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| <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> | ||
| <html> | ||
| <head> | ||
| <title>GRASS GIS manual: r.maxent.lambdas</title> | ||
| <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> | ||
| <link rel="stylesheet" href="grassdocs.css" type="text/css"> | ||
| </head> | ||
| <body bgcolor="white"> | ||
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| <img src="grass_logo.png" alt="GRASS logo"><hr align=center size=6 noshade> | ||
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| <h2>NAME</h2> | ||
| <em><b>r.maxent.lambdas</b></em> - Computes raw and/or logistic prediction maps from MaxEnt lambdas files | ||
| <h2>KEYWORDS</h2> | ||
| raster, MaxEnt, species distribution modelling | ||
| <h2>SYNOPSIS</h2> | ||
| <b>r.maxent.lambdas</b><br> | ||
| <b>r.maxent.lambdas help</b><br> | ||
| <b>r.maxent.lambdas</b> [-<b>rl</b>] <b>lambdas_file</b>=<em>string</em> <b>output_prefix</b>=<em>string</em> [<b>alias_file</b>=<em>string</em>] [<b>integer_output</b>=<em>integer</em>] [<b>output_mapcalc</b>=<em>string</em>] [--<b>overwrite</b>] [--<b>verbose</b>] [--<b>quiet</b>] | ||
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| <h3>Flags:</h3> | ||
| <dl> | ||
| <dt><b>-r</b></dt> | ||
| <dd>Produce only raw output (both are computed by default).</dd> | ||
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| <dt><b>-l</b></dt> | ||
| <dd>Produce only logistic output (both are computed by default).</dd> | ||
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| <dt><b>--overwrite</b></dt> | ||
| <dd>Allow output files to overwrite existing files</dd> | ||
| <dt><b>--verbose</b></dt> | ||
| <dd>Verbose module output</dd> | ||
| <dt><b>--quiet</b></dt> | ||
| <dd>Quiet module output</dd> | ||
| </dl> | ||
| <h2>DESCRIPTION</h2> | ||
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| <h3>Parameters:</h3> | ||
| <dl> | ||
| <dt><b>lambdas_file</b>=<em>string</em></dt> | ||
| <dd>MaxEnt lambdas-file to compute distribution-model from</dd> | ||
| The script is intended to compute raw and/or logistic prediction maps | ||
| from a lambdas file produced with MaxEnt 3.3.3e.<br> | ||
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| <dt><b>output_prefix</b>=<em>string</em></dt> | ||
| <dd>Prefix for output raster maps</dd> | ||
| It will parse the specified lambdas-file from MaxEnt 3.3.3e and | ||
| translate it into an r.mapcalc-expression which is then stored in a | ||
| temporary file and finally piped to r.mapcalc. If alias names had been | ||
| used in MaxEnt, these alias names can automatically be replaced | ||
| according to a CSV-like file provided by the user. This file should | ||
| contain alias names in the first column and map names in the second | ||
| column, seperated by comma, without header. It should look e.g. like | ||
| this: | ||
| <br> | ||
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| <dt><b>alias_file</b>=<em>string</em></dt> | ||
| <dd>CSV-file to replace alias names from MaxEnt by GRASS map names</dd> | ||
| <div class="code"><pre> | ||
| alias_1,map_1 | ||
| alias_2,map_2 | ||
| ...,... | ||
| </pre></div> | ||
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| <dt><b>integer_output</b>=<em>integer</em></dt> | ||
| <dd>Produce logistic integer output with this number of digits preserved</dd> | ||
| <dd>Default: <em>0</em></dd> | ||
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| <dt><b>output_mapcalc</b>=<em>string</em></dt> | ||
| <dd>Save r.mapcalc expression to file</dd> | ||
| </dl> | ||
| <h2>DESCRIPTION</h2> | ||
| The script is intended to compute raw and/or logistic prediction maps from a lambdas file produced with MaxEnt 3.3.3e.<br> | ||
| It will parse the specified lambdas-file from MaxEnt 3.3.3e and translate it into an r.mapcalc-expression | ||
| which is then stored in a temporary file and finally piped to r.mapcalc. If alias names had been used in MaxEnt, these | ||
| alias names can automatically be replaced according to a CSV-like file provided by the user. | ||
| This file should contain alias names in the first column and map names in the second column, seperated by comma, | ||
| without header. It should look e.g. like this:<br> | ||
| <br> | ||
| <em> | ||
| alias_1,map_1<br> | ||
| alias_2,map_2<br> | ||
| ...,...<br> | ||
| </em> | ||
| <br> | ||
| If such a CSV-file with alias names used in MaxEnt is provided, the alias names from MaxEnt are replaced by map names.<br> | ||
| <br> | ||
| A raw output map is always computed from the MaxEnt model as a first step. If logistic output is requested, the raw output | ||
| map can be deleted by the script ( using the l-flag). The logistic map can be produced as an integer map. To do so the user | ||
| has to specify the number of decimal places, that should be preserved in integer output.<br> | ||
| Optionally the map calculator expressions can be saved in a text file as especially the one for the raw output is likely to exceed | ||
| the space in the map history. | ||
| <p> | ||
| If such a CSV-file with alias names used in MaxEnt is provided, the alias | ||
| names from MaxEnt are replaced by map names. | ||
| <p> | ||
| A raw output map is always computed from the MaxEnt model as a first | ||
| step. If logistic output is requested, the raw output map can be | ||
| deleted by the script ( using the l-flag). The logistic map can be | ||
| produced as an integer map. To do so the user has to specify the number | ||
| of decimal places, that should be preserved in integer output. | ||
| <p> | ||
| Optionally the map calculator expressions can be saved in a text file | ||
| as especially the one for the raw output is likely to exceed the space | ||
| in the map history. | ||
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| <h2>NOTES</h2> | ||
| This script works only if the maps containing the input data to MaxEnt are accessible from the current region.<br> | ||
| Due to conversion from double to floating-point in exp()-function, a loss of precision from the 7th decimal place onwards may occur | ||
| in the logistic output. | ||
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| This script works only if the maps containing the input data to MaxEnt are | ||
| accessible from the current region. | ||
| <p> | ||
| Due to conversion from double to floating-point in exp()-function, a loss of | ||
| precision from the 7th decimal place onwards may occur in the logistic output. | ||
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| <h2>SEE ALSO</h2> | ||
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| r.out.maxent_swd, r.in.xyz<br> | ||
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| MaxEnt 3.3.3e <a href="http://biodiversityinformatics.amnh.org/open_source/maxent/">http://biodiversityinformatics.amnh.org/open_source/maxent/</a><br> | ||
| Jane Elith, Steven J. Phillips, Trevor Hastie, Miroslav Dudík, Yung En Chee, Colin J. Yates. 2011: A statistical explanation of MaxEnt | ||
| 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.<br> | ||
| Wilson, Peter D. 2009: Guidelines for computing MaxEnt model output values from a lambdas file. (Avaliable at <a href="http://groups.google.com/group/MaxEnt"> | ||
| http://groups.google.com/group/MaxEnt</a>) | ||
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| Wilson, Peter D. 2009: Guidelines for computing MaxEnt model output values from a lambdas file. (Available at <a href="https://groups.google.com/group/MaxEnt"> | ||
| https://groups.google.com/group/MaxEnt</a>) | ||
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| Steven J. Phillips, Robert P. Anderson, Robert E. Schapire. 2006: Maximum entropy modeling of species geographic distributions. | ||
| Ecological Modelling, (190):231-259, 2006.<br> | ||
| Steven J. Phillips, Miroslav Dudík, Robert E. Schapire. 2004: A maximum entropy approach to species distribution modeling. In: Proceedings | ||
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| 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, p. 655-662, 2004. | ||
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| <h2>AUTHOR</h2> | ||
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| Stefan Blumentrath, Norwegian Institute for Nature Research (NINA), <a href="http://www.nina.no">http://www.nina.no</a> | ||
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| </body> | ||
| </html> | ||
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