marindicators-package: Calculates Marine Ecosystem and Fishing Pressure Indicators
In marindicators: Marine Ecosystem and Fishing Pressure Indicators

Description Details References

The marindicators package provides functions to calculate indicators for four marine ecosystem attributes (Biodiversity, Ecosystem Structure and Functioning, Ecosystem Stability and Resistance to Perturbations, Resource Potential) and one marine ecosystem pressure (Fishing Pressure) from fishery independent trawl survey data and commercial landings data. All indicators were selected and evaluated using the “Indicator Selection Guidance Framework” developed by Bundy, Gomez, and Cook (2017).

A comprehensive evaluation and selection of robust ecological indicators is one of the key steps in the process of implementing an Ecosystem Approach to fisheries management and to track progress towards meeting ecosystem goals. The indicators included in this package were selected using the “Indicator Selection Guidance Framework” developed by Bundy, Gomez, and Cook (2017) to select and evaluate potential indicators for ecosystem monitoring and assessment at different spatial scales using established selection criteria.

The framework was successfully tested for the Scotian Shelf Bioregion, Canada. In Step 1, four ecosystem attributes and one pressure were defined: Biodiversity, Ecosystem Structure and Functioning, Ecosystem Stability and Resistance to Perturbations, Resource Potential, and Fishing Pressure. In Step 2, 186 indicators were selected to represent these attributes and pressure. The qualitative screening in Step 3 reduced this set to 68 indicators (Table 1), which were calculated in Step 4. The quantitative screening in Step 5 resulted in a final suite of 30 non-redundant ecological and fishing pressure indicators derived from fishery independent and dependent data (Step 6). For more information, including attribute definitions and the methods used to select the final suite of indicators, please refer to the guidance framework document (Bundy, Gomez, and Cook, 2017).

The marindicators package provides functions to calculate the suite of marine ecosystem indicators calculated in Step 4 of the guidance framework (Table 1; Bundy, Gomez, and Cook, 2017). Some functions may be used to calculate additional indicators, for example by specifying different species groups or using alternative values for arguments with default values.

Table 1: Indicators for each ecosystem attribute and pressure and the marindicators function used to calculate each indicator. Indicators included in the final suite for the Scotian Shelf Bioregion are highlighted in bold.

ATTRIBUTE	INDICATOR	FUNCTION
Biodiversity	All Biodiversity indicators	`allBiodiversity()`
Biodiversity	Margalef's Species Richness	`margalef()`
Biodiversity	Species Richness	`speciesRichness()`
Biodiversity	Shannon's Diversity Index	`shannon()`
Biodiversity	Hill's Diversity Index	`hillN1()`
Biodiversity	Kempton's Q	`kemptonQ()`
Biodiversity	Hill's Dominance	`hillN2()`
Biodiversity	Pielou's Species Evenness	`pielouEvenness()`
Biodiversity	`Heips Evenness Index`	`heips()`

Structure & Functioning	All Structure & Functioning indicators	`allStructure()`
Structure & Functioning	Large Fish Indicator	`largeFishIndicator()`
Structure & Functioning	Large Species Indicator	`largeSpeciesIndicator()`
Structure & Functioning	Proportion of Predatory Fish	`biomassRatio()`
Structure & Functioning	Biomass of Trophic Guilds^1	`resourcePotential`
Structure & Functioning	Biomass Ratio(s)	`biomassRatio()`
Structure & Functioning	Mean Length (weighted by abundance)	`meanLengthCommunity()`
Structure & Functioning	Mean Length (weighted by biomass)	`meanLengthCommunity()`
Structure & Functioning	Mean Trophic Level of Community	`meanTLCommunity()`
Structure & Functioning	Community Condition	`communityCondition()`
Structure & Functioning	Trophic Guild Condition^2	`communityCondition()`

Stability & Resistance	All Stability & Resistance indicators	`allStability()`
Stability & Resistance	Mean Lifespan	`meanMaxAge()`
Stability & Resistance	Mean Max Length (weighted by abundance)	`meanMaxLength()`
Stability & Resistance	Mean Max Length (weighted by biomass)	`meanMaxLength()`
Stability & Resistance	Intrinsic Vulnerability Index of Landings	`IVILandings()`
Stability & Resistance	Biomass per Trophic Level^3	`biomassPerTL()`
Stability & Resistance	Coefficient of Variation of Biomass	`CVBiomass()`

Resource Potential	All Resource Potential indicators	`allPotential()`
Resource Potential	Biomass	`resourcePotential()`
Resource Potential	Biomass of Key Groups^4	`resourcePotential()`
Resource Potential	Fishing in Balance	`fishingInBalance()`

Fishing Pressure	All Fishing Pressure indicators	`allPressure()`
Fishing Pressure	Fishing Pressure	`fishingPressure()`
Fishing Pressure	Fishing Pressure on Groups^5	`fishingPressure()`
Fishing Pressure	Marine Trophic Index	`meanTLLandings()`
Fishing Pressure	Mean Trophic Level of Landings	`meanTLLandings()`
Fishing Pressure	Diversity of Target Species	`speciesRichness()`
Fishing Pressure	Landings	`landings()`
Fishing Pressure	Landings of Fished Groups^6	`landings()`

^1Biomass of piscivores and zoopiscivores
^2Condition of large benthivores, medium benthivores, piscivores, and zoopiscivores
^3Biomass at trophic level 2
^4Biomass of invertebrates, gadoids, flatfish, and skates
^5Fishing Pressure on clupeids
^6 Landings of skates, flatfish, and large pelagics

The data required to apply the marindicators package depends on the indicator(s) to be calculated. In general, indicators related to ecosystem attributes require annual fishery independent survey data, while indicators related to the ecosystem pressure require annual commercial landings data. Additional species information is required to calculate some indicators, including: trophic level, intrinsic vulnerability index, maximum recorded age, maximum recorded length, and annual length-at-weight data. See the vignette or the help page for a specific function for more information on data requirements.

The functions in this package provide the user with three options for calculating indicators:
1. Individual functions, which calculate a single indicator for one or more user-defined species groups.
2. “allAttribute” functions, which call the individual functions to calculate and return all (or a subset) of the indicators for an attribute or pressure.
3. extractAll() function, which calls the “allAttribute” functions to calculate and return all of the indicators.

See the vignette "Introduction to marindicators" or the help files below for more details on these functions.

Bundy A, Gomez C, Cook AM. 2017. Guidance framework for the selection and evaluation of ecological indicators. Can. Tech. Rep. Fish. Aquat. Sci. 3232: xii + 212 p.

marindicators documentation built on Nov. 12, 2019, 5:07 p.m.