analysis of toy_outbreak_long dataset from the o2geosocial package
install package o2geosocial from "alxsrobert/o2geosocial". To generate all figures from main and supplement, run the script generate_figure.R.
install.packages("devtools")
library(devtools)
install_github("alxsrobert/o2geosocial")
library(o2geosocial)
source("R/generate_figures.R", echo = TRUE)To generate a new simulated dataset with different input parameters (number of cases, R0, spatial parameters...), edit the lines 8-40 in analysis_generated_data.R. Run the rest of the script to generate the o2geosocial runs on the dataset.
List of files in the repository:
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In data:
- State_initials.csv : Data table with state names and acronyms.
- pop_center.csv: Population centroid and population of every county (Source: https://www.census.gov/geographies/reference-files/2010/geo/2010-centers-population.html (per state : UNITED STATES)).
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In R:
- library_importation.R: import libraries for analysis.
- function_generate_dataset.R: Functions to generate toy_outbreak_long.
- function_prepare_for_figures.R: Function to generate summary statistics on run.
- function_generate_figures_main.R: function to generate figures similar to figure 3, 4, 5 and 6.
- function_supplement_figures.R: function to generate figures similar to figures in the supplement.
- load_all_analysis.R: Load all o2geosocial runs.
- generate_figs_analysis_threshold.R: Load o2geosocial runs with different import thresholds and save files to generate figures.
- generate_figs_analysis_likelihoods.R: Load o2geosocial runs with different likelihoods and save files to generate figures.
- generate_figs_analysis_genotype.R: Load o2geosocial runs with different proportion of genotyped cases and save files to generate figures.
- load_data_distributions.R: Load prior distributions.
- analysis_generated_data.R: Script to run o2geosocial on toy_outbreak_long.
- generate_figure.R: Generate all figures (main + supplement).