README.Rmd

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output: github_document
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<img src='man/figures/EPIONCHO-IBM_logo3.png' align="right" height="220" />  

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### An individual-based onchocerciasis dynamic model

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## Overview

A individual-based, stochastic model of the *Onchocerca volvulus* transmission system.

For full model details please see:
[Hamley JID, Milton P, Walker M, Basáñez M-G (2019) Modelling exposure heterogeneity and density dependence in onchocerciasis using a novel individual-based transmission model, EPIONCHO-IBM: Implications for elimination and data needs. PLoS Negl Trop Dis 13(12): e0007557](https://doi.org/10.1371/journal.pntd.0007557)

The process overview within EPIONCHO-IBM, describing the steps through a model run which reflect changes in the host/vector and parasite life-cycle, is presented here:

<img src='man/figures/oncho_oncho_processflowchart.png' align="below" height="800" /> 

Other publications utilizing and/or developing EPIONCHO-IBM include:

[Hamley JID, Walker M, Coffeng LE, Milton P, de Vlas SJ, Stolk WA, Basáñez MG. Structural Uncertainty in Onchocerciasis Transmission Models Influences the Estimation of Elimination Thresholds and Selection of Age Groups for Seromonitoring. J Infect Dis. 2020 Jun 11;221(Suppl 5):S510-S518.](https://doi.org/10.1093%2Finfdis%2Fjiz674)

[Walker M, Hamley JID, Milton P, Monnot F, Pedrique B, Basáñez MG. Designing antifilarial drug trials using clinical trial simulators. Nat Commun. 2020 Jun 1;11(1):2685.](https://doi.org/10.1038/s41467-020-16442-y)

[Hamley JID, Blok DJ, Walker M, Milton P, Hopkins AD, Hamill LC, Downs P, de Vlas SJ, Stolk WA, Basáñez MG. What does the COVID-19 pandemic mean for the next decade of onchocerciasis control and elimination? Trans R Soc Trop Med Hyg. 2021 Mar 6;115(3):269-280.](https://doi.org/10.1093/trstmh/traa193)

[Stolk WA, Blok DJ, Hamley JID, Cantey PT, de Vlas SJ, Walker M, Basáñez MG. Scaling-Down Mass Ivermectin Treatment for Onchocerciasis Elimination: Modeling the Impact of the Geographical Unit for Decision Making. Clin Infect Dis. 2021 Jun 14;72(Suppl 3):S165-S171.](https://doi.org/10.1093/cid/ciab238)

[Walker M, Hamley JID, Milton P, Monnot F, Kinrade S, Specht S, Pedrique B, Basáñez MG. Supporting Drug Development for Neglected Tropical Diseases Using Mathematical Modeling. Clin Infect Dis. 2021 Sep 15;73(6):e1391-e1396. doi: 10.1093/cid/ciab350.](https://doi.org/10.1093%2Fcid%2Fciab350)


## Installation

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

``` r
# install.packages("devtools")
# install.packages("remotes")
remotes::install_github("mrc-ide/EPIONCHO.IBM")
```

## Using EPIONCHO-IBM

For a detailed practical guide please see the [Installing and Running EPIONCHO-IBM](https://github.com/mrc-ide/EPIONCHO.IBM/blob/master/vignettes/Running_EPIONCHO_IBM.Rmd) vignette