mrc-ide/EPIONCHO.IBM: Source data and instructions to reproduce modelling analysis and figures for onchocerciasis in Togo

mrc-ide/EPIONCHO.IBM: Source data and instructions to reproduce modelling analysis and figures for onchocerciasis in Togo Amaral, Luis-Jorge (Contact person)1,2 (0000-0001-8155-9014); Basáñez, Maria-Gloria1 (0000-0001-5031-3361) Title: Reaching Elimination of Onchocerciasis Transmission with Long-term Vector Control and Ivermectin Treatment in Togo Authors: Luís-Jorge Amaral1,2,*, Rachel N. Bronzan3,4, Anders Seim5, Marie-Denise Milord3, Koffi Padjoudoum6, Ibrahim Gado Telou7, Sibabe Agoro7, Michel Datagni8, Piham Gnossike9, Jonathan I. D. Hamley1,10, Martin Walker1,11 & Maria-Gloria Basáñez1,* Affiliations: 1 MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; 2 Global Health Institute, University of Antwerp, Antwerp, Belgium; 3 Health & Development International, Newburyport, Massachusetts, USA; 4 Gates Foundation, Seattle, Washington, USA; 5 Health & Development International, Fjellstrand, Norway; 6 National Onchocerciasis Control Program, Kara, Togo; 7 Ministère de la Santé et de l'Hygiène Publique, Lomé, Togo; 8 Health and Development International, Lomé, Togo; 9 Neglected Tropical Diseases Coordinator, Ministère de la Santé et de l'Hygiène Publique, Lomé, Togo; 10 Department of Visceral Surgery and Medicine, and Multidisciplinary Center for Infectious Diseases, University of Bern, Switzerland; 11 Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK *Corresponding Authors Journal: Nature Communications Year: 2025 Overview of files This repository contains datasets and R code used to generate the results and figures in the main article and supplementary material: - datasets and simulations.RData: All datasets required for the analysis in the main article and its supplementary material. This includes the endemicity survey time series for Togo’s villages (object: E8) and the EPIONCHO‑IBM simulation scenarios used throughout the study. - Figures 2 to 6 main article.R: Scripts to reproduce Fig. 2–6 of the main article, showing EPIONCHO‑IBM simulated trends of Onchocerca volvulus microfilarial prevalence (to 2030) for Savanes, Kara, Centrale, Plateaux and Maritime regions, for villages with baseline microfilarial prevalence (BMP) estimates located within or outside Special Intervention Zone, under vector control (VC) and ivermectin mass drug administration (MDA), according to intervention scenario. - Figure 7 main article.R: Script to reproduce Fig. 7 of the main article, presenting the categorical likelihood of elimination of onchocerciasis transmission (EOT) in Togo’s prefectures if ivermectin mass drug administration (MDA) were stopped in 2027, based on EPIONCHO‑IBM projections and probabilities of elimination. - Figures 1 to 7 supplementary.R: Scripts to reproduce Supplementary Figures 1–7 and related statistical code, including: baseline endemicity by prefecture (Fig. 1), onchocerciasis control in Togo (Fig. 2), temporal trends of crude microfilarial prevalence for Special Intervention Zone (SIZ) and non‑SIZ villages (Fig. 3), box‑and‑whisker plots of crude microfilarial prevalence across intervention periods (Fig. 4), geographical distribution of villages for onchocerciasis monitoring (Fig. 5), linear relationship between crude and age‑/sex‑standardised microfilarial prevalence (Fig. 6), and box-and-whisker plots of the proportion of the population surveyed per village according to survey years (Fig. 7). - Figures 8 to 14 supplementary.R: Scripts to reproduce Supplementary Figures 8–14 showing EPIONCHO‑IBM simulated trends of Onchocerca volvulus microfilarial prevalence (to 2030) for Savanes, Kara, Centrale, Plateaux and Maritime regions, for SIZ or not SIZ villages lacking baseline microfilarial prevalence (BMP) estimates, under vector control (VC) and ivermectin mass drug administration (MDA), according to intervention scenario. - Mean Square error code.R: Code to identify best‑fit intervention scenarios via mean square error (MSE) across 100 model repeats for villages with and without recorded baseline microfilarial prevalence (BMP) estimates, stratified by region, SIZ status and endemicity category. - Model code availability: The underlying EPIONCHO-IBM model, source code and setup instructions are hosted publicly at: https://github.com/mrcide/EPIONCHO.IBM/tree/togo-elimination-analysis Instructions: 1) Open R (and optionally RStudio). 2) Set your working directory to this archive folder. 3) Load the data file: load("datasets and simulations.RData") This will make objects such as E8 and the EPIONCHO‑IBM simulation lists available in your session. 4) Run the desired script(s): source("Figures 2 to 6 main article.R") source("Figure 7 main article.R") source("Figures 1 to 7 supplementary.R") source("Figures 8 to 14 supplementary.R") 5) Outputs (e.g., figures) will be saved to the paths defined in each script. Software & dependencies • R (version ≥ 4.0 recommended) • Commonly used packages include: ggplot2, dplyr, patchwork/ggpubr. Install any missing packages. • EPIONCHO‑IBM simulation objects are included in the .RData file used by the scripts. Citation If you use these data or scripts, please cite the article and this dataset. Contact Luís‑Jorge Amaral (luis.amar[email protected]; luisjtmamara[email protected])