r.le.setup(1)

NAME
r.le.setup

DESCRIPTION
r.le.setup program is used to set up the sampling and analysis framework that will be used by the other r.le programs.

NOTES
Full instructions can be found in the r.le manual (see "REFERENCES" section below).

The first menu allows the user to define a rectangular sampling frame, select how sampling will be done (regions, sampling units, moving window), setup the limits for groups and classes, and change the color table. Use the left mouse button to make your choice.

Information about the structure of the landscape is obtained by overlaying a set of sampling areas on top of a specified part (the sampling frame of a map layer, and then calculating specific structural measures for the part of the map layer that corresponds to the area in each sampling area.

To setup a sampling frame click on SAMPLING FRAME in the main menu. The program will ask "Will the sampling frame (total area within which sampling units are distributed) be the whole map? (y/n) [y]" Just hit a carriage return to accept the default, which is to use the whole map. You do not need to setup a sampling frame if you want to use the whole map, as this is the default. To setup a different sampling frame type "n" in response to this question. Then use the mouse and a rubber band box to outline a rectangular sampling frame on screen. This box will be moved to the nearest row and column of the map. You will be asked last whether you want to "Refresh the screen before choosing more setup?" If you don't like the sampling frame you just setup, answer yes to this question, then click on SAMPLING FRAME again to redo this part of the setup. This sampling frame will be used in all subsequent setup procedures unless you change it. You can change it at any time by simply clicking on SAMPLING FRAME again.

A sampling area may be one of four things. First, it is possible to treat the entire map layer as the one (and only) sampling area. Second, if the map layer can be divided into meaningful geographical regions, then it is possible to treat the regions themselves as sampling areas. The third option is that the sampling areas may be sampling units of fixed shape and size (also called scale) that are placed within the map layer as a whole. The fourth and final option is that the sampling area may be moved systematically across the map as a moving window.

If regions are to be used as the sampling areas , then the user can use r.le.setup to draw regions or any existing map of regions can simply be used directly. To draw regions and create a new regions map in r.le.setup select "REGIONS" from the first r.le.setup menu, and the user is asked to do the following:
1. "ENTER THE NEW REGION MAP NAME:" Only a new raster map name is acceptable. The user can type LIST to find out the existing raster map names in this location and mapset.
2. "PLEASE OUTLINE REGION # 1" The user should move the mouse cursor into the graphic monitor window and use the mouse buttons as instructed:
- Left button: where am I.to display the current coordinates of the cursor.
- Middle button: Mark start (next) point. to enter a vertex of the region boundary.
- Right button: Finish region-connect to 1st point to close the region boundary by setting the last vertex to be equal to the first one.
3. A "REGION OPTIONS:" menu is displayed and the user should use the mouse to select one of the options:
- "DRAW MORE": repeat the above process and setup another region.
- "START OVER": abandon the previous setup and start all over again.
- "DONE-SAVE": save the regions outlined so far and exit this procedure.
- "QUIT-NO SAVE": quit the procedure without saving the regions.

Once the "DONE-SAVE" option is selected, the new raster map of the sampling regions is generated. It is displayed on the monitor window for several seconds, the monitor window is refreshed, the main menu is displayed again, and the program is ready for other setup work. Note that you cannot draw regions in areas outside the mask, if a mask is present (see r.mask command).

The user can also use the GRASS r.digit or v.digit programs to digitize circular or polygonal regions and to create a sampling regions map without using r.le.setup. Or, as mention above, an existing raster map can be used as a regions map.

If sampling units are to be used as the sampling areas (Fig. 2), then choose "SAMPLING UNITS" from the first r.le.setup menu. The program checks the r.le.para subdirectory for an existing "units" file from a previous setup session and allows the user to rename this file (to save it) before proceeding. The r.le.setup program will otherwise overwrite the "units" file. Then the following choice is displayed followed by a series of other choices:
    Which do you want to do?
       (1) Use the keyboard to enter sampling unit parameters
       (2) Draw the sampling units with the mouse
                        Enter 1 or 2:

When sampling units are defined using the keyboard, the user inputs the shape and size (scale) of the sampling units by specifying dimensions in pixels using the keyboard. When sampling units are drawn with the mouse, the user clicks the mouse to define the sampling units in the GRASS monitor window, and then actually places the sampling units for each scale onto the map. By placing the units with the mouse the user can directly determine the method of sampling unit distribution as well as the shape, size, and number of sampling units.

If the choice is made to define sampling units using the keyboard, the following series of questions must be answered:
    How many different SCALES do you want (1-15)?

The user is asked to specify the number of scales that will be used. The r.le programs allow the user to simultaneously sample the same map with the same measures using sampling areas of different sizes. Currently there can be between 1 and 15 scales that can be sampled simultaneously. Substantial output can be produced if many scales are used.

Sampling units must be placed spatially into the landscape. There are five options for doing this :

Random nonoverlapping
Sampling units are placed in the landscape by randomly choosing numbers that specify the location of the upper left corner of each sampling unit, subject to the constraint that successive sampling units not overlap other sampling units or the edge of the landscape, and that they must be entirely within the area defined by the mask (see r.mask command) if one exists.

Systematic contiguous
Sampling units are placed side by side across the rows. The user will be able to enter a row and column to indicate where the upper left corner of the systematic contiguous framework should be placed. Rows are numbered from the top down beginning with row 1 of the sampling frame. Columns are numbered from left to right, beginning with column 1 of the sampling frame. A random starting location can be obtained by using a standard random number table to choose the starting row and column. The r.le.setup program does not avoid placing the set of sampling units over areas outside the mask. The user will have to make sure that sampling units do not extend outside the mask by choosing a particular starting row and column or by drawing a sampling frame before placing the set of sampling units.

Systematic noncontiguous
The user must specify the starting row and column as in #2 above and the amount of spacing (in pixels) between sampling units. Horizontal and vertical spacing are identical. Sampling units are again placed side by side (but spaced) across the rows. As in #2 the program does not avoid placing sampling units outside the masked area; the user will have to position the set of units to avoid areas outside the mask.

Stratified random
The strata are rectangular areas within which single sampling units are randomly located. The user must first specify the starting row and column as in #2 above. Then the user must specify the number of strata in the horizontal and vertical directions. As in #2 the program does not avoid placing sampling units outside the masked area; the user will have to position the set of units to avoid areas outside the mask.

Centered over sites
The user must specify the name of a sitefile containing point locations. A single sampling unit is placed with its center over each site in the site file. This is a useful approach for determining the landscape structure around points, such as around the location of wildlife observations.

The user is prompted to enter a ratio that defines the shape of the sampling units. Sampling units may have any rectangular shape, including square as a special case of rectangular. Rectangular shapes are specified by entering the ratio of columns/rows (horizontal dimension/vertical dimension) as a real number. For example, to obtain a sampling unit 10 columns wide by 4 rows long specify the ratio as 2.5 (10/4).
    Recommended maximum SIZE is m in x cell total area.
    What size (in cells) for each sampling unit of scale n?

The user is then given the recommended maximum possible size for a sampling unit (in pixels) and asked to input the size of sampling units at each scale. Sampling units can be of any size, but the maximum size is the size of the landscape as a whole. All the sampling units, that make up a single sampling scale, are the same size. After specifying the size, the program determines the nearest actual number of rows and columns, and hence size, that is closest to the requested size, given the shape requested earlier.
    The nearest size is x cells wide X y cells high = xy cells
    Is this size OK? (y/n) [y]
    Maximum NUMBER of units in scale n is p?
    What NUMBER of sampling units do you want to try to use?

The maximum number of units that can be placed over the map, given the shape and size of the units, is then given. The user can then choose the number of sampling units to be used in the map layer. It may not always be possible to choose the maximum number, depending upon the shape of the sampling units. In the case of systematic contiguous and noncontiguous, the program will indicate how many units will fit across the columns and down the rows. The user can then specify a particular layout (e.g., 6 units could be placed as 2 rows of 3 per row or as 3 rows of 2 per row).
    Is this set of sampling units OK? (y/n) [y]

Finally, the set of sampling units is displayed on the screen (e.g., Fig. 1) and the user is asked whether it is acceptable. If the answer is no, then the user is asked if the screen should be refreshed before redisplaying the menu for "Methods of sampling unit distribution" so that the user can try the sampling unit setup again.

The choice is made to define sampling units using the mouse, then the following menu for use with the mouse is displayed:
    Outline the standard sampling unit of scale n.
       Left button:    Check unit size
       Middle button:    Move cursor
       Right button:    Lower right corner of unit here

The user can then use the mouse and the rubber band box to outline the standard sampling unit. Once it has been outlined, the number of columns and rows in the unit, the ratio of width/length and the size of the unit, in cells, will be displayed. After this first unit is outlined, then a new menu is displayed:
    Outline more sampling units of scale n?
       Left button:    Exit
       Middle button:    Check unit position
       Right button:    Lower right corner of next unit here

The user can then place more units identical to the standard unit by simply clicking the right mouse button where the lower right corner of the unit should be placed. The rest of the rubber band box can be ignored while placing additional units. The program is set up so that units cannot be placed so they overlap one another, so they overlap the area outside the mask, or so they overlap the edge of the sampling frame. Warning messages are issued for all three of these errors and a sampling unit is simply not placed.

Using this procedure a rectangular "window" or single sampling area is moved systematically across the map to produce a new map (Fig. 2,3). This sampling procedure can only be used with the measures that produce a single value or with a single class or group when measures produce distributions of values (Table 1). The first class or group specified when defining class or group limits (section 2.3.2.) is used if distributional measures are chosen with the moving window sampling method. In this case, the user should manually edit the r.le.para/recl_tb file so that the desired group is listed as the first group in this file.

Sampling begins with the upper left corner of the window placed over the upper left corner of the sampling frame. It is strongly recommended that the user read the section on the GRASS mask (section 2.2.2) prior to setting up the moving window, as this mask can be used to speed up the moving window operation. The value of the chosen measure is calculated for the window area. This value is assigned to the location on the new map layer corresponding to the center pixel in the window if the window has odd (e.g. 3 X 3) dimensions. The value is assigned to the location on the new map layer corresponding to the first pixel below and to the right of the center if the window has even dimensions (e.g. 6 X 10). If this pixel has the value "0," which means "no data" in GRASS, then this pixel is skipped and a value of "0" is assigned to the corresponding location in the new map. The window is then moved to the right (across the row) by one pixel, and the process is repeated. At the end of the row, the window is moved down one pixel, and then back across the row. This option produces a new map layer, whose dimensions are smaller by approximately (m-1)/2 rows and columns, where m is the number of rows or columns in the window.

If the "MOVE-WINDOW" option in the main menu is selected, first the program checks for an existing "move_wind" file, in the r.le.para subdirectory, containing moving window specifications from a previous session. The user is given the option to avoid overwriting this file by entering a new file name for the old "move_wind" file. Users should be aware that moving window analyses are very slow, because a large number of sampling units are, in effect, used. See the appendix on "Time needed to complete analyses with the r.le programs" for some ideas about how moving window size and sampling frame area affect the needed time to complete the analyses.

The r.le programs r.le.dist and r.le.patch allow the attribute categories in the input map to be reclassed into several attribute groups, and reports the analysis results by each of these attribute groups. It is necessary to setup group limits for all measures that say "by gp" when typing "r.le.dist help" or "r.le.patch help" at the GRASS prompt. The same reclassing can be done with the measurement indices (e.g., size), except that each "cohort" (class) of the reclassed indices is called an index class instead of a group. It is also necessary to setup class limits for all measures that say "by class" when typing "r.le.dist help" or "r.le.patch help" at the GRASS prompt.

Group/class limits are setup by choosing "GROUP/CLASS LIMITS" from the main menu upon starting r.le.setup, or you can create the files manually using a text editor. The program checks for existing group/class limit files in subdirectory r.le.para and allows the user to rename these files prior to continuing. If the files are not renamed the program will overwrite them. The files are named recl_tb (attribute group limits), size (size class limits), shape_PA (shape index class limits for perimeter/area index), shape_CPA (shape index class limits for corrected perimeter/area index), shape_RCC (shape index class limits for related circumscribing circle index), and from_to (for the r.le.dist program distance methods m7-m9).

Attribute groups and index classes are defined in a different way. In the r.le programs attribute groups are defined as in the following example:
    1, 3, 5, 7, 9 thru 21 = 1 (comment)
    31 thru 50 = 2 (comment)
    end

In this example, the existing categories 1, 3, 5, 7, {9, 10, ... 20, 21} are included in the new group 1, while {31, 32, 33, ..., 49, 50} are included in the new group 2. The characters in bold are the "key words" that are required in the definition. Each line is called one "reclass rule".

The GRASS reclass convention is adopted here with a little modification (see "r.reclass" command in the GRASS User's Manual). The difference is that r.le only allows one rule for each group while the GRASS r.reclass command allows more than one. The definition of "from" and "to" groups is simply the extension of the GRASS reclass rule. The advantage of using the GRASS reclass convention is that the user can generate a permanent reclassed map, using GRASS programs, directly from the r.le setup results.

The r.le measurement index classes are defined by the lower limits of the classes, as in the following example:
    0.0, 10.0, 50.0, 200.0, -999

This means:
    if v >= 0.0 and v < 10.0 then v belongs to index class 1;
    if v >= 10.0 and v < 50.0 then v belongs to index class 2;
    if v >= 50.0 and v < 200.0 then v belongs to index class 3;
    if v >= 200.0 then v belongs to index class 4;

where v is the calculated index value and -999 marks the end of the index class definition. The measurement index can be the size index, one of the three shape indices, or one of the three distance indices. The program is currently designed to allow no more than 25 attribute groups, 25 size classes, 25 shape index classes, and 25 distance index classes. As an alternative, the user may want to permanently group certain attributes prior to entering the r.le programs. For example, the user may want to group attributes 1-10, in a map whose attributes are ages, into a single attribute representing young patches. The user can do this using the GRASS r.reclass and r.resample commands, which will create a new map layer that can then be analyzed directly (without setting up group limits) with the r.le programs.

REFERENCES
Baker, W.L. and Y. Cai. 1992. The r.le programs for multiscale analysis of landscape structure using the GRASS geographical information system. Landscape Ecology 7(4):291-302.

The r.le manual: Quantitative analysis of landscape structures (GRASS 5; 2001)

SEE ALSO
r.le.patch, r.le.pixel, r.le.trace

AUTHOR
William L. Baker Department of Geography and Recreation University of Wyoming Laramie, Wyoming 82071 U.S.A.

Last changed: $Date: 2010-01-20 14:26:08 +0100 (Wed, 20 Jan 2010) $

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