lineage_info: lineage_info

In magnusnosnes/GeoLineages: Transmission Lineages From Maximum Likelihood Mappings

lineage_info

Description

The function takes in the output from the LineageHomology algorithm and a data frame with taxa names and numeric dates of sampling. It formats the output to be easily plotted by other functions, such as ridgeplot_lineagedensities and lineage_growth_cumulative. See the full tutorial at https://github.com/magnusnosnes/LineageHomology/blob/master/Examples_and_plotting_methods/Simple_example/Basic_plotting.md

Usage

lineage_info(Result_Lineage_homology, name_date)

Arguments

Result_Lineage_homology	The output from LineageHomology. This should be the object returned from running the LineageHomology algorithm.
name_date	A data frame with taxa names in one column and numeric dates of sampling in another. The column names should be c("name", "date"). This data frame is used to match the taxa names in the output from LineageHomology with the dates of sampling.

Value

A data frame with columns "dates", "group_no", "group_size", "range_group", and "lineage_state". These columns are used to plot the output from LineageHomology.

magnusnosnes/GeoLineages documentation built on April 17, 2025, 6:29 p.m.