freyja relgrowthrate

Calculates relative growth rates for each lineage using AGG_RESULTS and METADATA

freyja relgrowthrate [OPTIONS] AGG_RESULTS METADATA

Options

--thresh <thresh>

min lineage abundance in plot

Default:: 0.01

--scale_by_viral_load

scale by viral load

Default:: False

--nboots <nboots>

Number of Bootstrap iterations

Default:: 1000

--serial_interval <serial_interval>

Serial Interval

Default:: 5.5

--config <config>: control the colors and grouping of lineages in the plot

--mincov <mincov>

min genome coverage included

Default:: 60.0

--output <output>

Output html file

Default:: rel_growth_rates.csv

--days <days>

number of days for growth calculation

Default:: 56

--grthresh <grthresh>

minimum prevalence to calculate relative growth rate for

Default:: 0.001

--lineageyml <lineageyml>: lineage hierarchy file

Arguments

AGG_RESULTS: Required argument

METADATA: Required argument

Example Usage:

This command will generate the relative growth rates for each Lineage and output it as a CSV file. The lineages can also be grouped together by passing the --config [path-to-plot-config-file] option. This uses the same configuration file as the dash command. The lineages are grouped together based on the Lineage: field in the config file. The number of bootstraps can be specified with the --nboots [number-of-bootstraps] option and the serial interval can be specified with the --serial_interval option. The output will be a CSV file with the following columns:

Lineage

Estimated Advantage

Bootstrap 95% interval