marindicators (version 1.0.0)

communityCondition: Calculates Fulton's Condition Index for the community

Description

This function calculates Fulton's Condition Index for \(j\) areas and \(i\) years.

Usage

communityCondition(X_length, groups, species.table = NULL, LenWt.table,
  years)

Arguments

X_length

A dataframe of fishery independent data derived from research vessel survey data or model output, with columns YEAR, ID, SPECIES, LENGTH, and ABUNDANCE. YEAR indicates the year the observation was recorded, ID is an area code indicating where the observation was recorded, and SPECIES is a numeric code indicating the species sampled. LENGTH is the length class (cm) and ABUNDANCE is the corresponding abundance at length (stratified and corrected for catchability as required). Species for which there are no length data should be assigned LENGTH = -99. These observations are removed by the function.

groups

A vector indicating the species group(s) for which to calculate the indicator. If groups = "ALL", all species will be included; otherwise, each entry must be a character string matching the name of a column 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.

LenWt.table

A table of annual length at weight data with 5 columns. YEAR, ID, and SPECIES are as described in X_length. LENGTH is fish length at the corresponding WEIGHT (fish weight).

years

A vector of years for which to calculate indicator.

Value

Returns a dataframe with columns ID and YEAR, and a column CCondition_group for each entry in groups.

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

Details

Fulton's Condition Index (\(K\)): $$K = \Sigma(K_j * A_j)/\Sigma A_j$$ where the sum is over all species, \(j\), \(A_j\) is the abundance of species \(j\), and $$K_j = 100*W_j/L_j^3$$ where \(W_j\) is the mean weight at length \(L\) for species \(j\) (Ricker, 1975).

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.

DFO. 2003. State of the Eastern Scotian Shelf ecosystem. Dartmouth, Nova Scotia

Choi JS, Frank KT, Petrie BD, Leggett WC. 2005. Integrated Assessment of a Large Marine Ecosystem: a case study of the devolution of the Eastern Scotian Shelf, Canada. Oceanogr Mar Biol An Annu Rev 43:47<U+2013>67

Ricker, W. E. 1975. Computation and interpretation of biological statistics of fish populations. Bulletin of the Fisheries Research Board of Canada 191:1-382.

See Also

Other ecosystem structure and function indicators: allStructure, biomassRatio, largeFishIndicator, largeSpeciesIndicator, meanTLCommunity

Examples

# NOT RUN {
# Compile data
data(X_length)
data(species.table)
data(Length_Weight)

# Species groups of interest
condition.groups <- c("FINFISH", "LBENTHIVORE", "PISCIVORE", "PLANKTIVORE")

# Calculate indicators
communityCondition(X_length, LenWt.table = Length_Weight, groups = condition.groups,
   species.table = species.table, years = c(2014:2019))
# }