clusterwise_logistic: Estimate rate that clusters increase or decrease in frequency...

In emvolz-phylodynamics/variantAnalysis: sarscov2 variant analysis

Description

Estimate rate that clusters increase or decrease in frequency and transform into selection coefficients for different genotypes

Usage

clusterwise_logistic(
  s,
  mint = 2020.2,
  maxt = 2020.35,
  minClusterSize = 25,
  r = 73,
  quasi = F
)

Arguments

s	data frame with sequence_name(character), del_introduction(character), sample_time(numeric), genotype (wt or mutant)
mint	lower sample time bound. Clusters must have sample before this time
maxt	upper sample time bound. Clusters must have sample after this time
minClusterSize	exclude clusters with fewer samples than this
r	specifies generation time (1/r) when transforming to selection coefficients. Default 73 corresponds to five days.

Value

list with matrix of selection coefficients for different clusters and a t.test for difference in 'mutant' selection coefficients

emvolz-phylodynamics/variantAnalysis documentation built on Nov. 13, 2021, 7:16 p.m.