marindicators (version 1.0.0)

largeFishIndicator: Calculates the Large Fish Indicator

Description

This function calculates the Large Fish Indicator (LFI) for \(j\) areas and \(i\) years.

Usage

largeFishIndicator(X_length, group, species.table = NULL,
  metric = "BIOMASS", large.fish = 35, years)

Arguments

X_length

A dataframe of fishery independent data derived from research vessel survey data or model output, with columns YEAR, ID, SPECIES, LENGTH, and BIOMASS. YEAR indicates the year the observation was recorded, ID is an area code indicating where the observation was recorded, and SPECIES is a numeric code indicating the species sampled. LENGTH is the length class (cm) and BIOMASS is the corresponding abundance at length (stratified and corrected for catchability as required). Species for which there are no length data should be assigned LENGTH = -99. These observations are removed by the function.

group

character string indicating which species to include in the indicator calculation. If group = "ALL", all species will be included; otherwise, group should match a column name in species.table.

species.table

A table where the column names match the entries in groups. Column entries are species codes indicating the species from X included in each group. species.table may also include columns for other species groups; these will be ignored. If groups = "ALL", this table is not required. Default is species.table = NULL.

metric

A character string indicating which column in X to use to calculate indicator. Default is metric = "BIOMASS".

large.fish

Threshold for large fish (cm). Default is large.fish = 35 (i.e., large fish are those with X_length$LENGTH >= 35 cm).

years

A vector of years for which to calculate indicator.

Value

Returns a dataframe with 3 columns. ID, YEAR, and LargeFishIndicator.

If there are no observations of large fish or no observations in X for spatial scale \(j\) in year \(i\), indicator value is assigned NA.

Details

Large Fish Indicator (LFI): $$LFI = \Sigma B_m(L >35 cm)/\Sigma B_m$$ \(B_m\) is biomass of individuals in a body size class centered at mass m, and \(L\) is the length (cm) of an individual. This indicator describes the proportion (by weight) of the fish community that is larger than some length threshold (default here is 35 cm, i.e., the proportion of biomass occupying the top predator trophic level; Greenstreet and Rogers, 2006).

References

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.

Greenstreet SPR and Rogers SI. 2006. Indicators of the health of the fish community of the North Sea: identifying reference levels for an Ecosystem Approach to Management. ICES J. Mar. Sci., 63: 573<U+2013>593.

ICES. 2006. Report of the Working Group on Ecosystem Effects of Fishing Activities. ICES Document CM 2006/ACE: 05. 174 pp.

See Also

Other ecosystem structure and function indicators: allStructure, biomassRatio, communityCondition, largeSpeciesIndicator, meanTLCommunity

Examples

# NOT RUN {
# Compile data
data(X_length)
data(species.table)

# Calculate indicator
largeFishIndicator(X_length, group = "FINFISH", species.table = species.table,
   metric = "BIOMASS", years = c(2014:2019))
# }