s614_phylodynamics: Run skygrowth and treestructure on clades defined by s614...

In emvolz-phylodynamics/sarscov2Rutils: Scripts to support preparation and analysis of SARS CoV 2 analyses

Description

Run skygrowth and treestructure on clades defined by s614 polymorphism

Usage

s614_phylodynamics(tds, s614, ...)

Arguments

tds	List or multiPhylo of treedater trees or ape::phylo
s614	A data frame produced by compute_spike614genotype
...	Additional arguments passed to sarscov2::skygrowth1

Value

A list with skygrowth for G and D, and a list of treestructure tests for each tree

Examples

## Not run: 
library( sarscov2 ) 
 spikedf = compute_spike614genotype( 'algn3.fasta', 'algn4.fasta' )
 # inspect spikedf to make sure it a assigned D or G 
 # some precomputed treedater trees corersponding to algn3.fasta: 
 tds = readRDS('tds.rds' )  
 result = s614_phylodynamics( tds, spikedf)
 print( result$treestructureTests  )
 # make a plot 
 add_ggR_sarscov2skygrowth( result$sgD, result$sgG )

## End(Not run)

emvolz-phylodynamics/sarscov2Rutils documentation built on Nov. 17, 2020, 9:22 a.m.