josemalinga/Patterns-of-genetic-differences-in-Kilifi

Individual-based stochastic simulation model of malaria infections # Patterns-of-genetic-differences-in-Kilifi 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: 19018 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. There was an error in the original publication but this has now been corrected online and in the pdf. We erroneously stated that the mean of a half-normal distribution was sigma, but it is sigma*sqrt(2/pi). This lead to small changes throughout the manuscript. The parameter input to the model here is sigma (or 'rate' in the code), and the mean can be calculated afterwards. This does not lead to any changes in the conclusions in the paper.