imlouischan/ebola-ng

Estimating the protective effect of case isolation with transmission tree reconstruction during the Ebola outbreak in Nigeria, 2014 readme - 0a_main_mcmc.R The main script to create mcmc samples of all alternative models. - 0b_main_plot.R The main script to plot and present mcmc results. - 1a_data.R The script to read data, including time events and infectors. - 1b_bound.R The script to create the functions for boundaries of missing time points. - 2a_incubation.R (Figure S1A) The script to create the function for incubation period (and plot). - 2b_distribution.R (Figure S1B) The script to create the function for time lag distributions using MLE (and plot). - 3a_pmf_r.R The script to create the function for offspring distributions. - 3b_pmf_s.R The script to create the function for serial interval distributions. - 4a_L_ri.R The script to create the likelihood of offspring number of each case. - 4b_L_si.R The script to create the likelihood of serial interval of each case. - 4c_logL.R The script to create the likelihood of all cases. - 4d_pij.R The script to create the transmission probability used in each mcmc step to select an infector. - 5_mcmc.R The script to create mcmc samples using metropolis hastings. - 6a_parallel.R The script to run several mcmc chains in parallel using the package called "parallel". - 6b_combine_chains.R The script to combine mcmc chains. - 7a_plot_mixing.R The script to plot mcmc chain samples. - 7b_plot_dependence.R (Figure 3) The script to plot dependence between parameters. - 8a_plot_pmf_r.R (Figure 2D) The script to plot offspring distribution. - 8b_plot_pmf_s.R (Figure 2C) The script to plot serial interval distribution. - 9a_cal_pmf_r.R The script to calculate mean and SD of offspring distribution. - 9b_cal_pmf_s.R The script to calculate mean and SD of serial interval distribution. - 10a_comp_model.R (Table 1) The script to calculate criterion values to compare alternative distributions. - 10b_comp_para.R (Figure 4) The script to plot comparison of parameters in two scenarios. - 11_efficacy.R (Figure 2B) The script to plot efficacy (individual protect effect) …