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

Cysticercosis modelling project
https://github.com/mrc-ide/epicyst

Last synced: 10 days ago
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Cysticercosis modelling project

• Host: GitHub
• URL: https://github.com/mrc-ide/epicyst
• Owner: mrc-ide
• License: mit
• Created: 2019-11-04T12:20:35.000Z (about 5 years ago)
• Default Branch: master
• Last Pushed: 2024-06-05T15:18:51.000Z (7 months ago)
• Last Synced: 2024-11-06T02:31:05.051Z (about 2 months ago)
• Language: R
• Homepage: https://mrc-ide.github.io/epicyst/
• Size: 25.8 MB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE

Awesome Lists containing this project

README

        
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output: github_document

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[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)

[![R build status](https://github.com/mrc-ide/epicyst/workflows/R-CMD-check/badge.svg)](https://github.com/mrc-ide/epicyst/actions)

[![codecov](https://codecov.io/gh/mrc-ide/epicyst/branch/master/graph/badge.svg)](https://codecov.io/gh/mrc-ide/epicyst)

  




### A deterministic *Taenia solium* and Cysticercosis dynamic model

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### Overview

A deterministic, compartmental model of the Cysticercosis disease system.

For full model details please see:

[Winskill, P., Harrison, W.E., French, M. D., Dixon, M., Abela-Ridder, B. & Basáñez, M.-G. (2017) Assessing the impact of intervention strategies against Taenia solium cysticercosis using the epicyst transmission model. Parasites & Vectors, 10:73, DOI: 10.1186/s13071-017-1988-9](https://parasitesandvectors.biomedcentral.com/articles/10.1186/s13071-017-1988-9)

Other publications include:

[Dixon MA, Braae UC, Winskill P, Walker M, Devleesschauwer B, Gabriël S, et al. Strategies for tackling Taenia solium taeniosis/ cysticercosis: A systematic review and comparison of transmission models, including an assessment of the wider Taeniidae family transmission models. PLoS Negl Trop Dis. 2019;13(4):1–24](https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0007301)

[Dixon MA, Winskill P, Harrison WE, Whittaker C, Schmidt V, Sarti E, et al. Force ‑ of ‑ infection of Taenia solium porcine cysticercosis: a modelling analysis to assess global incidence and prevalence trends. Sci Rep. 2020;1–14](https://doi.org/10.1038/s41598-020-74007-x)

[Dixon MA, Braae UC, Winskill P, Devleesschauwer B, Trevisan C, Van Damme I, et al. Modelling for Taenia solium control strategies beyond 2020. Bull World Health Organ. 2020;98(3):198–205](https://apps.who.int/iris/handle/10665/331383)

    

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### Installation

To use the package, please install package devtools and install epicyst:

`remotes::install_github("mrc-ide/epicyst")`

You will need an [appropriate compiler](https://cran.r-project.org/bin/windows/Rtools/) installed.

The package ODEs are all driven by the [odin package](https://mrc-ide.github.io/odin/)

    

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### Use

For a detailed practical guide please see the [epicyst introduction vignette](https://mrc-ide.github.io/epicyst/articles/Introduction.html)

  

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Details on the model functionality and use can be found on the [epicyst Webpage](https://mrc-ide.github.io/epicyst/)  

Source code is available from the [epicyst Github](https://github.com/mrc-ide/epicyst/)  

Seen an issue? Please [Report a bug](https://github.com/mrc-ide/epicyst/issues)