Note: This document is for an older version of GRASS GIS that will be discontinued soon. You should upgrade, and read the current manual page.
NAME
v.maxent.swd - Export raster values at given point locations as text file in SWD format for input in Maxent. In addition, the addon can export the environmental raster layers as ascii files.
KEYWORDS
vector,
export,
Maxent
SYNOPSIS
v.maxent.swd
v.maxent.swd --help
v.maxent.swd [-teh] [species=string[,string,...]] [species_name=string] evp_maps=string[,string,...] [alias_names=string] [evp_cat=string[,string,...]] [alias_cat=string] [nbgp=number] [bgp=string] [species_output=name] [bgr_output=name] [alias_output=name] [export_rasters=name] [format=string] [nodata=number] [seed=integer] [--overwrite] [--help] [--verbose] [--quiet] [--ui]
Flags:
- -t
- Thin species and background points
- Select this flag if you want to limit the species and background points to maximum one point per raster cell. Note that this is already the case for the background points with the nbgp option.
- -e
- Automatically adapt resolution
- When the ns and ew resolution are not the same, nearest neighbor resampling will be used to ensure both are the same.
- -h
- skip header in csv
- --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:
- species=string[,string,...]
- vector map(s) of species occurence
- species_name=string
- Alias-name(s) for species (default: map names).
- evp_maps=string[,string,...] [required]
- Environmental parameter map(s)
- alias_names=string
- Alias names for environmental parameter(s)
- evp_cat=string[,string,...]
- Categorial environmental parameter map(s)
- alias_cat=string
- Alias names for categorial parameter(s)
- nbgp=number
- Number or percentage of background points
- bgp=string
- Vector layer with background / absence points
- species_output=name
- Species SWD file
- bgr_output=name
- Background SWD file
- alias_output=name
- CSV file with alias and map names
- export_rasters=name
- Folder where to export the predictor raster layers to
- format=string
- Raster data format to write (case sensitive, see r.out.gdal)
- Options: ascii, GeoTIFF
- nodata=number
- nodata value in output files
- Default: -9999
- seed=integer
- Seed for generating random points
- Default: 1
The
v.maxent.swd takes one or more point vector layers with
the location of species presence locations (parameter:
species),
and a set of raster layers representing relevant environmental
variables (parameter:
evp_maps). For all point locations, it
reads in the values of the environmental raster layers. The resulting
point layers(s) are combined in one layer and this is exported as a SWD
file that can be used as input for MaxEnd 3.4 or higher.
The user can also provide a point layer with background points
(parameter: bgp). Alternatively, a user-defined number of
background points can be generated automatically, respecting the
computational region and MASK. In either case, for all point locations,
the function reads in the values of the environmental raster layers.
The resulting point layer is exported as a SWD file.
If alias names are used, a CSV file (alias_file) can be created with
alias names in the first column and map names in the second column,
separated by comma, without a header.
The map names of both the species point layers and the environmental
parameters can be replaced by alias names, which will be used by
MaxEnt.
The SWD file format is a simple comma-delimited text files. The first
three fields provide the species name, x-coordinate and y-coordinate,
while subsequent fields contain the values of the user-selected
environmental parameters. The files can be easily read in for example,
R and subsequently used in other models / functions.
Maxent expects the n-s and e-w resolution to be the same. Following the
grass gis convention, the resolution of an exported raster is
determined by the region settings. So make sure to set the resolution
of the region so that the n-s and e-w resolution match. To accomplish
this, you can use (replaced the *** for the desired resolution):
Alternatively, you can set the -e flag. This will run g.region
for you, adjusting the resolution so both the ns and ew resolutionn
match the smallest of the two, using nearest neighbor resampling.
This addon is a vector-based alternative to r.out.maxent_swd.
It can be more efficient with sparse data points. The main difference
is that with this addon you can have more than one sample point per
raster cell. But note that you can use the -t flag to thin the
point layer so that there is never more than 1 point per raster cell.
Another difference is the option to export the predictor raster layers
to a user-defined folder. This can be used in Maxent, Maxnet addon for
R or other software.
The examples below use a dataset that you can download
from
here. It includes
vector point layer with
observation locations of the pale-throated sloth (
Bradypus
tridactylus) from
GBIF, a number of bioclim
raster layers from
WorldClim,
the
IUCN
RedList range map of the species, and a boundary layer of the South
American countries from
NaturalEarth.
The zip file contains a GRASS
location. Unzip it and put it in a GRASS GIS database. Next, open
GRASS GIS and go to the mapset southamerica. Download the zip
file, and unzip it in a GRASS GIS database.
v.maxent.swd -t species=Bradypus_tridactylus \
evp_maps=bio02,bio03@southamerica,bio08,bio09,bio13,bio15,bio17 \
evp_cat=sa_eco_l2 alias_cat=landuse nbgp=10000 \
bgr_output=maxentinput/bgrd_swd.csv \
species_output=maxentinput/spec_swd.csv \
export_rasters=maxentinput/envlayers
The output is a folder maxentinput with the SWD files
bgrd_swd.csv and spec_swd.csv and the accompanying proj files. The
latter provide information about the CRS, which might be useful if you
want to import the point layers in another software tools. In addition,
the example code creates the raster layers of the environmental layes
in ascii format in the folder envlayers.
The created data layers can be used as input for Maxent.
Alternatively, you can use it as input for the r.maxent.train
addon, which provides a convenient wrapper for the Maxent
software.
- r.maxent.train addon to
create/train a Maxent model. The addon provides a wrapper to the
Maxent software.
- r.out.maxent_swd, an
alternative implementation of this addon, using species
distribution data in raster format.
- r.maxent.lambdas addon to
compute raw or logistic prediction maps from MaxEnt lambdas
files.
- MaxEnt 3.4.1 (
http://biodiversityinformatics.amnh.org/open_source/maxent)
- Steven J. Phillips, Miroslav Dudík, Robert E. Schapire. 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.
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. A statistical explanation of MaxEnt
for ecologists. Diversity and Distributions, 17:43-57, 2011.
- GBIF.org (12 November 2023) GBIF Occurrence Download
https://doi.org/10.15468/dl.br8b4a
Paulo van Breugel, paulo at ecodiv.earth
HAS green academy University of Applied Sciences
Innovative
Biomonitoring research group
Climate-robust
Landscapes research group
SOURCE CODE
Available at:
v.maxent.swd source code
(history)
Latest change: Monday Jun 24 08:16:48 2024 in commit: 8939a985d18de5366340b88037ab0fe3a0814c9b
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GRASS Development Team,
GRASS GIS 8.3.3dev Reference Manual