Contains code and data from the paper:
Investigating the drivers of the spatio-temporal patterns of genetic differences between Plasmodium falciparum malaria infections in Kilifi County, Kenya. Malinga J, Mogeni P, Omedo I, Rockett K, Hubbart C, Jeffreys A, Williams T, Kwiatkowski D, Bejon P & Ross A. Scientific Reports 2019, 9(1): 19018 DOI: 10.1038/s41598-019-54348-y
The code runs a simulation model of Plasmodium falciparum malaria infections and fits it to genotyping data from Kilifi in order to estimate the mean distance between parent and offspring infections and to test simple hypotheses about drivers of the temporal and spatial genetic patterns observed.
"code index.docx" provides an index of the files.
An small error has been corrected in these files. The distribution for the mean distance was incorrect. Author Correction Sci Rep 2020 10(1): 22416 doi: 10.1038/s41598-020-78848-4.
This repository is a copy of the Swiss TPH repository.