This repository contains age-stratified seroprevalence data for dengue, obtained through a comprehensive literature review described in our paper entitled A scoping literature review of global dengue age-stratified seroprevalence: estimating dengue force of infection in endemic countries. The pre-print publication detailing the methodology and findings can be found here (DOI: https://doi.org/10.1101/2023.04.07.23288290).
Data Files In each file the "location" column specifies the location where the data was collected and the referenced paper.
dataset_modelA.csv: Contains the seroprevalence data analyzed with Model A.
dataset_modelB.csv: Contains the seroprevalence data analyzed with Model B.
dataset_modelC.csv: Contains the seroprevalence data analyzed with Model C.
dataset_model_D.csv: Contains the seroprevalence data analyzed with Model D.
dataset_Madagascar.csv: Contains the seroprevalence data analyzed with Model A in Madagascar.
dataset_Mexico.csv: Contains the seroprevalence data analyzed with Model A in Mexico.
dataset_Indonesia.csv: Contains the seroprevalence data analyzed with Model A in Indonesia.
Usage
Each model (Model A, B, C, and D) has its own R script and Stan model files that need to be executed to analyze the respective dataset. For Model A and B, the numeration 1 and 2 are used to separate the use of a binomial (1) or beta-binomial (2) log-likelihood. Ensure you have the necessary dependencies installed before running the scripts, the analysis was run in CmdStanR.
Model A1:
Script: Run_model_A1.R
Stan Model: Seromodel_A1.stan
Model A2:
Script: Run_model_A2.R
Stan Model: Seromodel_A2.stan
Model B1:
Script: Run_model_B1.R
Stan Model: Seromodel_B1.stan
Model B2:
Script: Run_model_B2.R
Stan Model: Seromodel_B2.stan
Model C:
Script: Run_model_C.R
Stan Model: Seromodel_C.stan
Model D:
Script: Run_model_D.R
Stan Model: Seromodel_D.stan
Refer to the individual scripts for specific instructions on how to execute the analysis for each model.