3. Input Files, Parameters and Variables
3.2 Required files
3.2.1 The Input Parameter File
3.2.1.5 Output
3.2.1.5.1 Screen Output Variable – ‘VERBOSITY’
Required: Yes
Description: This variable controls how much
information Marxan displays on the screen while it is running. In Inedit it is set using the drop down box labelled,
‘Screen Output’. Users can specify how much information Marxan prints to the screen (the verbosity) .
There are four different options for screen display:
0 Silent Running – Only the title of the program is displayed.
1 Results Only – Marxan will display which run it is up to, the basic results of each run and the total run time.
2 General Progress – In addition to the information about each run,
Marxan will display information on the data that has been read in as well as details o n any conservation features whose targets and requirements are such that they cannot be adequately reserved in the system.
3 Detailed Progress – Shows exactly where the program is up to and gives the value of the system each time the temperature changes.
Getting Started: The default for this variable is ‘General Progress’ and in most cases this will be the best choice. Printing results to the screen does not increase Marxan’s run time substantially unless 'Detailed Progress' is used. It is generally worthwhile to use at least ‘Results Only’ so that you have some idea of how many runs have been completed. ‘Detailed Progress’ is useful for seeing how the process of annealing works, and can also help identify problems Marxan runs (e.g. if the numbers do not change and it is “stalled”). For this reason, some users always use this setting, to
The ‘Output’ tab of Inedit.
visually check that the program appears to be running OK. Only apply ‘Silent
Running’ if you are confident in Marxan’s execution and you are saving all necessary outputs.
3.2.1.5.2 Save Files and Save File Name
Variables – ‘SAVERUN’, ‘SAVEBEST’, ‘SAVESUM’, ‘SAVESCEN’,
‘SAVETARGETMET’, ‘SAVESUMSOLN’, ‘SAVELOG’, ‘SAVESNAPSTEPS’,
‘SAVESNAPCHANGES’, ‘SAVESNAPFREQUENCY’ , and ‘SCENNAME’
Required: No
Description and Getting Started: With the exception of ‘SCENNAME’ and
‘SAVESNAPFREQUENCY’ , t hese variables are all used to tell Marxan what results it should save as output. When using Inedit you can tell Marxan to save any of these files simply by ticking the corresponding box. In the ‘input.dat’ file, set the value to ‘1’
for each output you want Marxan to save. If you wish to display the results in a GIS , tab delimited output should be used in preference to comma delimited. This can be done in Inedit by ticking the box labelled ‘ArcView Format’, and it is done directly in the ‘input.dat’ by setting the values for these variables to ‘2’. The different outputs and their uses are all described in detail in the next section.
If either SAVESNAPSTEPS (‘Save each n steps’ in Inedit) or SAVESNAPCHANGES (‘Save each n changes’ in Inedit) are selected then a SAVESNAPFREQUENCY (‘Frequency’ in Inedit) value must also be specified. This is the predetermined number of either system iterations (SAVESNAPSTEPS) or system changes
(SAVESNAPCHANGES) at which the solution progress of the optimisation procedure is saved.
Beware: saving snapshots can create enormous amounts of output files which swamp your output folder and drastically slow down the running of Marxan. They are for advanced diagnoses and should only be used by expert users. If you use them, make sure the snap frequency is large enough so that you are not left with tens of thousands of output files. The actual number you choose will depend on how many iterations you are using (see Section 3.2.1.3.1). For 1 million iterations , a snap frequency of 100,000 will give 10 output files.
The variable, ‘SCENNAME’ (or ‘Save File Name’ in Inedit), is the name you wish Marxan to append to all output files it saves (e.g. ‘scenario1_ssoln.dat’ would be the name given the summed solution output). The name should be something you can use to identify the scenario that generated the outputs.
3.2.1.5.3 Output Directory Variable – ‘OUTPUTDIR’
Required: Yes
Description and Getting Started: The variable is used to tell Marxan the name of the folder (called directory or DIR in Marxan) it should save the output files in. The
naming and location protocols for this folder are discussed in Section 5.1) and as with the input folder, it is critical this is correct or Marxan will not run.
3.2.1.5.4 Species missing proportion Variable – ‘MISSLEVEL’
Required: No
Description: This is the proportion of the target a conservation feature must reach in order for it to be reported as met. Using Inedit, it is specified in the box labelled
‘Species missing if proportion of target lower than’. There are situations where Marxan can get extremely close to the target (e.g. 99% of the desired level) without actually meeting the target. You can specify a level for which you are pragmatically satisfied that the amount of representation is close enough to the target to report it as met.
Getting Started: This value should always be high, i.e. greater than or equal to 0.95, if you are setting it lower than this you should probably think about changing your
targets. As a guide, it is often useful to run Marxan with the ‘MISSLEVEL’ set at ‘1’
and then re-run with it set at a slightly lower value and see if there is much of a difference in system cost. Setting this variable does not change the way the Marxan algorithm works, it merely changes the way target achievement is reported in screen and file output.
3.2.1.6 Cost Threshold