Data, analyses, and plots to characterize Newcastle disease virus transmission and impact of I-2 vaccination

Accompanies Sheen, Nguyen, Ravelomanantsoa, Randriamady, Andriamananjara-Cunderlik, Metcalf, Golden, "Characterizing Newcastle disease virus transmission dynamics and the impact of vaccination in village settings," Proceedings of the Royal Society B: Biological Sciences

To recreate analyses, make three directories:

• "vaxMada/code/" put all .R files
• "vaxMada-data/objects/data_obj/" put all .RData files
• "vaxMada-data/plots/" put all .png files

files to conduct analyses, save and load .RData objects for analysis, as well as to plot results

• 0_helper_functions.R: helper functions used throughout analyses
• 3a_characHH.R: creates .RData objects at household level of mortality rates and poultry husbandry.
• 4a_prep_pomp_vill1.R, 4b_prep_pomp_vill2.R, 4c_prep_pomp_vill3.R: prep data for maximum-likelihood estimation
• 5a_pomp_vill1.R, 5b_pomp_vill2.R, 5c_pomp_vill3.R: perform maximum-likelihood estimation
• 6a_plot_vill1.R, 6b_plot_vill2.R, 6c_plot_vill3.R: plot model performance of maximum-likelihood estimation
• 7_plot_additional.R: additional plots

plots created by the code

• plots: all plots of analyses, available in the main text and Supplementary Information