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131 changes: 66 additions & 65 deletions src/raster/r.boxplot/r.boxplot.html
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Expand Up @@ -7,32 +7,32 @@ <h2>DESCRIPTION</h2>
values of the input raster that fall within that zone.

<p>
If there is a zonal map, the user can add a line and band to represent
the median and interquartile range (IQR) of the input layer. Note that
all values of the input raster (within the region's extent) are used to
compute the median and IQR. If the zones of the zonal map cover only
part of the region, the user can mask out the non-covered parts of the
input map first by means of <em>r.mask</em>. That will result in an IQR
and median representing the values that fall within the zones of the
zonal map only. Otherwise, the computational region can be changed to
fit the extent of the zonal map with <em>g.region</em>
If there is a zonal map, the user can add a line and band to represent
the median and interquartile range (IQR) of the input layer. Note that
all values of the input raster (within the region's extent) are used to
compute the median and IQR. If the zones of the zonal map cover only
part of the region, the user can mask out the non-covered parts of the
input map first by means of <em>r.mask</em>. That will result in an IQR
and median representing the values that fall within the zones of the
zonal map only. Otherwise, the computational region can be changed to
fit the extent of the zonal map with <em>g.region</em>.

<p>
By default, the resulting plot is displayed on screen. However, the
user can also save the plot to file using the <b>output</b> option.
The format is determined by the extension given by the user. So, if
output = outputfile.png, the plot will be saved as a PNG file.
user can also save the plot to file using the <b>output</b> option. The
format is determined by the extension given by the user. So, if output
= outputfile.png, the plot will be saved as a PNG file.

<p>
The whiskers extend to the most extreme data point, which is no more
than <b>range</b> &#10005; the IQR from the box. By default, a
<b>range</b> of <tt>1.5</tt> is used, but the user can change this.
The whiskers extend to the most extreme data point, which is no more
than <b>range</b> &#10005; the IQR from the box. By default, a
<b>range</b> of <tt>1.5</tt> is used, but the user can change this.
Note that range values need to be larger than <tt>0</tt>.

<p>
By default, outliers are not included in the plot. Set the <b>-o</b>
flag to include them in the plot. To also create a point vector map
with the locations of the outliers, the user needs to provide the name
By default, outliers are not included in the plot. Set the <b>-o</b>
flag to include them in the plot. To also create a point vector map
with the locations of the outliers, the user needs to provide the name
of the output map using <b>map_outliers</b>.

<p>
Expand All @@ -47,31 +47,32 @@ <h2>DESCRIPTION</h2>

<h2>NOTE</h2>

The <em>r.boxplot</em> module operates on the raster array defined by
the current region settings, not the original extent and resolution of
the input map. See <a
href="https://grass.osgeo.org/grass-stable/manuals/r.univar.html">g.region</a>
The <em>r.boxplot</em> module operates on the raster array defined by
the current region settings, not the original extent and resolution of
the input map. See <a
href="https://grass.osgeo.org/grass-stable/manuals/r.univar.html">g.region</a>
to understand the impact of the region settings on the calculations.

To include outliers, the function converts the raster cell with outlier
values to a point vector layer. This may take some time if there are a
lot of outliers. So, if users are working with very large raster
layers, they should be cautious to not set the <b>range</b> value too
To include outliers, the function converts the raster cell with outlier
values to a point vector layer. This may take some time if there are a
lot of outliers. So, if users are working with very large raster
layers, they should be cautious to not set the <b>range</b> value too
low as that may result in a huge number of outliers.

<p>
The zonal map needs to be an integer map. If it is not, the function will exit
with the error message, 'The zonal raster must be of type CELL (integer)'.
The zonal map needs to be an integer map. If it is not, the function
will exit with the error message, 'The zonal raster must be of type
CELL (integer)'.

<p>
If the <b>-c</b> flag is used, the <b>bxp_color</b> and
<b>median_color</b> are ignored, even if set by the user. The option to
color boxploxs using the colors of the zonal raster categories
(<b>c</b> flag) only works if the zonal map contains a color table. If
it does not, the function exits with the error message that 'The zonal
map does not have a color table'. If the user thinks there is a color
table, run <em>r.colors.out</em> and check if the categories are
integers. If not, that is the problem. If they are all integers, you
If the <b>-c</b> flag is used, the <b>bxp_color</b> and
<b>median_color</b> are ignored, even if set by the user. The option to
color boxploxs using the colors of the zonal raster categories
(<b>c</b> flag) only works if the zonal map contains a color table. If
it does not, the function exits with the error message that 'The zonal
map does not have a color table'. If the user thinks there is a color
table, run <em>r.colors.out</em> and check if the categories are
integers. If not, that is the problem. If they are all integers, you
probably have caught a bug.

<p>
Expand All @@ -96,9 +97,9 @@ <h3>Example 1</h3>
<p>
<img src="r_boxplot_01.png"><br>

<h3>Example 2</h3> Draw boxplots of the values of the
<tt>elevation</tt> layer per category from the <tt>landclass96</tt>
layer from the same <a href="https://grass.osgeo.org/download/data/">NC
<h3>Example 2</h3> Draw boxplots of the values of the
<tt>elevation</tt> layer per category from the <tt>landclass96</tt>
layer from the same <a href="https://grass.osgeo.org/download/data/">NC
sample dataset</a>. Use the <b>-r</b> flag to rotate the x-asis labels.

<div class="code"><pre>
Expand All @@ -111,12 +112,12 @@ <h3>Example 2</h3> Draw boxplots of the values of the

<h3>Example 3</h3>

Draw boxplots of the values of the <tt>elevation</tt> layer per
category from the <tt>landclass96</tt> layer from the same <a
href="https://grass.osgeo.org/download/data/">NC sample dataset</a>.
Set the <b>-o</b> flag to include outliers. Use
<b>bx_sort=ascending</b> to order the boxplots from low to high median.
Provide a name for the outlier map to save the outlier locations as a
Draw boxplots of the values of the <tt>elevation</tt> layer per
category from the <tt>landclass96</tt> layer from the same <a
href="https://grass.osgeo.org/download/data/">NC sample dataset</a>.
Set the <b>-o</b> flag to include outliers. Use
<b>bx_sort=ascending</b> to order the boxplots from low to high median.
Provide a name for the outlier map to save the outlier locations as a
point vector map.

<div class="code"><pre>
Expand All @@ -128,20 +129,20 @@ <h3>Example 3</h3>
<img src="r_boxplot_03.png"><br>

<p>
Below, part of the <tt>landclass96</tt> raster map is shown, with the
vector point layer with location of outliers on top. Curiously, for
Below, part of the <tt>landclass96</tt> raster map is shown, with the
vector point layer with location of outliers on top. Curiously, for
some lakes, only part of the raster cells are outliers.

<p>
<img src="r_boxplot_map_03.png"><br>

<h3>Example 4</h3>

Draw boxplots of the values of the <tt>elevation</tt> layer per
category from the <tt>landclass96</tt> layer from the same <a
href="https://grass.osgeo.org/download/data/">NC sample dataset</a>.
Set the <b>-c</b> flag to color the boxplots, use
<b>bx_sort=ascending</b> to order the boxplots from low to high median,
Draw boxplots of the values of the <tt>elevation</tt> layer per
category from the <tt>landclass96</tt> layer from the same <a
href="https://grass.osgeo.org/download/data/">NC sample dataset</a>.
Set the <b>-c</b> flag to color the boxplots, use
<b>bx_sort=ascending</b> to order the boxplots from low to high median,
and set the font size to 11.

<div class="code"><pre>
Expand All @@ -152,7 +153,7 @@ <h3>Example 4</h3>
<h3>Example 5</h3>

To make it easier to compare the elevation distribution across the different
land classes, you can plot a line and band representing the median and
land classes, you can plot a line and band representing the median and
interquartile range of the whole raster layer.

<div class="code"><pre>
Expand All @@ -161,20 +162,20 @@ <h3>Example 5</h3>
</div><br>

<p>
Note, if the zones of your zonal map do not cover the entire area, you
may want to use <em>r.mask</em> to mask out the non-covered parts of
the input map, or alternatively, create a new input raster with only
Note, if the zones of your zonal map do not cover the entire area, you
may want to use <em>r.mask</em> to mask out the non-covered parts of
the input map, or alternatively, create a new input raster with only
values within the zones of the zonal layer.

<p>
<img src="r_boxplot_05.png"><br>

<h2>Acknowledgements</h2>

This work was carried in the framework of the <a
href="https://savethetiger.nl/" target="_blank">Save the tiger, save
the grassland, save the water</a> project by the <a
href="https://www.has.nl/en/has-research/research-groups/innovative-bio-monitoring-research-group"
This work was carried in the framework of the <a
href="https://savethetiger.nl/" target="_blank">Save the tiger, save
the grassland, save the water</a> project by the <a
href="https://www.has.nl/en/has-research/research-groups/innovative-bio-monitoring-research-group"
target="_blank">Innovative Bio-Monitoring research group</a>.

<h2>SEE ALSO</h2>
Expand All @@ -187,9 +188,9 @@ <h2>SEE ALSO</h2>

<h2>AUTHOR</h2>

<a href="https://ecodiv.earth">Paulo van Breugel</a>, <a
href="https://has.nl">HAS green academy</a>, <a
href="https://www.has.nl/en/research/professorships/innovative-bio-monitoring-professorship/">Innovative
Biomonitoring research group</a>, <a
href="https://www.has.nl/en/research/professorships/climate-robust-landscapes-professorship/">Climate-robust
<a href="https://ecodiv.earth">Paulo van Breugel</a>, <a
href="https://has.nl">HAS green academy</a>, <a
href="https://www.has.nl/en/research/professorships/innovative-bio-monitoring-professorship/">Innovative
Biomonitoring research group</a>, <a
href="https://www.has.nl/en/research/professorships/climate-robust-landscapes-professorship/">Climate-robust
Landscapes research group</a>
86 changes: 43 additions & 43 deletions src/raster/r.maxent.predict/r.maxent.predict.html
Original file line number Diff line number Diff line change
@@ -1,39 +1,39 @@
<h2>DESCRIPTION</h2>


The <em>r.maxent.predict</em> module is a front-end to the Maxent
software, providing a convenient way to run the Maxent software, and
create output layers in GRASS GIS.
The <em>r.maxent.predict</em> module is a front-end to the Maxent
software, providing a convenient way to run the Maxent software, and
create output layers in GRASS GIS.

<p>
<div align="left" style="margin: 10px"> <a
href="r_maxent_predict_workflow.png"> <img
src="r_maxent_predict_workflow.png" alt="workflow, from data
preparation, training a model to model prediction" border="0">
</a><br><i>A workflow, from data preparation, training a model to model
<div align="left" style="margin: 10px"> <a
href="r_maxent_predict_workflow.png"> <img
src="r_maxent_predict_workflow.png" alt="workflow, from data
preparation, training a model to model prediction" border="0">
</a><br><i>A workflow, from data preparation, training a model to model
prediction using three GRASS GIS addons.</i> </div>

<p>
It is part of a set of three addons that can be used to prepare the
input data for the Maxent model (<em>v.maxent.sdm</em>), to train a
maxent presence only model (<em>r.maxent.train</em>), and to use the model to
create prediction layers (this module).

The <em>r.maxent.predict</em> modules uses the model (the
<i>.lambdas</i> file) created with <em>r.maxent.train</em> (or the
Maxent software directly) and applies this to a set of environmental
raster layers. These should represent the same variables as used to
create the model, but can represent a different area, of future
It is part of a set of three addons that can be used to prepare the
input data for the Maxent model (<em>v.maxent.sdm</em>), to train a
maxent presence only model (<em>r.maxent.train</em>), and to use the model to
create prediction layers (this module).

The <em>r.maxent.predict</em> modules uses the model (the
<i>.lambdas</i> file) created with <em>r.maxent.train</em> (or the
Maxent software directly) and applies this to a set of environmental
raster layers. These should represent the same variables as used to
create the model, but can represent a different area, of future
conditions.


<p>
The <em>r.maxent.train</em> creates a file
<i>maxent_explanatory_variable_names.csv</i>, which you can check for
the names of the predictor variables. If these are different from the
input raster layers, you can provide the variable names using the
<em>variables</em> parameter. Alternatively, you can provide a CSV file
with the names of the explanatory variables (first column) and the
The <em>r.maxent.train</em> creates a file
<i>maxent_explanatory_variable_names.csv</i>, which you can check for
the names of the predictor variables. If these are different from the
input raster layers, you can provide the variable names using the
<em>variables</em> parameter. Alternatively, you can provide a CSV file
with the names of the explanatory variables (first column) and the
names of the corresponding raster layers (second column).

<p>
Expand All @@ -48,10 +48,10 @@ <h2>DESCRIPTION</h2>

<h2>NOTES</h2>

This addon requires the Maxent software (version &ge; 3.4). You can download the software
from the <a
href="https://biodiversityinformatics.amnh.org/open_source/maxent">Maxent
website</a>. The <em>r.maxent.setup</em> module provides an helper
This addon requires the Maxent software (version &ge; 3.4). You can download the software
from the <a
href="https://biodiversityinformatics.amnh.org/open_source/maxent">Maxent
website</a>. The <em>r.maxent.setup</em> module provides an helper
function to enable GRASS GIS to use the Maxent software.


Expand Down Expand Up @@ -230,23 +230,23 @@ <h2>REFERENCES</h2>

<h2>SEE ALSO</h2>

<ul> <li><a href="v.maxent.swd.html">v.maxent.swd</a>, creating species
and background swd files and prediction rasters that can be used
directly by the <em>r.maxent.train</em> addon (or the Maxent software
itself) to create species distribution models.</li> <li><a
href="r.out.maxent_swd.html">r.out.maxent_swd</a>, creating species and
background swd files based on species distribution data in raster
format.</li> <li><a href="r.maxent.train.html">r.maxent.train</a>,
creates a maxent model based on presence point data a set of
environmental predictor layers.</li> <li><a
href="r.maxent.setup.html">r.maxent.setup</a>, helper function to
<ul> <li><a href="v.maxent.swd.html">v.maxent.swd</a>, creating species
and background swd files and prediction rasters that can be used
directly by the <em>r.maxent.train</em> addon (or the Maxent software
itself) to create species distribution models.</li> <li><a
href="r.out.maxent_swd.html">r.out.maxent_swd</a>, creating species and
background swd files based on species distribution data in raster
format.</li> <li><a href="r.maxent.train.html">r.maxent.train</a>,
creates a maxent model based on presence point data a set of
environmental predictor layers.</li> <li><a
href="r.maxent.setup.html">r.maxent.setup</a>, helper function to
allow GRASS to use Maxent.</li> </ul>

<h2>AUTHOR</h2>

<a href="https:ecodiv.earth">Paulo van Breugel</a>, <a
href="https://has.nl">HAS green academy</a>, <a
href="https://www.has.nl/en/research/professorships/innovative-bio-monitoring-professorship/">Innovative
Biomonitoring research group</a>, <a
href="https://www.has.nl/en/research/professorships/climate-robust-landscapes-professorship/">Climate-robust
<a href="https:ecodiv.earth">Paulo van Breugel</a>, <a
href="https://has.nl">HAS green academy</a>, <a
href="https://www.has.nl/en/research/professorships/innovative-bio-monitoring-professorship/">Innovative
Biomonitoring research group</a>, <a
href="https://www.has.nl/en/research/professorships/climate-robust-landscapes-professorship/">Climate-robust
Landscapes research group</a>
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