NAME
r.out.maxent_swd - Exports map data as input to MaxEnt in SWD format
KEYWORDS
raster, MaxEnt, species distribution modelling
SYNOPSIS
r.out.maxent_swd
r.out.maxent_swd help
r.out.maxent_swd [-bz] [alias_input=string] [evp_maps=string[,string,...]] [alias_names=string] [alias_output=string] [bgr_output=string] [bgr_mask=string] [specie_mask=string[,string,...]] [specie_output=string] [specie_name=string] [nv=integer] [--verbose] [--quiet]
Flags:
- -b
- Produce only background output
- -z
- Zoom computational region to species data
Setting this flag may speed up processing for very large regions and locally distributed
species. But it may decrease processing time in other cases. Use with care.
- --verbose
- Verbose module output
- --quiet
- Quiet module output
Parameters:
- alias_input=string
- File containg map and alias name(s) for environmental parameter(s)
This file should contain alias names in the first column and map names in the second column, separated by comma,
without header. It should look e.g. like this:
alias_1,map_1
alias_2,map_2
...,...
- evp_maps=string[,string,...]
- Environmental parameter map(s)
Multiple maps containing the environmental parameter(s) to be used in MaxEnt.
- alias_names=string
- Alias names for environmental parameter
A list of names to be used as alias names for the environmental parameter map names.
- alias_output=string
- Save alias names for the environmental parameters to file
When using alias names for the environmental parameter map names, it is advantageous to save the alias names to file.
In this case the alias file can be used to re-translate the alias names back to map names when using the script r.maxent.lambdas.
- bgr_output=string
- Output SWD file for the environmental data of the background landscape
- bgr_mask=string
- Map to be used as mask for the background landscape
- specie_mask=string[,string,...]
- Raster map(s) of specie occurence
- specie_output=string
- Output SWD file for the specie(s) related environmental data
- specie_name=string
- Alias-name(s) for species to be used in MaxEnt SWD file instead of map names, separated by comma (default: map names).
- nv=integer
- Integer representing NO DATA cell value
- Default: -9999
DESCRIPTION
The script is intended to produce a set of SWD files as input to MaxEnt 3.3.3e using r.stats.
The SWD file format is a simple CSV-like file file format as described in Elith et al. 2011.
Generally it looks like:
specie_name,X,Y,parameter_1,parameter_2,...
your_specie,1.1,1.1,2,4.7,...
The first column always contains the name of the species, followed by
two colums for the X- and Y-coordinates. Then each column
represents one environmental parameter. In contrast to r.stats
only integer values are accepted to represent NO DATA.
A background SWD file is allways produced while specie output can be omitted.
Multiple species can be processed, but each has to be in an
individual raster map. Map names of the maps containing the environmental
parameters can be replaced by short names, which should be used
in MaxEnt 3.3.3.e.
Results from MaxEnt can either be imported using r.in.xyz or
calculated from MaxEnt lambdas file using the script
r.maxent.lambdas.
NOTES
SEE ALSO
r.stats
MaxEnt 3.3.3e http://www.cs.princeton.edu/~schapire/maxent/
Wilson, Peter D. 2009: Guidlelines for computing MaxEnt model output values from a lambdas file. (Avaliable at
http://groups.google.com/group/MaxEnt)
Steven J. Phillips, Miroslav Dudík, Robert E. Schapire. 2004: A maximum entropy approach to species distribution modeling. In Proceedings
of the Twenty-First International Conference on Machine Learning, pages 655-662, 2004.
Steven J. Phillips, Robert P. Anderson, Robert E. Schapire. 2006: Maximum entropy modeling of species geographic distributions.
Ecological Modelling, 190:231-259, 2006.
Jane Elith, Steven J. Phillips, Trevor Hastie, Miroslav Dudík, Yung En Chee, Colin J. Yates. 2011: A statistical explanation of MaxEnt
for ecologists. Diversity and Distributions, 17:43-57, 2011.
AUTHOR
Stefan Blumentrath, Norwegian Institute for Nature Research (NINA), http://www.nina.no