marindicators (version 1.0.0)

meanTLCommunity: Calculates the Mean Trophic Level of the community

Description

This function calculates the Mean Trophic Level of the community weighted by biomass for \(j\) areas and \(i\) years.

Usage

meanTLCommunity(X, TL.table, 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).

TL.table

A dataframe with columns SPECIES and the corresponding TL (trophic level). Entries in the SPECIES column should be the unique values of species codes in X (or a subset thereof). Other columns in TL.table are ignored.

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 MeanTLCommunity.

If there is no data for spatial scale \(j\) in year \(i\), indicator value is assigned NA.

Details

Mean trophic level (TL): $$TL = \Sigma (TL_i*B_i)/\Sigma B_i$$ \(TL_i\) is trophic level of species \(i\), and \(B_i\) is the biomass of species \(i\).

This indicator is based on trophic levels of all species with available biomass time series, weighted by annual species-specific biomass, to reflect the structure of the community (Christensen, 1998).

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.

Christensen V. 1998. Fishery-induced changes in a marine ecosystem: insight from models of the Gulf of Thailand. J. Fish Bio. 53:128-142. Article No. jb980809

Shannon L, Coll M, Bundy A, Gascuel D, Heymans JJ, Kleisner K, Lynam CP, Piroddi C, Tam J, Travers-Trolet M, Shin Y. 2014. Trophic level-based indicators to track fishing impacts across marine ecosystems. Mar. Ecol. Prog. Ser. 512, 115<U+2013>140.

See Also

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

Examples

# NOT RUN {
# Compile data
data(X)
data(species.info)

# Calculate indicator
meanTLCommunity(X, TL.table = species.info, metric = "BIOMASS", years = c(2014:2019))
# }