kde

Documentation

Overview

Package kde implements a command to estimate a range distribution using a kernel density estimator.

Index

• Variables

Variables

var Command = &command.Command{
	Usage: `kde --timepix <time-pixelation> [--prior <prior-file>]
	[--lambda <value>] [--bound <value>]
	[-o|--output <file>] [<rng-file>...]`,
	Short: "estimate a geographic range using a KDE",
	Long: `
Command kde reads one or more geographic range files, and produce a new range
map using a Kernel Density Estimation, based on an spherical normal.

One or more range files can be given as arguments. If no file is given, the
ranges will be read from the standard input.

The flag --timepix is required an defines the time pixelation that will contain
the raster values for each pixel. Prior probabilities for each pixel type can
be defined on a file and read with the flag --prior. The pixel prior file is a
tab-delimited file with the following columns:

	-key	the value used as identifier
	-prior	the prior probability for a pixel with that value

Any other columns, will be ignored. Here is an example of a pixel prior file:

	key	prior	comment
	0	0.000000	deep ocean
	1	0.010000	oceanic plateaus
	2	0.050000	continental shelf
	3	0.950000	lowlands
	4	1.000000	highlands
	5	0.001000	ice sheets

The flag --lambda defines the concentration parameter of the spherical normal
(equivalent to kappa parameter of the von Mises-Fisher distribution) in
1/radian^2 units. If no value is defined, it will use the 1/size^2 of a pixel
in the pixelation used for the range files.

By default only pixels at .95 of the spherical normal CDF will be used. Use
the flag --bound to set the bound for the normal CDF.

By default the output will be printed in the standard output. If the flag
--output, or -o, is defined, the indicated file will be used as output. If the
file exists, existing taxons will be replaced, and new taxon will be added to
the indicated file.
	`,
	SetFlags: setFlags,
	Run:      run,
}