NAME
r.out.maxent_swd - Exports map data as input to MaxEnt in SWD formatKEYWORDS
raster, export, maxent, ecology, nicheSYNOPSIS
r.out.maxent_swd
r.out.maxent_swd --helpr.out.maxent_swd [-z] [alias_input=name] [env_maps=name[,name,...]] [alias_names=string] [bgr_output=name] [alias_output=name] [bgr_mask=name] [species_masks=name[,name,...]] [species_output=name] [species_names=string] [null_value=integer] [--overwrite] [--help] [--verbose] [--quiet] [--ui]
Flags:
- -z
- Zoom computational region to species data (may speed up processing)
- --overwrite
- Allow output files to overwrite existing files
- --help
- Print usage summary
- --verbose
- Verbose module output
- --quiet
- Quiet module output
- --ui
- Force launching GUI dialog
Parameters:
- alias_input=name
- File containg map and alias name(s) for environmental parameter(s)
- env_maps=name[,name,...]
- Environmental parameter map(s)
- alias_names=string
- Alias names for environmental parameter map(s)
- bgr_output=name
- Output SWD file for the environmental data of the background landscape
- alias_output=name
- CSV-like output file with alias names in first column and map names in second column, separated by comma
- bgr_mask=name
- Map to be used as mask for the background landscape
- species_masks=name[,name,...]
- Raster map(s) of specie occurence
- species_output=name
- Output SWD file for the specie(s) related environmental data
- species_names=string
- Alias-name(s) for species to be used in MaxEnt SWD file instead of map names, separated by comma (default: map names).
- null_value=integer
- Integer representing NO DATA cell value (default: -9999)
- Default: -9999
Table of contents
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 columns 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 always produced while species 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 r.maxent.lambdas.
SEE ALSO
r.stats, r.what, r.in.xyz,, r.maxent.lambdas- Steven J. Phillips, Miroslav Dudík, Robert E. Schapire. 2020: Maxent software for modeling species niches and distributions (Version 3.4.1). Available from url: http://biodiversityinformatics.amnh.org/open_source/maxent and https://github.com/mrmaxent/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.noSOURCE CODE
Available at: r.out.maxent_swd source code (history)
Latest change: Thu Feb 3 09:32:35 2022 in commit: f17c792f5de56c64ecfbe63ec315307872cf9d5c
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