meanTLCommunity: Calculates the Mean Trophic Level of the community
In marindicators: Marine Ecosystem and Fishing Pressure Indicators

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

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

1	meanTLCommunity(X, TL.table, 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).
`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.

Mean trophic level (TL):

TL = Σ (TL_i*B_i)/Σ 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).

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.

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.

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, 115–140.

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

# Compile data
data(X)
data(species.info)

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