communityCondition: Calculates Fulton's Condition Index for the community
In marindicators: Marine Ecosystem and Fishing Pressure Indicators

Description Usage Arguments Details Value Author(s) References See Also Examples

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

1 2	communityCondition(X_length, groups, species.table = NULL, LenWt.table, years)

`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.

Fulton's Condition Index (K):

K = Σ(K_j * A_j)/Σ 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).

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.

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

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 43:47–67

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

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

# 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))