fishingPressure: Calculates Fishing Pressure
In marindicators: Marine Ecosystem and Fishing Pressure Indicators

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

This function calculates Fishing Pressure on a fished group for j areas and i years.

1	fishingPressure(X, land, FP.groups, species.table, years)

`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).
`land`	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 (in the same units as `BIOMASS` in `X`).
`FP.groups`	A dataframe with two columns, which must be named `group.land` and `group.X`. Each row holds the group names to calculate the fishing pressure on a target group, with the numerator in column `group.land` and the denominator in column `group.X`. Each entry must be a character string matching the name of a column in `species.table`.
`species.table`	A table with column names that match the entries of `FP.groups`. The entries in each column are the species codes for the species included in that group. Species codes should be a subset of those in the `SPECIES` column of `land` (for groups in `group.land`) or `X` (for groups in `group.X`). `species.table` may also include columns for other species groups; these will be ignored. Note that an entry in `FP.groups` could be `"ALL"`. In this case, a column in `species.table` named `"ALL"` is not required; the function will automatically include all species in `land` and/or `X`.
`years`	A vector of years for which to calculate indicator.

Fishing pressure (FP):

FP = Landings_{FG}/Biomass_{FG}

where Landings_{FG} is the landed catch of the fished group and Biomass_{FG} is the biomass of the fished group.

This indicator measures the level of exploitation or total fishing pressure at the ecosystem or species group level. Change in this indicator can result from change in Landings_{FG}, Biomass_{FG} or both. If Landings_{FG} and Biomass_{FG} change in the same direction, exploitation rate may not change.

Returns a dataframe with columns: ID and YEAR, and a column for each target group, named FP_group.X.

If biomass of group.X is NA and landings of group.land are zero, fishing pressure is set to zero. Otherwise, if biomass of group.X is NA, fishing pressure is set to 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.

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, Möllmann 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

Other fishing pressure indicators: allPressure, landings, meanTLLandings, speciesRichness

# Compile data
data(X)
data(land)
data(species.table)

# Species groups of interest
FP.groups <- data.frame(rbind(c("ALL", "ALL"), 
   c("CLUPEIDS", "CLUPEIDS.L"),
   c("FLATFISH", "FLATFISH.L"),
   c("GROUNDFISH", "GROUNDFISH.L")))
names(FP.groups) <- c("group.X", "group.land")

# Calculate indicators
fishingPressure(X = X, land = land, FP.groups = FP.groups, 
   species.table = species.table,  years = c(2014:2019))