marindicators (version 1.0.0)

largeSpeciesIndicator: Calculates the Large Species Indicator

Description

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

Usage

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

Arguments

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.

Value

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.

Details

Large Species Indicator (LSI): $$LSI = \Sigma B_i(L_{max} > 85 cm)/\Sigma B_i$$ 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).

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.

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, M<U+00F6>llmann 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

See Also

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

Examples

# NOT RUN {
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))
# }