lineage_growth_cumulative: Lineage growth cumulative

In magnusnosnes/LineageHomology: Transmission Lineages From Maximum Likelihood Mappings

Lineage growth cumulative

Description

The lineage_growth_cumulative function takes the input from the lineage_info function and plots the cumulative number of observed tips that belong to each transmission lineage (TL). Each line corresponds to a different TL and the function can be used to visualize the difference in growth rates and size reached over time. See the full tutorial at https://github.com/magnusnosnes/LineageHomology/blob/master/Examples_and_plotting_methods/Simple_example/Basic_plotting.md

Usage

lineage_growth_cumulative(
  Result_lineage_info,
  datelims,
  color_by_state = FALSE
)

Arguments

Result_lineage_info	The output from the lineage_info function. A typical workflow would run the functions in the order LineageHomology -> lineage_info -> lineage_growth_cumulative.
datelims	Limits of the dates in format c("yyyy-mm-dd","yyyy-mm-dd", ""). The last argument can be e.g. "1 week"/"1 year"/"1 month".
color_by_state	A logical value indicating whether to color the lines by the state of the TL.

Value

A plot showing the cumulative number of observed tips that belong to each transmission lineage.

magnusnosnes/LineageHomology documentation built on April 17, 2025, 6:30 p.m.