biomassPerTL: Calculates the biomass per discrete trophic level
In marindicators: Marine Ecosystem and Fishing Pressure Indicators

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

This function calculates the biomass per discrete trophic level for j areas and i years.

1	biomassPerTL(X, TL.table, metric = "BIOMASS", TL.grouping = 1, 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` will be ignored.
`metric`	A character string indicating which column in `X` to use to calculate indicator. Default is `metric = "BIOMASS"`.
`TL.grouping`	Size of the trophic level bin for which to aggregate biomass. For example, if `TL.grouping = 1`, trophic levels are binned from 1.00 - 1.99, 2.00 - 2.99, etc. If `TL.grouping = 0.5`, trophic levels are binned from 1.00 - 1.49, 1.50 - 1.99, 2.00 - 2.49, 2.50 - 2.99, etc. Default is `TL.grouping = 1`.
`years`	A vector of years for which to calculate indicator.

Returns a dataframe with columns ID, YEAR, and the corresponding biomass for each trophic level grouping. For example: for TL.grouping = 1, function will return columns BIOMASS_TL2, BIOMASS_TL3, BIOMASS_TL4. For TL.grouping = 0.5, function will return columns BIOMASS_TL2, BIOMASS_TL2.5, BIOMASS_TL3, BIOMASS_TL3.5, BIOMASS_TL4, BIOMASS_TL4.5.

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.

Bundy, A. 2005. Structure and functioning of the eastern Scotian Shelf ecosystem before and after the collapse of groundfish stocks in the early 1990s. Canadian Journal of Fisheries and Aquatic Sciences, 62(7), pp.1453-1473.

Coll M, Shannon LJ, Moloney CL, Palomera I, Tudela S, 2006. Comparing trophic flows and fishing impacts of a NW Mediterranean ecosystem with coastal upwellings by means of standardized ecological models and indicators. Ecol. Model. 198, 53-70.

Other stability and resistance indicators: CVBiomass, IVILandings, allStability, meanMaxAge, meanMaxLength

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

# Calculate indicators
biomassPerTL(X = X, TL.table = species.info, metric = "BIOMASS",
TL.grouping = 1, years = c(2014:2019))