[GRASS-SVN] r59100 - grass-addons/grass7/raster/r.mess

Thu Feb 20 02:04:31 PST 2014

Author: pvanbosgeo
Date: 2014-02-20 02:04:31 -0800 (Thu, 20 Feb 2014)
New Revision: 59100

Modified:
   grass-addons/grass7/raster/r.mess/r.mess.html
Log:
Added option to define vector with current and new set of environmental conditions. This will allow to calculate the MES between to time steps rather than between locations. If no set of environmental variables is given, the old ones are used.

Modified: grass-addons/grass7/raster/r.mess/r.mess.html
===================================================================

--- grass-addons/grass7/raster/r.mess/r.mess.html	2014-02-20 09:13:23 UTC (rev 59099)
+++ grass-addons/grass7/raster/r.mess/r.mess.html	2014-02-20 10:04:31 UTC (rev 59100)
@@ -1,125 +1,27 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-<title>GRASS GIS manual: r.mess</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">
-
-<img src="grass_logo.png" alt="GRASS logo"><hr align=center size=6 noshade>
-
-<h2>NAME</h2>
-<em><b>r.mess</b></em>  - Computes multivariate environmental similarity surface
-<h2>KEYWORDS</h2>
-<h2>SYNOPSIS</h2>
-<div id="name"><b>r.mess</b><br></div>
-<b>r.mess help</b><br>
-<div id="synopsis"><b>r.mess</b> [-<b>mkl</b>]  [<b>ref_rast</b>=<em>name</em>]   [<b>ref_vect</b>=<em>name</em>]  <b>env_var</b>=<em>names</em>[,<i>names</i>,...] <b>output</b>=<em>name</em> <b>digits</b>=<em>string</em>  [--<b>overwrite</b>]  [--<b>verbose</b>]  [--<b>quiet</b>] 
-</div>
-
-<div id="flags">
-<h3>Flags:</h3>
-<dl>
-<dt><b>-m</b></dt>
-<dd>Calculate Most dissimilar variable (MoD)</dd>
-
-<dt><b>-k</b></dt>
-<dd>Calculate mean of IES layers</dd>
-
-<dt><b>-l</b></dt>
-<dd>Calculate median of IES layers</dd>
-
-<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>
-</div>
-
-<div id="parameters">
-<h3>Parameters:</h3>
-<dl>
-<dt><b>ref_rast</b>=<em>name</em></dt>
-<dd>Reference distribution as raster</dd>
-
-<dt><b>ref_vect</b>=<em>name</em></dt>
-<dd>Reference distribution as point vector layer</dd>
-
-<dt><b>env_var</b>=<em>names[,<i>names</i>,...]</em> <b>[required]</b></dt>
-<dd>Input (predictor) raster map(s)</dd>
-
-<dt><b>output</b>=<em>name</em> <b>[required]</b></dt>
-<dd>Root name of the output MESS data layers</dd>
-
-<dt><b>digits</b>=<em>string</em> <b>[required]</b></dt>
-<dd>Precision of your input layers values</dd>
-<dd>Default: <em>0.001</em></dd>
-
-</dl>
-</div>
-
 <h2>DESCRIPTION</h2>
 
-<em>r.mess</em> computes the "Multivariate Environmental
-Similarity Surfaces" (MESS) in GRASS using R as backend. The
-MESS index was proposed by Elith et al (2010) and is also
-implemented in the Maxent software. The MESS approach
-can be described as follows (from Elith et al 2010):
-"The multivariate environmental similarity surface (MESS) calculation
-represents how similar a point is to a reference set of points, with
-respect to a set of predictor variables (V1, V2, ...). The values in
-the MESS are influenced by the full distribution of the reference points, so that
-sites within the environmental range of the reference points but in
-relatively unusual environments will have a smaller value than those in
-very common environments."
+<em>r.mess</em> computes the Multivariate Environmental Similarity (MES) surfaces in GRASS using R as backend. The MES index was proposed by Elith et al (2010) and is also implemented in the Maxent software. The MES approach can be described as follows (from Elith et al 2010): "The multivariate environmental similarity surface (MESS) calculation represents how similar a point is to a reference set of points, with respect to a set of predictor variables (V1, V2, ...). The values in the MESS are influenced by the full distribution of the reference points, so that sites within the environmental range of the reference points but in relatively unusual environments will have a smaller value than those in very common environments."
 
-<p>This module will also compute the individual environmental
-similarity surfaces (IESS), which represents how similar a point is to
-a set of reference points for each of the input variable. MESS
-is then simply calculated as the minimum of its similarity with respect
-to each variable. 
+<p>This module will compute the individual environmental similarity surfaces (IES), which represents how similar each raster cell in a raster layer is to a set of reference points for each of the input variable. MES is then simply calculated as the minimum of its similarity with respect to each variable. Note that if a given raster cell has a negative IES value, it means that that value falls outside the range of values found in the reference set. A negative MESS thus represents sites where at least one variable has a value that is outside the range of environments over the reference set.
 
-<p>Any sample of interest can be used for the reference set. For example,
-it can be occurrence records for the species; a sample of a region, or a sample of
-current climate conditions in a given area. The input layer representing the
-reference distribution can be a vector point layer or a raster layer.
+<p>The IES/MES compares the similarity between all raster cells in the current region and a subset of the raster cells in the region (the reference points). Any sample of interest can be used for the reference set. For example, it can be occurrence records for the species or a random sample of a region. The input layer representing the reference distribution can be a vector point layer or a raster layer.
 
-<p>
-The IESS can have negative values – these are sites where the variable
-has a value that is outside the range in the reference set. A negative MESS
-thus represents sites where at least one variable has a value that is
-outside the range of environments over the reference set, so these are
-novel environments.
+<p>Besides the obligatory set of environmental variables used to calculate the IES/MES, the user can define a second set of environmental variables (env1). This allows the user to compute how similar current conditions in given area are to those under e.g., future climates. This is for example useful to identify areas with novel future climates.
 
-<p>
-In addition to the MESS, which is the minimum(IESS), the r.mess
-function also allows to compute mean and medium of the IESS layers.
+<p>In addition to the MES, which is the minimum IES, the r.mess function also allows to compute mean and median of the IES layers and a MoD layer, which identifies for each raster cells the IESS with the lowest value. Note that the mean and median of the IES should be used with care as negative and positive IES values have different meanings.
 
 <h2>NOTES</h2>
-Digits should reflect the level of precision of the input layers. I.e., if
-values of the input layers are recorded with three digits behind the comma,
-Digits should be set to 0.001 or smaller.
+Digits should reflect the level of precision of the input layers. I.e., if values of the input layers are recorded with three digits behind the comma, Digits should be set to 0.001 or smaller.
 
 <h2>SEE ALSO</h2>
-There is also a similar function implemented for R using the R package
-<em>raster</em>, and which is part of the dismo package in R now. See <a href="http://rossijeanpierre.wordpress.com/2012/08/13/computing-the-multivariate-environmental-similarity-surfaces-mess-index-in-r/">here</a>.
-for more information and the script.
+There is also a similar function implemented for R using the R package <em>raster</em>, and which is part of the dismo package in R now. See <a href="http://rossijeanpierre.wordpress.com/2012/08/13/computing-the-multivariate-environmental-similarity-surfaces-mess-index-in-r/">here</a> for more information and the script.
 
+<h2>REFERENCES</h2>
+<p>Elith, J., Kearney, M., & Phillips, S. 2010. The art of modelling range-shifting species. Methods in Ecology and Evolution 1:330–342.
+
 <h2>AUTHOR</h2>
 
 Paulo van Breugel <paulo at ecodiv.org>
 
-<h2>REFERENCES</h2>
-<ul>
-<li>Elith, J., Kearney, M., & Phillips, S. 2010. The art of
-modelling range-shifting species. Methods in Ecology and Evolution 1:
-330–342.</li>
-</ul>
 
-<p>
-<i>Last changed: $Date$</i>
-</body>
-</html>
+<p><i>Last changed: $Date$</i>

