imlouischan / ebola-ng Goto Github PK
View Code? Open in Web Editor NEWEstimating the protective effect of case isolation with transmission tree reconstruction during the Ebola outbreak in Nigeria, 2014
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) of all cases. - 12_infector.R (Figure 2A) The script to plot distribution of infector of Case 20. - 13_timelines.R (Figure 1) The script to plot observed and reconstructed time events of all cases. - ebola_ng.xlsx The data including time events and infectors of 20 cases. - samples_alt_N1e+06.Rdata The mcmc samples of all alternative models, of each one million iterations. - figure The folder storing all figures generated using the codes.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.