largeFishIndicator: Calculates the Large Fish Indicator
In marindicators: Marine Ecosystem and Fishing Pressure Indicators

Description Usage Arguments Details Value Author(s) References See Also Examples

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

1 2	largeFishIndicator(X_length, group, species.table = NULL, metric = "BIOMASS", large.fish = 35, years)

`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.

Large Fish Indicator (LFI):

LFI = Σ B_m(L >35 cm)/Σ 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).

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.

Danielle Dempsey Danielle.Dempsey@dfo-mpo.gc.ca, Adam Cook, Catalina Gomez, Alida Bundy

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: 573–593.

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

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

# 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))