FAQ – Frequently Asked Questions

What is an ecosystem?

What format of an ecosystem model does this program work with?

What is ecosystem-based management?

What is a “gap” that is identified by the MINOE program?

Why is this only for the California Current Large Marine Ecosystem?

What is the California Current?

Can I import my laws for my region?

Can I enter more than one term for a single ecosystem component?

Can I use phrases?

What kind of questions can this program help me answer?

Can I run an analysis on a terrestrial ecosystem?

What is QAP?

What is Jaccard’s Coefficient?

What is G value?

What is p value?

What is the difference between this version one and the beta version?


What is an ecosystem?

An ecosystem, as defined by the Millennium Ecosystem Assessment (2005), “is a dynamic complex of plant, animal, and microorganism communities and the nonliving environment interacting as a functional unit.” This concept incorporates any scale of interest based on boundaries and criteria defined by interested party.


What format of an ecosystem model does this program work with?

The user must input an ecosystem model in a symmetrical matrix. Each row and column represents a single ecosystem element. Each element can be defined by a single or multiple terms or phrases. Each cell of the model contains the information about the relationship between the two elements (corresponding by row/column).

A model can either be


What is ecosystem-based management?

Ecosystem-based management (EBM) is a coordinated approach to management of the oceans and coasts in which ecosystem components, their interdependencies and impacts, and ecosystem processes and services are taken into account. In many cases this requires cross-sector and cross-jurisdictional coordination, given that many ecosystem relationships occur across such boundaries.

Please refer to the following sites for additional information about ecosystem-based management:


What is a “gap” that is identified by the MINOE program?

One of the primary goals of the MINOE program is to help identify which ecosystem relationships are accounted for in law and those that are not. The relationships that are not accounted for are refered to as “gaps”. A gap occurs when two components in the ecosystem are linked in the model but do not co-occur in any section of law.


Why is this only for the California Current Large Marine Ecosystem?

The first version of this software only contains laws and regulations that pertain to the Pacific coast of the United States (state and federal). If there is enough interest, we will extend the program to incorporate laws and regulations from other regions and countries, update the California laws, and include other types of documents that contain management information (such as management or action plans or agency policies).


What is the California Current Large Marine Ecosystem?

Bounded by ocean currents, bathymetry, and bioregional zones, this region, extends from the Washington-Canada border to just south of Baja California Sur, extending ocean-bound out to approximately 500 nautical miles. Please see http://www.lme.noaa.gov

Can I import my laws for my region?

Yes. Via the Import Documents module.


Can I enter more than one term for a single ecosystem element?

Yes, you can enter as many terms and/or phrases as you would like to represent a single ecosystem element. By default, all terms listed for the element are searched with an implied “OR” between each. To search so that multiple terms are included (implying the “AND” function), use the “+” before each term.


Can I use phrases?

Yes, a phrase must be in double quotations otherwise the program will recognize it as a multiple (isolated) terms, assuming “or” between them. For example, to search for kelp harvest, the phrase must be entered within quotes. Otherwise the program will search for all documents containing kelp OR harvest.


What kind of questions can this program help answer?

There are several different results and types of questions that this program can help answer:


Can I run an analysis on a terrestrial ecosystem?

The laws and regulations we have in this version specifically were compiled for systems related to marine and coastal regions. Please contact us if you’re interested in using this program for terrestrial ecosystems because we are interested in collaborating to test the utility of applying this method to other domains of natural resources (terrestrial, aquatic, atmospheric/climate, energy, and others).


What is QAP?

Used for non-dichotomous ecosystem models only: QAP stands for the Quadratic Assignment Procedure, which is a network correlation calculation to test the similarity between two symmetric matrices of the same size. This is the same calculation as used for the Mantel Test in ecology and geography. In this program, QAP is only useful in cases where the ecosystem model contains various strengths of relationships between elements (meaning the cells must contain more numbers than 1 and zero). The higher the QAP result (one is the highest, indicating an exact match between the ecosystem model and the law matrix) indicates that more of the relationships in the ecosystem may be accounted for in law. The closer the QAP result is to zero indicates that relationships in the ecosystem are not accounted for in law. The more negative (down to -1) the QAP result indicates that the relationships in the ecosystem are not accounted for in law, but the laws account for relationships between components of the ecosystem that are not modeled.


What is Jaccard’s Coefficient?

Used for dichotomous ecosystems only: Jaccard’s coefficient is used to calculate similarity (or correlation) between the ecosystem model and the law matrix result (for each geopolitical jurisdiction). Use this result only when the ecosystem model entered contained dichotomous data (ones and zeroes). The higher (up to one) the result indicates a higher similarity between the ecosystem modeled and the laws associated with these elements. The coefficient closer to zero indicates little or no similarity between whether ecosystem linkages are accounted for in law. A negative result indicates that the relationships in the ecosystem are not accounted for in law, but the laws account for relationships between components of the ecosystem that are not modeled.


What is G value?

G value is another measure indicating the degree to which the ecosystem model relationships are accounted for in law. The higher the G (up to 1), the more gaps are found in the system. If G is zero, this means all ecosystem links are potentially accounted for in law.


What is p value?

The p-value represents the probability that the correlation measure occurs at random. Therefore, the lower the p-value of G, the more likely this G was not generated at random. This value is calculated using a random permutation of the law matrix (cells are mixed at random) from which the correlation metric is generated. Ten thousand of these random generations are calculated. The proportion of the randomly generated metric that is the same as or higher than the actual metric is the p-value.


What is the difference between this version one and the beta version?

MINOE Version One includes a variety of added features compared to the beta version released in January 2009. Version One now enables users:

- to import their own documents for analysis (representing different years, levels of jurisdictions, other regions, or other indicators of management)

- to identify co-occurences based on word distance rather than simple co-occurence in a section of law (more about this subject coming soon)

- to define this word distance, which means that someone may choose how they want to define a co-occurrence. For example, one may prefer to find laws that talk about two concepts (ie. dredging and eelgrass) within 10 words of each other. For more broad concepts representing ecosystem components (ie. ecosystem and climate change), one may prefer to find laws that talk more loosely about two concepts within larger portions of text. In the latter example, the user could define cooccurrence with a word distance of 25 or 100 (or any number entered).

- to view agency involvement estimates based on a single component or ecosystem linkage, or a selected portion of or the entire ecosystem model. The beta version only allowed users to determine agencies related to a single linkage or individual component in the ecosystem model.

- to calculate "M" which is the proportion of the ecosystem's linkages that are potentially accounted for in the laws (by virtue of the co-occurrences). This represents one metric of the degree of institutional fit to the ecosystem. See Help and/or Ekstrom and Young 2009 (http://www.ecologyandsociety.org/vol14/iss2/art16/) for more information about this calculation.