Learn R Programming

marindicators

November 6, 2019 - Danielle Dempsey (danielle.dempsey@dfo-mpo.gc.ca)

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).

For information on the Guidance Framework, including definitions of ecosystem attributes and sub-attributes, and methods for screening indicators, please refer to: 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.

For general information on the marindicators package, including the indicators that can be calculated, descriptions of data, and examples, please refer to the vignette: Introduction to marindicators.

For information on the functions, for example arguments, data requirements, and indicator calculations, please refer to the help file for the function of interest.

Copy Link

Version

Install

install.packages('marindicators')

Monthly Downloads

9

Version

1.0.0

License

GPL-3 | file LICENSE

Maintainer

Danielle Dempsey

Last Published

November 12th, 2019

Functions in marindicators (1.0.0)

largeSpeciesIndicator

Calculates the Large Species Indicator
meanLengthCommunity

Calculates the Mean Length of the Community weighted by biomass or abundance
fishingInBalance

Calculates the Fishing-in-Balance Index
X

Example fishery independent survey data
Length_Weight

Example length-weight data
speciesRichness

Calculates Species Richness of the community or the Diversity of Target Species
extractAll

Calculates indicators from all attributes
marindicators-package

Calculates Marine Ecosystem and Fishing Pressure Indicators
species.table

Example input for argument species.table
margalef

Calculates Margalef's Species Richness
hillN1

Calculates Hill's Index of Diversity (N1)
landings

Calculates the Landings per fished group
allStability

Calculates all Stability and Resistance indicators
allStructure

Calculates all Structure and Functioning indicators
communityCondition

Calculates Fulton's Condition Index for the community
example_inds

Indicators calculated from the example data included in the package
largeFishIndicator

Calculates the Large Fish Indicator
hillN2

Calculates Hill's Species Dominance (N2)
resourcePotential

Calculates the Resource Potential of species groups
pielouEvenness

Calculates Pielou's Species Evenness
kemptonQ

Calculates Kempton's Biodiversity Index
land

Example commercial landings data
heips

Calculates Heip's Evenness Index
meanMaxAge

Calculates the Mean Maximum Age of fish in the community
meanMaxLength

Calculates the Mean Maximum Length of fish in the community
shannon

Calculates Shannon's Index of Diversity
species.info

Species information
meanTLLandings

Calculates the Mean Trophic Level or Marine Trophic Index of fisheries landings
meanTLCommunity

Calculates the Mean Trophic Level of the community
IVILandings

Calculates the Intrinsic Vulnerability Index of commercial landings
allBiodiversity

Calculates all Biodiversity indicators
X_length

Example length-based fishery independent survey data
allPotential

Calculates all Resource Potential indicators
CVBiomass

Calculates the Coefficient of Variation of the Biomass
allPressure

Calculates all Pressure indicators
biomassPerTL

Calculates the biomass per discrete trophic level
fishingPressure

Calculates Fishing Pressure
biomassRatio

Calculates the biomass ratio between two species groups