CLUZ functions

CLUZ is an ArcView GIS extension that consists of the CLUZ menu, which contains 25 items, as well as 6 buttons and 2 tools. Each of these elements carries out a different function and these are listed below. A pdf version of this information is also available and can be obtained by clicking here.

CLUZ is also constantly being updated and modified, so check the details of the latest version by visiting the CLUZ update history page here.

1) CLUZ menu

View and edit CLUZ setup file
The CLUZ setup file contains information on the location of the MARXAN program, the folders that contain the MARXAN data and where the MARXAN output information will be stored. It also lists the location details of the planning unit theme, the abundance table and the target table. All of the CLUZ functions use information from the CLUZ setup file, so you will need to load a suitable file or create a new one before carrying out any analysis. This function allows you to create or load an existing file and to edit the details.

Import MARXAN files
This module allows you to import existing MARXAN data files into CLUZ to create new abundance, target and planning unit theme tables. You need to use an existing planning unit theme and to use the Recalculate target table data function once you have created the target table.

Import C-Plan data
This module allows you to import C-Plan data into CLUZ. The module can import planning unit, target and abundance data, and converts them into dBASE files with the correct CLUZ format.

Create unit theme from shapefile
This module converts an existing polygon theme into a correctly formatted planning unit theme by adding fields called Unit_id, Area, Cost and Status. Each polygon is given a unique identifier, which is listed in the Unit_id field, and its status is set as Available. The Area value of each polygon is calculated and there is also an option to use this as the Cost value as well, if no other cost data exists.

Create blank target table
This module produces a new CLUZ target table in the correct format with the necessary fields. A row is added to this table so that it can be saved correctly but this row should be removed when rows describing actual conservation features are added.

Create blank abundance table from unit theme
This module produces a new CLUZ abundance table by copying the Unit_id field from the specified planning unit theme.

Calculate % of unit that falls within PAs
This module allows you to calculate the percentage of each unit that falls within a specified protected area theme. The module adds a field to the unit theme table called Pc_in_PA that lists the information and displays the data in a new theme. Use this information to choose a cut-off point above which a planning unit is assumed to be Conserved and then use the Change Status panel to select units above this threshold and change their status.

Recalculate target table data
This function calculates the total amount of each target and the amount that is conserved (ie in Earmarked or Conserved units) based on the abundance and planning unit theme tables. It should be used whenever changes have been made to the conservation portfolio without using CLUZ.

Troubleshoot all CLUZ files
This function inspects the format of all of the CLUZ tables to check that they have the correct format.

Remove features from abundance and target tables
This function allows the user to delete records on unwanted conservation features from the CLUZ system by removing the relevant fields and rows in the abundance and target tables.

Convert themes to abundance data
This function allows you to select polygon, line and point data that describes the distribution of different conservation features and calculate the amount of each feature in each planning unit. The distribution themes must contain a field named ID that gives the MARXAN numeric identifier code of each biodiversity element.

This function also allows you to divide each value by a specified number to convert from one measurement system to another. For example, if a vegetation map uses a UTM reference system that is measured in metres but you want to record the area of each vegetation type in hectares then you can state that you want to divide each area value by 10000.

Import fields from table to abundance table
This function allows you to add data from an existing table into the abundance table. The existing table must contain a field named Unit_id that is identical to the Unit_id field in the abundance table. This function also allows you to divide each value by a specified number to convert abundance values from one measurement system to another.

Show distribution of feature
This allows you to show the distribution of any of the conservation features listed in the target table based on the data stored in the abundance table.

Show details of selected units
Choosing this module brings up a table showing the total amount of each conservation feature found in the planning units that have been selected in the View. The table provides information on the target amount, the target shortfall and the amount of each feature in planning units with Available, Earmarked, Conserved and Excluded status.

Show portfolio cost and area details
This module shows the combined area, total planning unit cost, total boundary cost and total penalty factor cost of the portfolio of Conserved and Earmarked planning units displayed in the View. It also uses these results to calculate the total portfolio cost (not including any clump and cost threshold costs). The module needs data from the planning unit theme, target table, bound.dat file and setup file to produce all this information, but it will also display more limited information if some of these files have not been created.

Count number of features in each planning unit
Choosing this module counts the number of conservation features recorded in each planning unit, adds this information to a new field in the planning unit table and displays the results as a new theme. If the target table contains a field called Type then this module can also be used to count the number of a subset of conservation features, where the subsets are defined by the number code in the Type field. For example, if the Type field codes vegetation types as 1 and species as 2, then you can use this module to just show the number of species found in each planning unit.

Create abundance.dat
This converts the data in the abundance table into a text file with the suitable MARXAN format.

Create target.dat
This converts the data in the target table into a text file with the suitable MARXAN format.

Create unit.dat
This converts the data in the planning unit theme table into a text file with the suitable MARXAN format.

Create bound.dat
This calculates the boundary length shared between each planning unit and saves the data into a text file with the suitable MARXAN format. This function allows you to specify that data on external edges (ie edges of units on the boundaries of the study area that are not shared with other units) should be excluded.

Add to bound.dat to group selected units
This module allows the user to link selected units so that they will always appear together in any conservation portfolio identified by MARXAN. This is useful when different units make up part of an ecological unit that needs to be intact to be viable. For example, you may want to link different bat feeding and roosting sites, so you don't conserve the feeding site of one population and the roosting site of another. This is achieved by editing the bound.dat file to specify a very large boundary cost between the selected units, so that MARXAN chooses both to minimise the total boundary cost.

Load previous MARXAN results
This allows you to add results from previous MARXAN analyses to new fields in the planning unit theme table and display them in the View.

Copy unit field contents into new field
This copies information from one field into another new named field. This should be used to permanently save information from the Status, Best or Con_scr field, as the data in these fields are overwritten when using the Change Status panel (for the Status field) or when running MARXAN (for the Best or Con_scr fields).

RUN MARXAN
This function opens the RUN MARXAN dialog window, which allows you to specify different parameters before running the program. Parameters are the number of iterations per run, the number of runs, the output file name and whether boundary cost values should be included. The Advanced button allows the user to specify whether clumps of features smaller than a specified amount should be treated differently and whether targets should be set for clumps of specified features.

Modify Earmarked units using MARXAN
This module runs MARXAN using the standard settings but with one difference. It specifies that the Earmarked planning units should be included in the portfolio at the beginning of each run but allows them to be removed and replaced during each run. This means that MARXAN uses the portfolio displayed in the View as the starting point for each run but then lets the simulated annealing process make changes.

In general, some of the resultant portfolios produced by this process will improve on the original portfolio, but this will partly depend on the number of runs and iterations. The status of the Conserved and Excluded units remains the same throughout the process.

2) CLUZ Tools

Abundance Tool
Choosing this tool and clicking on a planning unit will produce a window showing the conservation features that are found in the unit, together with the amount of each feature, its target and the percentage of that target that has been met.

Earmarked Similarity Tool
Choosing this tool and clicking on an Earmarked planning unit identifies Available units that are most similar to the Earmarked unit in terms of achieving the conservation feature targets. These Available units would be the best to swap with the Earmarked units in the portfolio. This tool will also identify whether an Earmarked unit could be removed from the portfolio without affecting the number of conservation targets that have been met.

3) CLUZ Buttons

Open Abundance Table
Clicking on this button will open the abundance table.

Open Target Table
Clicking on this button will open the target table, allowing the user to change the target values or rename the conservation features. The values in the Pc_target field are automatically updated each time the table is opened.

Open MARXAN Target Results
Running MARXAN through CLUZ produces the best theme, which shows the most efficient of the conservation portfolios that MARXAN identified. Clicking on this button open a table that lists how many of the targets were met by this best portfolio. CLUZ will only display a target results table if MARXAN has been run since turning on the CLUZ extension. Use the Add table function in the Project Window if you wish to look at an older MARXAN target result table.

Display theme with CLUZ palette
Clicking on this button will allow you to select a theme to display with the CLUZ best or summed palette. CLUZ will identify fields in the selected theme with the correct format and will then display it using the best palette for text fields (where Selected planning units are displayed) or the summed palette for numerical fields.

Change the status of the Best units to Earmarked
Clicking on this button will give Earmarked status to any planning unit that was identified by MARXAN as being part of the best portfolio. To do this, CLUZ uses information from the Best field, which is added to the planning unit theme table whenever MARXAN is run.

Open Change Status Panel
Clicking on this will open the Change Status panel, which allows the user to select units and change their status to Conserved, Earmarked, Available or Excluded. Conserved units are those that are part of existing protected areas or those that will definitely be protected in the future. Earmarked units are that have been selected by the user as belonging to a proposed conservation portfolio and Available units are those that have not been selected by the user to belong to the portfolio. Excluded units are those that definitely will not belong to any portfolio for ecological, economic or political reasons.

At its simplest level, conservation planning in CLUZ involves identifying and setting the Conserved and Excluded units at the beginning of the process and then deciding whether the remaining units should have Earmarked or Available status. The Change Status panel consists of three main parts. The Selection tools are shown at the top of the panel, the Status section is in the middle and the action buttons are at the bottom. These are described in more detail below:

Select rectangle
This tool is identical to the one found in the View and allows the user to select rectangular blocks of units by left-clicking on the mouse, holding the mouse button down, moving the mouse icon to a new position and then releasing the mouse button. Several blocks of units can be selected at once by pressing down on the shift button on the keyboard whilst selecting a new block.

Select polygon
This tool allows the user to select irregularly shaped blocks of units by digitising the boundary of a polygon of the required block. The user must left-click once to start digitising and then set the boundary of the polygon by continue to left click. Double-clicking on the left mouse button finishes the process and several blocks can be selected at once by pressing down on the shift button on the keyboard whilst selecting a new block.

Build query
The build query tool allows planning units to be selected based on their attributes described in the planning unit theme table. The build query dialog box is exactly the same as that accessed from the Query Builder button in the View and allows the user to select new sets of planning units.

The status section of the Change Status panel allows you to specify the value you want to set by choosing the relevant radio button . Turning off the Allow changes in conserved and excluded status check box means that only the status of Earmarked and Available units can be changed.

Turning on the check box allows the user to change units to Conserved or Excluded status and also allows the status of Conserved or Excluded units to be modified. This should genrally only be done at the beginning of the planning process.

Change Status
Clicking on this button will change the status of any selected units to that specified in the status section of the panel.

Undo
Clicking on this button will undo the results of clicking on the Change Status button. The button is only active after the Change Status button has been used and cannot undo actions that were undertaken in previous sessions. The Undo function recalculates the values in the target table based on the restored status values, and can take a relatively long time to process this information.

Update MARXAN file
This function updates the MARXAN unit.dat file so that it reflects the changes to the Status field in the planning unit theme table.