plotLineage: Plot lineage as successes/failures over time, and fit...

In JacobLemieux/sars2phylo: Functions for analyzing SARS-CoV-2 phylogenetic data

Description

Plot lineage as successes/failures over time, and fit logistic regression as smoother

Usage

plotLineage(
  SS,
  LIN,
  bystate = FALSE,
  xlower = "2020-05-01",
  xupper = "2021-05-01"
)

Arguments

SS	dataframe of sample set, with one-hot encoding of each lineage as a column
LIN	character string of particular lineage
bystate	subset by state; SS must have state as a column
xlower	lower bound of x range
xupper	upper bound of x range, will extrapolate the logistic regression smoother

Value

creates a plot of successes (samples belong to lineage) vs failures (not lineage) over time

Examples

plotLineage(ss, "B.1.1.7", bystate = TRUE);

JacobLemieux/sars2phylo documentation built on Dec. 18, 2021, 12:29 a.m.