ntncmch/ebola_sierra_leone

Simple SEIR fit of the Ebola outbreak in Sierra Leone # Modelling the Ebola outbreak in Sierra-Leone Modelling work presented in a recent Nature Comment by Whitty et al. suggests that, without any intervention, the Ebola outbreak in Sierra Leone could peak early December, reaching a maximum of 1600 weekly cases. Here, we show that this figure is misleading and provide a fully transparent and reproducible analysis of the same data-set. All data, models, outputs and figures are provided in this repository (see for instance here for the baseline model). Alternatively you can re-run our analysis using the instructions below. A detailed step-by-step description of our analysis can be found here. # Run our analysis At the core of our analysis is the SSM (for State Space Models) library, which allows us to * implement a transmission model * fit this model to time-series data and estimate key parameters * forecast this fitted model by integrating the uncertainty of parameter estimates To re-run our analysis: 1. Install SSM 2. Clone or download this repository ``` git clone github.com ``` 3. Compile the model ``` cd ebola_sierra_leone/SSM ssm ``` 4. Fit the data ``` cd bin cat ../theta.json | ./simplex --iter 10000 --prior | ./pmcmc --iter 10000 --eps_switch 20 --switch 500 --cooling 0.99 | ./pmcmc --iter 100000 --eps_switch 20 --trace --acc --traj --n_traj 1000 -v ``` 5. Forecast the fitted model ``` ssm-predict mcmc_0.json X_0.csv trace_0.csv 2014-09-28 | ./simul --traj --start 2014-09-28 --end 2016-08-01 --freq 7 --id 1 ``` All outputs were processed using R.