sample_lineage: Produce a random sample of given global lineage and sample...
In emvolz-phylodynamics/variantAnalysis: sarscov2 variant analysis

Sampling is repeated multiple times and over multiple sample sizes. Can confine sampling to a particular time frame. A proportion of samples can be stratified through time rather than being drawn completely at random (weighted smapling is still used within each week)

sample_lineage(
  lineage = "B.1.1.7",
  weightsfn = "/cephfs/covid/bham/climb-covid19-volze/b0-weightsdf-2021-01-04.csv",
  mindate = as.Date("2020-10-15"),
  maxdate = as.Date(Sys.Date() - 12),
  nreps = 100,
  ns = c(250, 500, 750, 1000),
  prop_stratified = 0.25,
  deduplicate = TRUE
)

`lineage`	Global lineage
`weightsfn`	output produced by coverage_weights
`mindate`	minimum date
`maxdate`	maximum date; note it takes about 12 days for P2 sampling to stabilize
`nreps`	replicates
`ns`	sample sizes to use
`prop_stratified`	proportion of sample to reserve for stratified sampling
`deduplicate`	if TRUE, duplicate samples will be removed