marindicators (version 1.0.0)

meanMaxLength: Calculates the Mean Maximum Length of fish in the community

Description

This function calculates the Mean Maximum Length of fish in the community weighted by biomass or abundance for \(j\) areas and \(i\) years.

Usage

meanMaxLength(X, group, species.table = NULL, maxlength.table, metric,
  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).

group

character string indicating which species to include in the indicator calculation. If group = "ALL", all species will be included; otherwise, group should match a column name in species.table.

species.table

A table where the column names match the entries in groups. Column entries are species codes indicating the species from X included in each group. species.table may also include columns for other species groups; these will be ignored. If groups = "ALL", this table is not required. Default is species.table = NULL.

maxlength.table

A dataframe with columns SPECIES and MAXLENGTH, the maximum recorded length 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 maxlength.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 MMLength_metric.

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

Details

Mean Maximum Length: $$Mean Maximum Length = \Sigma (L_{max,i}*M_i)/\Sigma M_i$$ where \(L_{max,i}\) is the maximum asymptotic length (cm) of species \(i\), and \(M_i\) is biomass or abundance of species \(i\) (excluding invertebrates; Shin et al., 2005).

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, Rochet MJ, Jennings S, Field JG, Gislason H. 2005. Using size-based indicators to evaluate the ecosystem effects of fishing. In: ICES Journal of Marine Science. p 384-396

See Also

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

Examples

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

# Calculate indicators
# Weighted by abundance
meanMaxLength(X, group = "FINFISH", species.table = species.table, 
   maxlength.table = species.info, metric = "ABUNDANCE", years = c(2014:2019))
#Weighted by biomass
meanMaxLength(X, group = "FINFISH", species.table = species.table, 
   maxlength.table = species.info, metric = "BIOMASS", years = c(2014:2019))

# }