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v.maxent.swd: update manual page, added option to thin point layers a…
…nd bugfixes (OSGeo#1022) - Included an example - Added option to thin species presence and background point layers. - Bug fixes Co-authored-by: Markus Neteler <[email protected]>
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| <h2>DESCRIPTION</h2> | ||
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| <em>v.maxent.swd</em> Produce a set of SWD files as input to MaxEnt | ||
| 3.3.3k+, based on a point vector layer(s) of species distribution(s), a | ||
| point layer with background points and user-defined raster layers. The | ||
| user can also let the function create the background point file. | ||
| (respecting region and mask, if set). | ||
| The <em>v.maxent.swd</em> takes one or more point vector layers with | ||
| the location of species presence locations (parameter: <b>species</b>), | ||
| and a set of raster layers representing relevant environmental | ||
| variables (parameter: <b>evp_maps</b>). 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. | ||
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| <p> | ||
| The SWD file format is a simple CSV-like file format as described | ||
| in Elith et al. 2011. 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. Note that the | ||
| coordinates are not used by the MaxEnt program if all environmental | ||
| data is given in the SWD format file. | ||
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| <p> | ||
| The user can provide one or more species point files, which will be | ||
| combined in one SWD file. 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 user can also provide a point layer with background points | ||
| (parameter: <b>bgp</b>). 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. | ||
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| <p> | ||
| 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 header. This can be used as input in | ||
| r.maxent.lambdas (but note that this addon does not seem to work with | ||
| outputs from Maxent 3.4+). | ||
| separated by comma, without a header. | ||
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| <h2>NOTES</h2> | ||
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| The SWD output files are simple comma delimited text | ||
| files (.csv) and can therefore be easily read in in for example R | ||
| and subsequently used in other models / functions. | ||
| 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. | ||
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| <p> | ||
| Maxent expects the raster cells to be perfectly square. I.e., the n-s | ||
| and e-w resolution need to be the same. v.maxent.swd will fail if this | ||
| is not the case. If this happens, you should change the resolution. | ||
| 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. | ||
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| <p> | ||
| 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): | ||
| 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): | ||
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| <div class="code"><pre> | ||
| g.region -a res=*** | ||
| </pre></div> | ||
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| <p> | ||
| Alternatively, you can set the <i>-e flag</i>. This will run g.region | ||
| Alternatively, you can set the <b>-e flag</b>. 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. | ||
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| <p> | ||
| This addon is a vector based alternative to <em>r.out.maxent_swd</em>. | ||
| This addon is a vector-based alternative to <em>r.out.maxent_swd</em>. | ||
| 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. points per raster cell. If this is not desired, use | ||
| r.out.maxent_swd. 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. | ||
| raster cell. But note that you can use the <b>-t</b> 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. | ||
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| <h2>EXAMPLES</h2> | ||
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| The examples below use a dataset that you can download <a | ||
| href="https://ecodiv.earth/share/reader_SDM/grassmaxent_sampledata.zip">from | ||
| here</a>. It includes <a href="">vector point layer</a> with | ||
| observation locations of the pale-throated sloth (<i>Bradypus | ||
| tridactylus</i>) from <a | ||
| href="https://doi.org/10.15468/dl.br8b4a">GBIF</a>, a number of bioclim | ||
| raster layers from <a | ||
| href="https://www.worldclim.org/data/worldclim21.html">WorldClim</a>, | ||
| the <a href="https://www.iucnredlist.org/species/3037/210442660">IUCN | ||
| RedList range map</a> of the species, and a boundary layer of the South | ||
| American countries from <a | ||
| href="https://www.naturalearthdata.com/downloads/50m-cultural-vectors/">NaturalEarth</a>. | ||
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| <p> | ||
| The zip file contains a <a | ||
| href="https://grass.osgeo.org/grass-stable/manuals/grass_database.html#grass-locations">GRASS | ||
| location</a>. Unzip it and put it in a GRASS GIS database. Next, open | ||
| GRASS GIS and go to the mapset <i>southamerica</i>. Download the zip | ||
| file, and unzip it in a GRASS GIS database. | ||
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| <div class="code"> | ||
| <pre> | ||
| 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 | ||
| </pre> | ||
| </div> | ||
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| <p> | ||
| The output is a folder <i>maxentinput</i> 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 <i>envlayers</i>. | ||
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| <p> | ||
| The created data layers can be used as input for <a | ||
| href="http://biodiversityinformatics.amnh.org/open_source/maxent/">Maxent</a>. | ||
| Alternatively, you can use it as input for the <em>r.maxent.train</em> | ||
| addon, which provides a convenient wrapper for the <i>Maxent</i> | ||
| software. | ||
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| <h2>SEE ALSO</h2> | ||
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| <ul> | ||
| <li>MaxEnt 3.4.1 (<a | ||
| href="http://biodiversityinformatics.amnh.org/open_source/maxent/"> | ||
| http://biodiversityinformatics.amnh.org/open_source/maxent/</a>)</li> | ||
| <li><a href="r.out.maxent_swd.html">r.out.maxent_swd</a>, the original | ||
| implementation using species distribution data in raster format.</li> | ||
| <li><a href="r.maxent.lambdas.html">r.maxent.lambdas</a> addon to | ||
| compute raw or logistic prediction maps from MaxEnt lambdas files.</li> | ||
| <li><a href="r.maxent.train.html">r.maxent.train</a> addon to | ||
| create/train a Maxent model. The addon provides a wrapper to the | ||
| Maxent software.</li> | ||
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| <li><a href="r.out.maxent_swd.html">r.out.maxent_swd</a>, an | ||
| alternative implementation of this addon, using species | ||
| distribution data in raster format.</li> | ||
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| <li><a href="r.maxent.lambdas.html">r.maxent.lambdas</a> addon to | ||
| compute raw or logistic prediction maps from MaxEnt lambdas | ||
| files.</li> | ||
| </ul> | ||
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| <h2>REFERENCES</h2> | ||
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| <ul> | ||
| <li> Steven J. Phillips, Miroslav Dudík, Robert E. Schapire.A | ||
| <li>MaxEnt 3.4.1 (<a | ||
| href="http://biodiversityinformatics.amnh.org/open_source/maxent/"> | ||
| http://biodiversityinformatics.amnh.org/open_source/maxent</a>)</li> | ||
| <li> 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.</li> | ||
| <li>Steven J. Phillips, Robert | ||
| P. Anderson, Robert E. Schapire. Maximum entropy modeling of | ||
| species geographic distributions. Ecological Modelling, | ||
| 190:231-259, 2006.</li> | ||
| <li>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. </li> | ||
| <li>Steven J. Phillips, Robert P. Anderson, Robert E. Schapire. | ||
| Maximum entropy modeling of species geographic distributions. | ||
| Ecological Modelling, 190:231-259, 2006.</li> | ||
| <li>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. </li> | ||
| <li>GBIF.org (12 November 2023) GBIF Occurrence Download | ||
| https://doi.org/10.15468/dl.br8b4a </li> | ||
| </ul> | ||
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| <h2>AUTHOR</h2> | ||
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| Paulo van Breugel, paulo at ecodiv.earth | ||
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| <p> | ||
| HAS green academy University of Applied Sciences<br> | ||
| <a | ||
| href="https://www.has.nl/en/research/professorships/innovative-bio-monitoring-professorship/">Innovative | ||
| Biomonitoring research group</a><br> | ||
| <a | ||
| href="https://www.has.nl/en/research/professorships/climate-robust-landscapes-professorship/">Climate-robust | ||
| Landscapes research group</a> | ||
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