like

Documentation

Overview

Package like implements a command to perform a biogeographic reconstruction using likelihood.

Index

• Variables

Variables

var Command = &command.Command{
	Usage: `like [--ranges] [--stem <age>] [--lambda <value>]
	[-p|--particles <number>]
	[-o|--output <file>]
	[--cpu <number>] [--nomat] <project-file>`,
	Short: "perform a likelihood reconstruction",
	Long: `
Command like reads a PhyGeo project, perform a likelihood reconstruction for
the trees in the project, using a diffusion model over a sphere, and write the
results of an stochastic mapping.

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.

The flag --lambda defines the concentration parameter of the spherical normal
(equivalent to kappa parameter of the von Mises-Fisher distribution) for a
diffusion process on a million year using 1/radian^2 units. If no value is
defined, it will use 100. As the kappa parameter, lager values indicate low
diffusivity while smaller values indicate high diffusivity.

By default, 1000 particles will be simulated for the stochastic mapping. The
number of particles can be changed with the flag -p, or --particles.

The results will be writing on a TSV file using the project name, the tree
name, the lambda value, and the number of particles. If the flag -o, or
--output is defined, the indicated string will be used as a prefix for the
file. For example, in the project 'rhododendron.tab', and the tree 'vireya'
using default parameters will result in a file called:
'rhododendron.tab-vireya-1.000000x1000.tab'. If the flag -o is set to 'out' the
resulting file will be: 'out-rhododendron.tab-vireya-1.000000x1000.tab'.

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,
}