marindicators (version 1.0.0)

meanMaxAge: Calculates the Mean Maximum Age of fish in the community

Description

This function calculates the Mean Maximum Age (MMA) of fish in the community for \(j\) areas and \(i\) years.

Usage

meanMaxAge(X, age.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).

age.table

A dataframe with columns SPECIES and MAXAGE, the maximum recorded age of the corresponding species. Entries in the SPECIES column should be the unique values of species codes in X (or a subset thereof). Other columns in age.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 MeanLifespan.

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

Details

Mean Maximum Age: $$Mean Maximum Age = \Sigma (age_{max,i}*B_i)/\Sigma B_i$$ where the sum is over all species \(i\), and \(B_i\) is biomass of species \(i\). The mean lifespan or longevity is considered to be a fixed parameter per species. Lifespan may vary under fishing pressure, so Shin et al. (2010) adopted the maximum longevity observed for each species (\(age_{max,i}\)). The variation of this indicator captures changes in species composition, and therefore changes in average lifespan (Shin et al., 2010).

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.

Shin, YJ, Shannon LJ, Bundy A, Coll M, Aydin K, Bez N, Blanchard JL, Borges, MF, Diallo I, Diaz E, Heymans JJ, Hill L, Johannesen E, Jouffre D, Kifani S, Labrosse P, Link JS, Mackinson S, Masski H, M<U+00F6>llmann C, Neira S, Ojaveer H, Abdallahi KM, Perry I, Thiao D, Yemane D, and Cury PM. 2010. Using indicators for evaluating, comparing and communicating the ecological status of exploited marine ecosystems. Part 2: Setting the scene. ICES Journal of Marine Science, 67: 692-716

See Also

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

Examples

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

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