skygrowth1: Compute skygrowth Ne(t) and R(t) estimates for a given list...

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

Description

If tstart is provided than you can supply a list of ape::phylo trees instead of treedater trees

Usage

skygrowth1(
  tds,
  X = NULL,
  formula = ~transit_stations_percent_change_from_baseline,
  tstart = decimal_date(as.Date("2020-03-01")),
  tau0 = 30/365/36.5^2,
  res = 5,
  numpb = 10,
  ncpu = 6,
  gamma1 = (-log(0.5)) * 365/6.5,
  logRmean = NULL,
  logRsd = 0.5,
  ...
)

Arguments

tds	A list or multiPhylo, containing ape::phylo or treedater trees
X	A data frame with covariate data, must include numeric column 'time'
formula	Specify the relationship between Change in growth rate and covariates. Should have empty lhs and only specify rhs
tstart	A numeric time to consider as the beginning of the epidemic in region; for best results, select a time when exponential growth in region is well underway. Can be NULL in which case the sarscov2::timports function is used to guess an appropriate date
tau0	Precision parameter for skygrowth. Default value corresponds to 1 per cent change in growth per week
numpb	Number of parametric bootstrap to use if using timports
ncpu	Number CPUs to use
gamma1	Death/recovery rates used for translating growth rates into R(t)
...	Additional arguments passed to skygrowth (eg mhsteps)
see	skygrowth, if omitted will guess a good value

Value

A list with dataframes for Ne, growth, and R(t)

Examples

## Not run: 
library( ape ) ; library( sarscov2 )
tres = read.tree( 'startTrees.nwk' ) 
o = skygrowth0 ( tres, start = decimal_date( as.Date('2020-02-15') ) )

## End(Not run)

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