.TH r.li.setup 1grass "" "GRASS 6.4.4" "Grass User's Manual"
.SH NAME
\fI\fBr.li.setup\fR\fR  - Configuration editor for r.li.'index'
.SH KEYWORDS
raster, landscape structure analysis
.SH SYNOPSIS
\fBr.li.setup\fR
.br
\fBr.li.setup help\fR
.br
\fBr.li.setup\fR  [\-\-\fBverbose\fR]  [\-\-\fBquiet\fR] 
.SH DESCRIPTION
\fIr.li.setup\fR  creates and shows configuration files for the 
other analytical \fIr.li\fR modules. For a general introduction, see 
r.li.
.br
The configurations are raster map independent, 
it means that you can use a file created on a raster map for analyze any 
other you have. 
.br
The program is completely interactive and uses a GUI to help you 
in your choices.
.SS Analysis methods
Definition of region for analysis:
.RS
.IP
 Whole map layer: entire map (current region),
.IP
 Keyboard setting: based on keyboard selection for region definition,
.IP
 Draw the sampling frame: based on interactive region selection via mouse.
.RE
Definition of creation of sampling area:
.RS
.IP
 Whole map layer: use entire area selected above,
.IP
 Regions: select one to many subareas via mouse,
.IP
 Sample units: automated selection of sampling area (for details see below)
.RS
.IP
 Random nonoverlapping,
.IP
 Systematic contiguous,
.IP
 Systematic noncontiguous,
.IP
 Stratified random,
.IP
 Centered over sites (vector points).
.RE
Moving window: rectangular or circular with size
Select areas from the overlaid vector map (for details see below)
.RE
.SS Usage details
The startup window shows your configuration files, you can: 
..IP
.IP \fB1\fR
\fI\fBLoad a file\fR\fR: the configuration is printed using 
rectangles with differents colors (green for the raster map, red for 
the sample frame and blue for the sample areas), and other notes 
(disposition of sample areas etc). The configuration file is saved 
in ~/.r.li/history/my_conf (the file name can be defined by 
the user). The output can either be a new raster map (in case of 
using a "moving window" analysis) or be an ASCII text file (when not 
performing a "moving window" analysis) containing the result which 
is then saved to the folder $HOME/.r.li/output/.
.br
All dimensions are percentages of raster rows or columns.
.IP \fB2\fR
\fI\fBCreate a new file:\fR\fR this create a new configuration 
file in an interactive way, in three steps:
..IP
 
.IP \fB2.1\fR
 Choose file name and maps to use for setting:
.RS
.IP
 \fIConfiguration file name \fR(required): the name
of new configuration file
.IP
 \fIRaster map name to use to select areas\fR (required): the name of raster
map to use for setting 
.IP
 \fIVector areas map to overlay\fR (optional): name of a vector 
map to overlay in setting
.IP
 \fIVector points map to overlay\fR (optional): name of vector map 
of points type to overlay in setting
.RE
.IP \fB2.6\fR
 Set the sampling frame. The sample frame is a rectangular area 
which contains all the areas to analyze. It can be defined in three 
ways: 
.RS
.IP
\fIWhole map layer\fR: the sample frame is the whole map
.IP
\fIKeyboard setting\fR: the user enters the coordinates in
cells of upper left corner of sampling frame and its length in
rows and columns.
.IP
\fIDraw the sample frame\fR: the user draws the sample frame
on map using mouse.
.RE
.IP \fB2.10\fR
 Set the sample areas. The sample areas are simply the areas to 
analyze. They can be defined in five ways (see the picture below):
.RS
.IP
\fIWhole map layer\fR: the sample area is the whole sample 
frame
.IP
\fIRegions\fR: the user enters the number of areas and then 
draws them using mouse. 
.IP
\fISample units\fR: they are areas of rectangular or circular 
shape. The user can define them using keyboard or mouse.
.RS
.IP
keyboard: the user define the shape of sample unists and 
their disposition:
.RS
.IP
\fIRandom non overlapping\fR: the user specifies 
the number of sample units and they are placed in a 
random way at runtime. It is guaranteed that the 
areas do not intersect themselves.
.IP
\fISystematic contiguous\fR: the defined sample
is placed covering the sample frame, side by side 
across rows.
.IP
\fISystematic non contiguous\fR: the same as above, 
but here ever rectangle is spaced from another by
a specified number of cells.
.IP
\fIStratified random\fR: the sample frame is
divided in \fIn\fR strats of rows and \fIm\fR strats of columns 
(\fIn\fR and \fIm\fR are given by user), then the specified 
number of sample areas are placed in a random way, 
one for every \fIm*n\fR areas defined by strats.
.IP
\fICentered over sites\fR: the sample areas
are placed into sample frame centering them on points 
in site file.
.RE
.IP \fB2.20\fR
mouse: the user chooses the shape and then draws the 
specified number of sample areas on map.
.RE
.IP \fB2.21\fR
\fIMoving Window:\fR the user defines a rectangular or 
circular area, it is moved over all the raster increasing only
of a cell for every move(in columns if possible, if not in rows). 
It produces a new raster containing the result of all analysis.
.IP \fB2.22\fR
\fISelect areas from the overlaid vector map\fR: 
the sample areas are defined by the vector map selected above.
For every cat in vector map, the procedure prompts the 
user if he wants to include it as sample area.
The resulting configuration file can be used only with the 
specified raster map, and the procedure can be used only if
whole map layer is selected as sampling frame.
.RE
.PP
.IP \fB3\fR
\fI\fBRemove a file\fR\fR the selected file is deleted from the
available configuration files.
.IP \fB4\fR
\fI\fBHelp\fR\fR: open this help text.
.IP \fB5\fR
\fI\fBClose\fR\fR module window.
.PP
.SH NOTES
Configuration files are raster map independent because areas are saved using
relative coordinates.
.SH EXAMPLES
.SS Moving window analysis on full region
Example for a 7x7 moving window analysis on full region, the output 
is a raster map:
.PP
Click on "New", then:
.RS
.IP
 Configuration file name: "movwindow7"
.IP
 Raster map name to use to select areas: "forests"
.RE
1. Setup sampling frame:
.RS
.IP
 Define a sampling frame (region for analysis): "Whole map layer", then "OK"
.RE
2. Setup sampling frame
.RS
.IP
 Define sampling areas: "Moving window", then "OK"
.IP
 Then click on "Use keyboard to define moving window dimension"
.RE
Select type of shape:
.RS
.IP
 [x] Rectangular
.IP
 Width size (in cells)?: "7"
.IP
 Height size (in cells)?: "7"
.IP
 Then "Save settings"
.RE
3. Save settings: click on button
.br
(4.) Close
.PP
Now an anaysis can be performed using one of the analytical modules, e.g.
\fC
.DS
.br
g.region rast=forests \-p
.br
r.li.patchdensity map=forests conf=movwindow7 output=forests_p_dens7
.br
r.univar forests_p_dens7
.br
.DE
\fR
The result is the new raster map "forests_p_dens7" which shows (in this example)
the patch density of the forest areas.
.br
See the respective modules for further examples.
.SS Whole region analysis
Example for a whole region analysis, the output is a text file:
Click on "New", then:
.RS
.IP
 Configuration file name: "whole_region"
.IP
 Raster map name to use to select areas: "lsat7_2000_40"
.RE
1. Setup sampling frame:
.RS
.IP
 Define a sampling frame (region for analysis): "Whole map layer", then "OK"
.RE
2. Setup sampling frame
.RS
.IP
 Define sampling areas: "Whole map layer", then "OK"
.RE
3. Save settings: click on button
.br
(4.) Close
.PP
Now an anaysis can be performed using one of the analytical modules, e.g.
\fC
.DS
.br
g.region rast=lsat7_2002_40 \-p
.br
r.li.shannon map=lsat7_2000_40 conf=whole_region output=lsat7_2000_40_shannon
.br
.DE
\fR
The result is the new text file "forests_p_dens7" (stored in folder $HOME/.r.li/output/.
.br
See the respective modules for further examples.
.SH SEE ALSO
\fI
r.li - package overview
.br
r.li.daemon
\fR
.PP
\fI
Old r.le suite manual
\fR
.SH REFERENCES
McGarigal, K., and B. J. Marks. 1995. FRAGSTATS: spatial pattern
analysis program for quantifying landscape structure. USDA For. Serv.
Gen. Tech. Rep. PNW-351. (PDF)
.SH AUTHORS
Claudio Porta and Lucio Davide Spano, students of Computer Science
.br
University of Pisa (Italy).
.br
Commission from Faunalia Pontedera (PI)
.br
Rewritten from \fIr.le.setup\fR by William L. Baker
.PP
\fILast changed: $Date: 2014-02-11 17:25:15 +0100 (Tue, 11 Feb 2014) $\fR
.PP
Full index
.PP
© 2003-2014 GRASS Development Team