Marxan User Manual: Getting Started

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2.1 System requirements
The system requirements for running Marxan are quite modest. Any Microsoft operating system will suffice, even a really old one. As a rule of thumb, if a computer is powerful enough to run commercial GIS software, then it will be more than adequate for running Marxan. The more planning units, conservation features and optional advanced Marxan settings you have, the slower Marxan will run. Of course, the more powerful your computer (MHz and RAM), the faster Marxan will run. Depending on these factors, the time required for Marxan to provide 100 good solutions to you problem can range from minutes to days. WARNING: Plugin disabled TAG!5

WARNING: Plugin disabled TAG!5It is usually the advanced features of Marxan (such as separation distance and minimum clump size) that can slow the analysis down significantly, especially with large numbers of planning units. We therefore recommend that initial test runs do not make use of these advanced features, such that the basic operationally of the Marxan input is first tested and verified.

2.2 Software installation
Chances are that if you are reading this manual you have already downloaded Marxan. If not, Marxan can be downloaded from You will require around 2 MB of free disk space to install Marxan and the associated files.

When you download Marxan you will receive the following files:
  1. Marxan.exe (the Marxan program executable)
  2. Inedit.exe (a program that allows you to easily generate the Input Parameter File – the file that controls how Marxan works)
  3. input.dat (an example Input Parameter File)
  4. A folder labelled ‘Sample’, containing examples of the other input files used to run Marxan (the details of these files are explained later).
  5. This manual

These files can be saved anywhere on the computer. For simplicity when running Marxan, the executable, ‘Marxan.exe’, should be located in the same folder as the input files for that project (see Section 3.1.2). Rather than continually move files around, we recommend simply copying the Marxan executable to each folder containing a Marxan project.

2.3 Supporting Freeware
In this manual we describe how to run Marxan as a stand-alone program, however, there are several, freely available, user interfaces that can assist in running Marxan. Many users have found these interfaces particularly helpful for generating appropriate input files and displaying Marxan outputs. Guidance on using these programs (described below) can be obtained from their websites or user manuals.

2.3.1 CLUZ (Conservation Land Use Zoning)
CLUZ is an ArcView? GIS interface that links to Marxan. It was developed by Bob Smith at the Durrell Institute of Conservation and Ecology and is available from CLUZ provides a dynamic connection with Marxan so the user can easily run Marxan and map the results of Marxan runs. It also contains tools to help develop the input files required by Marxan. CLUZ comes with useful tutorial exercises to guide users through developing input files, modifying run parameters and displaying Marxan results.

2.3.2 P.A.N.D.A. (Protected Areas Network Design Application)
P.A.N.D.A. is a stand-alone application that uses the Visual Basic and ArcObjects? software. It was developed by Francesca Riolo to provide ArcGIS users with a user friendly framework for systematic protected areas network design. ArcGIS is required to run the program. It is available from

2.3.3 C-Plan?
C-Plan? is conservation decision support software that links with GIS to map options for achieving explicit conservation targets. It was developed by Matt Watts and Bob Pressey. C-Plan? allows users to decide which planning units should be placed under some form of conservation management through manual selection. It also allows automated selection using heuristic selection algorithms. The newer version, C-Plan? 3.4, has a Marxan interface which can generate Marxan input files from C-Plan? files. It also allows users to run Marxan from C-Plan? and import Marxan outputs back into C-Plan? to be displayed in GIS. C-Plan? is available from

2.4 Overview of what is required to run Marxan
There are four main steps to running Marxan:
  1. Setting up the input files
  2. Setting the scenario parameters
  3. Running Marxan
  4. Interpreting the results

This section is intended to provide a brief guide to the essential steps of using Marxan. A more detailed treatment of each step follows in subsequent chapters. The successful use of Marxan will never involve a once-off, sequential application of these steps. Instead, in any given project these steps should be repeated numerous times, particularly the last three, and the results of each run used to refine the details of following runs. Because of this, it is important to be well organised and have an efficient file management protocol. Suggestions of possible protocols are provided in the sections below. Once the input files have been set up it should be quite easy to modify the scenario, re-run Marxan and investigate the results.

Marxan is a decision support tool to help guide the selection of efficient reserve systems; its output should never be interpreted as “the answer.” Although the results of a single Marxan run will represent a good solution to your reserve design problem, it will not necessarily be the preferred solution. Because Marxan tests the utility of planning units in a pseudo-random fashion (see Appendix B for more details), each run is likely to be subtly (and sometimes extensively) different. In most cases there will be many good solutions to the problem at hand. This is a positive attribute as it allows flexibility in planning and stakeholder negotiations. It is possible to sample the range of different possible solutions (the solution space) by running Marxan many times.

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