Author: pvanbosgeo
Date: 2015-01-10 15:44:09 -0800 (Sat, 10 Jan 2015)
New Revision: 64050
Modified:
grass-addons/grass7/raster/r.mess/r.mess.html
grass-addons/grass7/raster/r.mess/r.mess.py
Log:
correct text about requirements reference input layer
Modified: grass-addons/grass7/raster/r.mess/r.mess.html
===================================================================
--- grass-addons/grass7/raster/r.mess/r.mess.html 2015-01-10 23:04:51 UTC (rev 64049)
+++ grass-addons/grass7/raster/r.mess/r.mess.html 2015-01-10 23:44:09 UTC (rev 64050)
@@ -1,6 +1,6 @@
<h2>DESCRIPTION</h2>
-The Multivariate Environmental Similarity (MES) surfaces was
+<p>The Multivariate Environmental Similarity (MES) surfaces was
proposed by Elith et al (2010) and originally implemented in the
Maxent software. They described the MES approach as: "The
multivariate environmental similarity surface (MESS) calculation
@@ -17,41 +17,37 @@
the MES values
<ul>
- <li>the area where for at least one of the variables has a value
- that falls outside the range of values found in the reference set
- </li>
- <li>the most dissimilar variable (MoD)</li>
- <li>the mean
- of the IES layers where IES < 0</li>
- <li>the number of layers
- with negative values</li>
+ <li>the area where for at least one of the variables has a value that falls outside the range of values found in the reference set</li>
+ <li>the most dissimilar variable (MoD)</li>
+ <li>the mean of the IES layers where IES < 0</li>
+ <li>the number of layers with negative values</li>
</ul>
-<p> The reference points can be a binary raster layer (with 1
-representing presence and 0 representing absence) or a vector point
-layer as reference points. Any sample of interest can be used for
-the reference set. Examples are points representing occurrence
-records for the species and areas that represent protected areas.
+<p>The reference points can be a binary raster layer (with all
+none-NULL values representing presence and NULL values representing
+absence) or a vector point layer as reference points. Any sample of
+interest can be used for the reference set. Examples are points
+representing occurrence records for the species and areas that
+represent protected areas.
-<p> To compare e.g., current and future environmental conditions the
+<p>To compare e.g., current and future environmental conditions the
user needs to define a reference set of environmental variables
(env_old) and a set of future environmnental variables (env_new).
This is for example used to identify areas with novel future climates.
-<p> One can also test for the similarity between two different
-areas. For this one needs to provide a set of environmental
-variables (env_old) and a reference layer (ref_rast) for one region
-and a second set of environmental variables for another region
-(env_new).
+<p>One can also test for the similarity between two different areas.
+For this one needs to provide a set of environmental variables
+(env_old) and a reference layer (ref_rast) for one region and a
+second set of environmental variables for another region (env_new).
-<h2>REFERENCES</h2>
-<p>Elith, J., Kearney, M., & Phillips, S.
+<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.
+Ecology and Evolution 1:330–342.
<h2>AUTHOR</h2>
Paulo van Breugel, paulo at ecodiv.org
+
<p><i>Last changed: $Date$</i>
Modified: grass-addons/grass7/raster/r.mess/r.mess.py
===================================================================
--- grass-addons/grass7/raster/r.mess/r.mess.py 2015-01-10 23:04:51 UTC (rev 64049)
+++ grass-addons/grass7/raster/r.mess/r.mess.py 2015-01-10 23:44:09 UTC (rev 64050)
@@ -28,7 +28,7 @@
#% key: ref_rast
#% type: string
#% gisprompt: old,cell,raster
-#% description: Reference distribution as raster
+#% description: Reference distribution as raster (1 = presence, 0 = absence)
#% key_desc: name
#% required: no
#% multiple: no
@@ -242,6 +242,7 @@
tmpf0 = "rmess_tmp_" + str(uuid.uuid4())
tmpf0 = string.replace(tmpf0, '-', '_')
grass.mapcalc("$tmpf0 = $vtl * 1", vtl = vtl, tmpf0=tmpf0, quiet=True)
+ grass.run_command("r.null", map=tmpf0, setnull=0, quiet=True)
clean_rast.add(tmpf0)
# Remove mask