emvolz-phylodynamics/ebola2014-practical

Worked example of exploratory phylodynamics of EBOV epidemic in Western Africa # Exploratory phylodynamics of early EBOV epidemic in Sierra Leone In this practical, we will re-analyse whole-genome EBOV sequences collected over the course of the 2013-2015 Ebola virus epidemic in Western Africa. The data and analysis were first described here: * Dudas G. et al.(2017) _Virus genomes reveal factors that spread and sustained the ebola epidemic_, Nature, 544/7650: 309-15. Details of the original analysis of these data can be found here By the way, here is an interesting TED talk by the chief scientist responsible for collecting the data: * P Sabeti: How we'll fight the next deadly virus ## Installation and setup For these analyses, we'll use the `ape`, `treedater`, and `skygrowth` packages. If you need to install this on MS Windows, run the installation script like this: ``` source('msc_epi_ebola_installScript.R') ``` On Mac or Linux, we will compile the packages from source: ``` install.packages('ape') install.packages('devtools') require(devtools) install_github( 'mrc-ide/skygrowth') install_github( 'emvolz/treedater') ``` Now we load the package as follows: ```r suppressPackageStartupMessages( require(ape) ) suppressPackageStartupMessages( require(skygrowth) ) suppressPackageStartupMessages( require(treedater) ) ``` ## Experimental design The original analysis by Dudas et al. was based on 1610 whole EBOV genomes. We will do a fast exploratory analysis of a random subsample of these sequences. In the `resamples/` directory you will find 30 replicate data sets. Each alignment (_.fas_ file) contains 300 sequences sampled at random. Corresponding to each alignment, there is also a comma-separated table which provides the time of sampling of each sequence. In the rest of this tutorial, we will work with the first replicate, 'resamples/aln-1.fas` and 'resamples/sts-1.csv', but you can generate your own unique results using a different replicate. ## Loading and exploring the data Let's load the multiple sequence alignment and inspect it: ``` …