This function calculates the Mean Trophic Level or Marine Trophic Index of fisheries landings for \(j\) areas and \(i\) years.
meanTLLandings(land, TL.table, minTL = 0, years)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.
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.
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.
A vector of years for which to calculate indicator.
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.
Mean trophic level of fisheries landings (\(TL_{Land}\)): $$TL_{Land} = \Sigma (TL_i*Y_i)/Y$$ 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).
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
# NOT RUN {
# 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))
# }
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