Estimating the elimination feasibility in the ‘end game’ of control efforts for parasites subjected to regular mass drug administration: a schistosomiasis case study

Outputs_Refs folder

Contains outputs of simulations and parameter sets used in plotting scripts to produce manuscript figures. Contains all .Rdata files that are ignored in GitHub due to their size, but available by request by contacting @cmhoove14 or choover@berkeley.edu or by running the scripts in the order below and storing the necessary outputs

Savio folder

Contains scripts with minor modifications that allow them to be run on savio, the Berkeley supercomputing cluster

Stochastic folder

Stochastic versions of the models

Scripts contained in this folder (in order that they would be run to reproduce results presented in the manuscript)

• schisto_mods_pdd_nopdd.R -- Deterministic models used to simulate schisto dynamics in the presence of different density dependencies. Also contain best-fitting parameter set
• model_fit_profile.R -- Fits the model with density dependencies to observed data from a study site in Senegal and stores the resulting transmission parameter sets in Outputs_Refs folder as model_fit_profile_likelihood_parameters.Rdata (run on savio with savio version)
• Reff_BBR_fns -- Functions to estimate Reff and BBR, derived from models in schisto_mods_pdd_nopdd.R
• Reff_addNDDs_BBR_plots.R -- Estimates Reff, BBR, and dW/dt across a range of worm burdens for the best fitting parameter set. Used to produce Figures 1 and 2 that demonstrate difference between model predictions with and without influence of positive density dependence
• Get_eqbm_for_trans_parameter_sets.R -- For each transmission parameter set, simulates pdd and pdd-free models over long time period to reach equilibrium and saves the resulting equilibrium values in Outputs_Refs folder
• PDD_noPDD_sims.R -- For each transmission parameter set and each model: Gets equilibrium estimates produced with Get_eqbm_for_trans_parameter_sets.R and simulates 20 years of annual MDA, then simulates 40 years of intervention-free transmission. During the 20 years of MDA, estimates BBR between each MDA, epsilon over entire MDA sequence for that transmission parameter set. Stores all outputs in Outputs_Refs folder
• PDD_noPDD_plots_analyze -- Processes simulations produced in PDD_noPDD_sims.R to produce Figure 3 showing (a) worm burden trajectory for the pdd and pdd-free models over the course of simulated 20 years MDA and 40 years intervention-free transmission (b) estimates of BBR in each MDA interval for each model and (c) Estimate of epsilon for each year >3 in the 20 years of MDA. Also produces Figure 4 which shows the same three panels but based on prevalence data rather than worm burden data
• stochModSims_postProcess -- takes stochastic simulations run on Savio (see Savio folder) and process them, plots results shown in Figure 5 of relationship between probabilioty of elimination (P(e)) from stochastic simulations to elimination feasibility coefficient/estimator (epsilon)
• eps_surface_kap_lam.R -- For a range of positive density dependence (k) and transmission intensity (lambda) estimates epsilon over 20 years of simulated MDA
• eps_surface_kap_lam_plots.R -- Takes output from eps_surface_kap_lam.R and produces a surface plot (Figure 6) showing how epsilon varies across the two key parameters