MeanTLLandings: Calculates the Mean Trophic Level or Marine Trophic Index of...
In dempseydanielle/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 or Marine Trophic Index of fisheries landings for j areas and i years.

1	meanTLLandings(land, TL.table, minTL = 0, years)

`land`	A dataframe of commercial landings data with columns `YEAR`, `ID`, `SPECIES` and `CATCH`. `YEAR` indicates the year the landing was recorded, `ID` is an area code indicating where the landing was recorded, `SPECIES` is a numeric code indicating the species landed, and `CATCH` is the corresponding landed weight.
`TL.table`	A dataframe with columns `SPECIES` and the corresponding `TL_LAND` (trophic level). Entries in the `SPECIES` column should be the unique values of species codes in `land` (or a subset thereof). Other columns in `TL.table` are ignored.
`minTL`	The minimum trophic level of species to include. Set `minTL = 0` to calculate the mean trophic level of the landings; Set `minTL = 3.25` to calculate the marine trophic index. Default is `minTL = 0`.
`years`	A vector of years for which to calculate indicator.

Mean trophic level of fisheries landings (TL_{Land}):

TL_{Land} = Σ (TL_i*Y_i)/Y

where TL_i is the trophic level of species i, Y_i is the landings of species i, and Y is the total landings of all species. Trophic Level of individual species can be estimated either through an Ecopath model or dietary analysis, or taken from a global database such as Fishbase.

This indicator captures the average trophic level of the species exploited in the fishery. In general, it reflects a transition from long-lived, high trophic level, demersal fish toward short-lived, low trophic level pelagic fish and invertebrates (Pauly et al., 1998).

The marine trophic index is calculated similarly to TL_{Land}, but only includes species with trophic level greater than or equal to an explicitly stated trophic level minTL. For instance, Pauly and Watson 2005 adopted a trophic level minTL of 3.25 to emphasize changes in the relative abundance of higher trophic level fishes, and Shannon et al. 2014 used a minTL of 4.0 to examine changes within the apex predator community. If used in this way, this indicator highlights changes in the relative abundance of the more threatened high-trophic level fishes (Pauly et al., 1998).

Returns a dataframe with three columns: ID, YEAR, and if minTL = 0: MeanTL.Landings, if minTL = 3.25: MTI.Landings, or if minTL is a different value: MeanTL.Landings_minTL.

If there are no observations in land for spatial scale j in year i, indicator value is set to NA.

Danielle Dempsey, Adam Cook Adam.Cook@dfo-mpo.gc.ca, 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.

Pauly D, Christensen V, Dalsgaard J, Froese R, Torres F. 1998. Fishing Down Marine Food Webs. Science 279:860-863

Pauly D, Watson R. 2005. Background and interpretation of the Marine Trophic Index as a measure of biodiversity. Philos Trans R Soc B Biol Sci 360:415 423

Shannon L, Coll M, Bundy A, Gascuel D, Heymans, JJ, Kleisner K, Lynam CP, Piroddi C, Tam J, Travers-Trolet M and Shin Y. 2014. Trophic level-based indicators to track fishing impacts across marine ecosystems. Marine Ecology Progress Series, 512, pp.115-140.

Other fishing pressure indicators: allPressure(), fishingPressure(), landings(), speciesRichness()

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

# Calculate indicators
# Mean trophic level of landings
meanTLLandings(land, TL.table = species.info, minTL = 0, years = c(2014:2019))
# Marine trophic index
meanTLLandings(land, TL.table = species.info, minTL = 3.25, years = c(2014:2019))