: lubridate
  abstract: 'lubridate: Make Dealing with Dates a Little Easier'
  notes: Imports
  url: https://lubridate.tidyverse.org
  repository: https://CRAN.R-project.org/package=lubridate
  authors:
  - family-names: Spinu
    given-names: Vitalie
    email: spinuvit@gmail.com
  - family-names: Grolemund
    given-names: Garrett
  - family-names: Wickham
    given-names: Hadley
  year: '2024'
  doi: 10.32614/CRAN.package.lubridate
- type: software
  title: magrittr
  abstract: 'magrittr: A Forward-Pipe Operator for R'
  notes: Imports
  url: https://magrittr.tidyverse.org
  repository: https://CRAN.R-project.org/package=magrittr
  authors:
  - family-names: Bache
    given-names: Stefan Milton
    email: stefan@stefanbache.dk
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2024'
  doi: 10.32614/CRAN.package.magrittr
- type: software
  title: rlang
  abstract: 'rlang: Functions for Base Types and Core R and ''Tidyverse'' Features'
  notes: Imports
  url: https://rlang.r-lib.org
  repository: https://CRAN.R-project.org/package=rlang
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2024'
  doi: 10.32614/CRAN.package.rlang
- type: software
  title: scales
  abstract: 'scales: Scale Functions for Visualization'
  notes: Imports
  url: https://scales.r-lib.org
  repository: https://CRAN.R-project.org/package=scales
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Seidel
    given-names: Dana
  year: '2024'
  doi: 10.32614/CRAN.package.scales
- type: software
  title: spdep
  abstract: 'spdep: Spatial Dependence: Weighting Schemes, Statistics'
  notes: Imports
  url: https://github.com/r-spatial/spdep/
  repository: https://CRAN.R-project.org/package=spdep
  authors:
  - family-names: Bivand
    given-names: Roger
    email: Roger.Bivand@nhh.no
    orcid: https://orcid.org/0000-0003-2392-6140
  year: '2024'
  doi: 10.32614/CRAN.package.spdep
- type: software
  title: stats
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2024'
- type: software
  title: treemapify
  abstract: 'treemapify: Draw Treemaps in ''ggplot2'''
  notes: Imports
  url: https://wilkox.org/treemapify/
  repository: https://CRAN.R-project.org/package=treemapify
  authors:
  - family-names: Wilkins
    given-names: David
    email: david@wilkox.org
    orcid: https://orcid.org/0000-0002-3385-8981
  year: '2024'
  doi: 10.32614/CRAN.package.treemapify
- type: software
  title: utils
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2024'
- type: software
  title: checkmate
  abstract: 'checkmate: Fast and Versatile Argument Checks'
  notes: Suggests
  url: https://mllg.github.io/checkmate/
  repository: https://CRAN.R-project.org/package=checkmate
  authors:
  - family-names: Lang
    given-names: Michel
    email: michellang@gmail.com
    orcid: https://orcid.org/0000-0001-9754-0393
  year: '2024'
  doi: 10.32614/CRAN.package.checkmate
- type: software
  title: covr
  abstract: 'covr: Test Coverage for Packages'
  notes: Suggests
  url: https://covr.r-lib.org
  repository: https://CRAN.R-project.org/package=covr
  authors:
  - family-names: Hester
    given-names: Jim
    email: james.f.hester@gmail.com
  year: '2024'
  doi: 10.32614/CRAN.package.covr
- 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: '2024'
  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: '2024'
  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: jeroen@berkeley.edu
    orcid: https://orcid.org/0000-0002-4035-0289
  - family-names: Hester
    given-names: Jim
    email: james.hester@rstudio.com
  year: '2024'
  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: '2024'
  doi: 10.32614/CRAN.package.testthat
  version: '>= 3.0.0'

GitHub Events

Total
  • Issues event: 7
  • Watch event: 1
  • Delete event: 3
  • Issue comment event: 2
  • Push event: 29
  • Pull request review event: 2
  • Pull request review comment event: 1
  • Pull request event: 9
  • Fork event: 1
  • Create event: 6
Last Year
  • Issues event: 7
  • Watch event: 1
  • Delete event: 3
  • Issue comment event: 2
  • Push event: 29
  • Pull request review event: 2
  • Pull request review comment event: 1
  • Pull request event: 9
  • Fork event: 1
  • Create event: 6

Committers

Last synced: 8 months ago

All Time
  • Total Commits: 246
  • Total Committers: 6
  • Avg Commits per committer: 41.0
  • Development Distribution Score (DDS): 0.402
Past Year
  • Commits: 30
  • Committers: 5
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.433
Top Committers
Name Email Commits
Juan D. Umaña j****o@g****m 147
Juan Montenegro Torres 6****9 47
jd-otero j****o@o****m 31
Hugo Gruson 1****o 17
github-actions[bot] 4****] 3
Hadley Wickham h****y@p****o 1
Committer Domains (Top 20 + Academic)
posit.co: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 64
  • Total pull requests: 97
  • Average time to close issues: 2 months
  • Average time to close pull requests: 9 days
  • Total issue authors: 15
  • Total pull request authors: 6
  • Average comments per issue: 0.38
  • Average comments per pull request: 0.59
  • Merged pull requests: 81
  • Bot issues: 0
  • Bot pull requests: 6
Past Year
  • Issues: 7
  • Pull requests: 11
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 3 days
  • Issue authors: 3
  • Pull request authors: 5
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.09
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 2
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Issue Authors
  • juan-umana (27)
  • Juanmontenegro99 (17)
  • Deedado71 (3)
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Pull Request Authors
  • Juanmontenegro99 (56)
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Top Labels
Issue Labels
enhancement (15) bug (10) documentation (3) test (2)
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Packages

  • Total packages: 1
  • Total downloads:
    • cran 246 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 1
cran.r-project.org: epiCo

Statistical and Viz Tools for Vector-Borne Diseases in Colombia

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 246 Last month
Rankings
Dependent packages count: 28.6%
Dependent repos count: 35.3%
Average: 50.1%
Downloads: 86.5%
Maintainers (1)
jd.umana10@uniandes.edu.co
Last synced: 6 months ago