largeSpeciesIndicator: Calculates the Large Species 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 Species Indicator (LSI) for j areas and i years.

1 2	largeSpeciesIndicator(X, group, species.table = NULL, maxlength.table, max.length = 85, metric = "BIOMASS", years)

`X`	A dataframe of fishery independent data derived from research vessel survey data or model output, with columns `YEAR`, `ID`, `SPECIES`, and `BIOMASS`. `YEAR` indicates the year the observation was recorded, `ID` is an area code indicating where the observation was recorded, `SPECIES` is a numeric code indicating the species sampled, and `BIOMASS` is the corresponding biomass (stratified and corrected for catchability as required).
`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`.
`maxlength.table`	A dataframe with columns `SPECIES` and `MAXLENGTH`, the maximum recorded length of the corresponding species. Entries in the `SPECIES` column should be the unique values of species codes in `X` (or a subset thereof). Other columns in `maxlength.table` are ignored.
`max.length`	The threshold for large species (cm). Default is `max.length = 85` (i.e., large species are those with `MAXLENGTH` >= 85 cm).
`metric`	A character string indicating which column in `X` to use to calculate indicator. Default is `metric = "BIOMASS"`.
`years`	A vector of years for which to calculate indicator.

Large Species Indicator (LSI):

LSI = Σ B_i(L_{max} > 85 cm)/Σ B_i

where B_i is biomass of individual species, i, and L_{max} is the maximum asymptotic length in cm (threshold default here is 85 cm; Shin et al., 2010).

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

If there are no observations of large species 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.

Shephard S, Fung T, Houle JE, Farnsworth KD, Reid DG, Rossberg AG. 2012. Size-selective fishing drives species composition in the Celtic Sea. ICES J Mar Sci 69:223-234

Shin, YJ, Shannon LJ, Bundy A, Coll M, Aydin K, Bez N, Blanchard JL, Borges, MF, Diallo I, Diaz E, Heymans JJ, Hill L, Johannesen E, Jouffre D, Kifani S, Labrosse P, Link JS, Mackinson S, Masski H, Möllmann C, Neira S, Ojaveer H, Abdallahi KM, Perry I, Thiao D, Yemane D, and Cury PM. 2010. Using indicators for evaluating, comparing and communicating the ecological status of exploited marine ecosystems. Part 2: Setting the scene. ICES Journal of Marine Science, 67: 692-716

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

data(X)
data(species.table)
largeSpeciesIndicator(X, group = "ALL", species.table = species.table,
   maxlength.table = species.info, max.length=85,  metric = "BIOMASS", years = c(2014:2019))