ml

Documentation

Overview

Package ml implements a command to search for the maximum likelihood estimation of a biogeographic reconstruction.

Index

• Variables

Variables

var Command = &command.Command{
	Usage: `ml [--ranges] [--stem <age>]
	[--lambda <value>] [--step <value>] [--stop <value>]
	[--cpu <number>] [--nomat] <project-file>`,
	Short: "search the maximum likelihood estimate",
	Long: `
Command ml reads a PhyGeo project, and search for the maximum likelihood
estimation of the lambda parameter.

The algorithm is a simple hill climbing search. By default it starts at a
lambda value of zero. The flag --lambda changes this starting point. By
default, the initial step has a value of 100, use the flag --step to change
the value. At each cycle the step value is reduced a 50%, and stop when step
has a size of 1. Use flag --stop to set a different stop value.

By default, it will use geographic distributions stored as points (presence-
absence maps). If no there are no point distribution, or the flags --ranges is
defined, the continuous range maps will be used.

By default, an stem branch will be added to each tree using the 10% of the root
age. To set a different stem age use the flag --stem, the value should be in
million years.

By default, all available CPUs will be used in the processing. Set --cpu flag
to use a different number of CPUs.

By default, if the base pixelation is smaller than 500 pixels at the equator,
it will build a distance matrix to speed up the search. As this matrix
consumes a lot of memory, this procedure can be disabled using the flag
--nomat.
	`,
	SetFlags: setFlags,
	Run:      run,
}