compute_marxan_species_penalty_factor: Compute marxan species penalty factor
In langfob/bdpg: Package For Building and Testing Biodiversity Problem Generators

compute_marxan_species_penalty_factor

R Documentation

Compute marxan species penalty factor

Description

Choosing spf values

Usage

compute_marxan_species_penalty_factor(spf_rule_to_use, num_spp, parameters)

Arguments

`spf_rule_to_use`	character string
`num_spp`	integer
`parameters`	list

Details

Taken from pp. 38-39 of Marxan_User_Manual_2008.pdf. Particularly note the second paragraph, titled "Getting Started".

3.2.2.4 Conservation Feature Penalty Factor

Variable – ‘spf’ Required: Yes Description: The letters ‘spf’ stands for Species Penalty Factor. This variable is more correctly referred to as the Conservation Feature Penalty Factor. The penalty factor is a multiplier that determines the size of the penalty that will be added to the objective function if the target for a conservation feature is not met in the current reserve scenario (see Appendix B -1.4 for details of how this penalty is calculated and applied). The higher the value, the greater the relative penalty, and the more emphasis Marxan will place on ensuring that feature’s target is met. The SPF thus serves as a way of distinguishing the relative importance of different conservation features. Features of high conservation value, for example highly threatened features or those of significant social or economic importance, should have higher SPF values than less important features. This signifies that you are less willing to compromise their representation in the reserve system. Choosing a suitable value for this variable is essential to achieving good solutions in Marxan. If it is too low, the representation of conservation features may fall short of the targets. If it is too high, Marxan’s ability to find good solutions will be impaired (i.e. it will sacrifice other system properties such as lower cost and greater compactness in an effort to fully meet the conservation feature targets).

Getting Started: It will often require some experimentation to determine appropriate SPFs. This should be done in an iterative fashion. A good place to start is to choose the lowest value that is of the same order of magnitude as the number of conservation features, e.g. if you have 30 features, start with test SPFs of, say, 10 for all features. Do a number of repeat of runs (perhaps 10) and see if your targets are being met in the solutions. If not all targets are being met try increasing the SPF by a factor of two and doing the repeat runs again. When you get to a point where all targets are being met, decrease the SPFs slightly and see if they are still being met.

After test runs are sorted out, then differing relative values can be applied, based on considerations such as rarity, ecological significance, etc., as outlined above. Even if all your targets are being met, always try lower values . By trying to achieve the lowest SPF that produces satisfactory solutions, Marxan has the greatest flexibility to find good solutions. In general, unless you have some a priori reason to weight the inclusion of features in your reserve system, you should start all features with the same SPF. If however, the targets for one or two features are consistently being missed even when all other features are adequately represented , it may be appropriate to raise the SPF for these features. Once again, see the MGPH for more detail on setting SPFs.