Illustrating methods used in: Routledge, Isobel, et al. "Estimating spatiotemporally varying malaria reproduction numbers in a near elimination setting." Nature communications 9.1 (2018): 2476 (https://www.nature.com/articles/s41467-018-04577-y).
"MultiTree_illustrative.R" provides all code required to generate and vizualise individual case reproduction number estimates. "dummy_data.csv" is a csv file which provides simulated line list data containing date of symptom onset, imported/locally acquired case classification and latitude/longitude of case residential address.