README
¶
Ranges
Package ranges implements a pixelation
for data about species distribution ranges.
Authorship and license
Copyright © 2022 J. Salvador Arias jsalarias@gmail.com. All rights reserved. Distributed under BSD2 licenses that can be found in the LICENSE file.
Documentation
¶
Overview ¶
Package ranges implements a pixelation for data about species distribution ranges.
A range is a representation of a taxon distribution, and it can be either explicit sampling points, or a probability density for the presence of a taxon at a pixel.
Index ¶
- type Collection
- func (c *Collection) Add(name string, age int64, lat, lon float64)
- func (c *Collection) AddPixel(name string, age int64, pixID int)
- func (c *Collection) Age(name string) int64
- func (c *Collection) Delete(name string)
- func (c *Collection) HasTaxon(name string) bool
- func (c *Collection) Pixelation() *earth.Pixelation
- func (c *Collection) Range(name string) map[int]float64
- func (c *Collection) Set(name string, age int64, rng map[int]float64)
- func (c *Collection) SetPixels(name string, age int64, rng map[int]float64)
- func (c *Collection) TSV(w io.Writer) error
- func (c *Collection) Taxa() []string
- func (c *Collection) Type(name string) Type
- type Type
Constants ¶
This section is empty.
Variables ¶
This section is empty.
Functions ¶
This section is empty.
Types ¶
type Collection ¶
type Collection struct {
// contains filtered or unexported fields
}
A Collection is a collection of distribution ranges with an associated pixelation.
func New ¶
func New(pix *earth.Pixelation) *Collection
New creates a new collection of taxon ranges using an isolatitude pixelation.
func ReadTSV ¶
func ReadTSV(r io.Reader, pix *earth.Pixelation) (*Collection, error)
ReadTSV reads a collection of range maps from a TSV file.
The TSV must contain the following columns:
- taxon, the name of the taxon
- type, the type of the range model. Can be "points" (for presence-absence pixelation), or "range" (for a pixelated range map).
- age, for the age stage of the pixels (in million years)
- equator, for the number of pixels in the equator
- pixel, the ID of a pixel (from the pixelation)
- density, the density for the presence at that pixel
Here is an example file:
# range distribution models taxon type age equator pixel density Brontostoma discus points 0 360 17319 1.000000 Brontostoma discus points 0 360 19117 1.000000 Eoraptor lunensis range 230000000 360 34661 0.200000 Eoraptor lunensis range 230000000 360 34662 0.500000 Eoraptor lunensis range 230000000 360 34663 1.000000 Eoraptor lunensis range 230000000 360 34664 0.500000 Eoraptor lunensis range 230000000 360 34665 0.200000 Rhododendron ericoides points 0 360 18588 1.000000 Rhododendron ericoides points 0 360 19305 1.000000 Rhododendron ericoides points 0 360 19308 1.000000
func (*Collection) Add ¶
func (c *Collection) Add(name string, age int64, lat, lon float64)
Add adds a point to a taxon at an specific age (in years).
To add a point the range of the taxon must be defined as 'points' (i.e. a presence-absence pixelation).
func (*Collection) AddPixel ¶
func (c *Collection) AddPixel(name string, age int64, pixID int)
AddPixel adds a pixel. using the pixel ID in the underlying pixelation, to a taxon at an specific age (in years).
To add a pixel the range of the taxon must be defined as 'points' (i.e. a presence-absence pixelation).
func (*Collection) Age ¶
func (c *Collection) Age(name string) int64
Age returns the age (in years) used to set a range map for a taxon.
func (*Collection) Delete ¶
func (c *Collection) Delete(name string)
Delete removes the indicated taxon from the collection.
func (*Collection) HasTaxon ¶
func (c *Collection) HasTaxon(name string) bool
HasTaxon returns true if the indicated taxon is in the collection.
func (*Collection) Pixelation ¶
func (c *Collection) Pixelation() *earth.Pixelation
Pixelation returns the underlying pixelation of a Collection.
func (*Collection) Range ¶
func (c *Collection) Range(name string) map[int]float64
Range returns a range map of a taxon.
The range map is a map of pixel IDs to the probability field scaled to set the maximum value equal to 1.0 (so in the case of points, all points will be set to be 1.0, and all other pixels will be 0.0).
func (*Collection) Set ¶
func (c *Collection) Set(name string, age int64, rng map[int]float64)
Set sets a range map for a taxon at the indicated age (in years). The range is a map of pixel IDs to a probability. The values will be scaled so the max value will be 1, and values smaller than 0.0000005 will be ignored. It will overwrite any range map previously set for the taxon.
func (*Collection) SetPixels ¶
func (c *Collection) SetPixels(name string, age int64, rng map[int]float64)
SetPixels sets pixel points for a taxon at the indicated age (in years). All pixel points will set to 1.0 no matter the stored value in the range. It will overwrite any data previously set for the taxon.
func (*Collection) TSV ¶
func (c *Collection) TSV(w io.Writer) error
TSV encodes range maps in a collection to a TSV file.
func (*Collection) Taxa ¶
func (c *Collection) Taxa() []string
Taxa returns an slice with the taxon names of the taxa in the collection of ranges.
func (*Collection) Type ¶
func (c *Collection) Type(name string) Type
Type returns the type of a range map for a given taxon.
type Type ¶
type Type string
Type is the type of range map.
const ( // Points is a range map made of points // (i.e. a presence-absence pixelation). Points Type = "points" // A Range is a continuous range map // (for example a pixelation of a range map from literature, // the output from a distribution model, // or a density estimation for a set of points). Range Type = "range" )
Type valid values.
Source Files
Directories
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| Path | Synopsis |
|---|---|
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cmd
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taxrange
TaxRange is a tool to dealt with pixelated range maps.
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TaxRange is a tool to dealt with pixelated range maps. |
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taxrange/imppoints
Package imppoints implements a command to import taxon distribution ranges from a list of specimen records.
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Package imppoints implements a command to import taxon distribution ranges from a list of specimen records. |
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taxrange/kde
Package kde implements a command to estimate a range distribution using a kernel density estimator.
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Package kde implements a command to estimate a range distribution using a kernel density estimator. |
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taxrange/mapcmd
Package mapcmd implements a command to draw the geographic range of taxon in a map.
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Package mapcmd implements a command to draw the geographic range of taxon in a map. |
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taxrange/rotate
Package rotate implements a command to rotate the points of a range distribution.
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Package rotate implements a command to rotate the points of a range distribution. |
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taxrange/taxa
Package taxa implements a command to print the list of taxa in a taxon range collection.
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Package taxa implements a command to print the list of taxa in a taxon range collection. |