kkotokwe-bot/pangeabot

Analysis and R scripts for data from Botswana # pangeabot Analysis and R scripts for data from Botswana. We show the phylodynamic analysis of the Botswana HIV Epidemic using treestructure and mlesky.The methods are described in Volz, E., Wiuf, C., Grad, Y., Frost, S., Dennis, A., & Didelot, X. (2020) and Model design for nonparametric phylodynamic inference and applications to pathogen surveillance. Xavier Didelot, Vinicius Franceschi, Simon D. W Frost, Ann Dennis, Erik M Volz Virus Evolution, Volume 9, Issue 1, 2023, vead028, doi.org #script 1 treedater is used to time-resolve the gag and pol phylogenies, including inference of dates for Genbank sequences with missing date information. #script 2 treestructure is used to partition phylogenies. #script 3 mlesky model used to estimate effective population size though time in each phylogenetic partition #script 4 epi analysis, comparing the demographic (age, sex, sample date), clinical (treatment status, inferred stage of infection) and geographical (districts) characteristics using χ2 tests, ANOVA and tukey analysis across partitions and genes