Introduction

Calculations of outbreak risk for Djibouti, Somalia and Yemen.

Running the code

The code can be found in the src folder; reports are run in order as shown below

Initialize (ensure repository folder is working directory):

path=getwd()
orderly2::orderly_init(path)
library(YEPaux)

Calculate epidemiological parameter values from Markov chain parameter outputs and environmental data:

orderly2::orderly_run("get_FOI_R0_values_from_saved_chain_data",
list(n_param_sets=1000,
enviro_filename="enviro_data_IAregions_6covs_new_labelling.csv",
chain_filename="markov_chain_data_combined_paper_latest.Rds"))

Create maps of epidemiological parameter values:

orderly2::orderly_run("map_FOI_R0_values")

Calculate case data:

orderly2::orderly_run("case_data_calc_R0_case_seeding",
list(p_severe_inf=0.12,
p_death_severe_inf=0.39,
deterministic=FALSE,
n_sets_to_run=1000,
n_reps=10,
mode_parallel=TRUE,
n_cores=4))

Calculate outbreak risk:

orderly2::orderly_run("get_outbreak_risk_R0_case_seeding")

Calculate outbreak risk weighted by Raptor data:

orderly2::orderly_run("outbreak_risk_seeded_weighted_by_raptor_data",
list(raptor_results_filename="all_DS_results_neighbours 1.rds"))

Map outbreak risk data:

orderly2::orderly_run("maps_create")

orderly2

This is an orderly project. The directories are:

• src: create new reports here
• archive: versioned results of running your report
• shared : common data files
• R : common functions