MAGPIE-SFU/tb-malawi-phylogeo-public

A publicly available version of the analysis in the manuscript "Genomic epidemiology of Mycobacterium tuberculosis in Malawi: using global phylogeography to understand the impact of geographically-focused interventions"" # tb-malawi-phylogeo-public This publicly available repository accompanies the manuscript Beams et. al, *Genomic epidemiology of Mycobacterium tuberculosis in Malawi: using global phylogeography to understand the impact of geographically-focused interventions*, submitted to Microbial Genomics. The paper describes a phylogeographic analysis of Mtb sequences collected from within the city of Blantyre, Malawi, and supplemented with additional publicly-available sequences collected across the world and maintained on the European Nucleotide Archive (ENA). The focus of the paper is to account for heterogeneous sampling using a method called sampling-aware ancestral state inference (SAASI) in order to arrive at more accurate estimates for lineage movements than can be obtained with other approaches that do not account for sampling heterogeneity by location. The study includes a simulated intervention within Blantyre to help us understand how migration patterns of TB might affect public health interventions in local settings. Please note that to respect patient privacy, TB sequences collected from Blantyre have had zone information redacted. The data and codes in this repository will run SAASI using large geographic regions (Blantyre, Proximal, Global, Global-LSA) but will not reconstruct movements of Mtb lineages between different zones of the city of Blantyre. Consequently, some of the figures will differ from those seen in the manuscript. ## Required packages: - ape - dplyr - ggplot2 - ggtree - ggtreeExtra - ggnewscale - ggpubr - sf - tidyverse - ggalluvial - rnaturalearth - rnaturalearthdata - saasi To install the version of saasi used in this work, you will need to use a branch of the main project that accounts for the timeframe of sampling for the data. To do this, you may run ```{r} remotes::install_github("MAGPIE-SFU/saasi@try-sampling-vary-through-time") ``` Note that this is different from the main branch of the saasi package. We are planning to merge these …