R/FishingPressure.R

In dempseydanielle/marindicators: Marine Ecosystem and Fishing Pressure Indicators

#'@title Calculates Fishing Pressure
#'@description This function calculates Fishing Pressure on a fished group for
#'  \eqn{j} areas and \eqn{i} years.
#'@details Fishing pressure (FP): \deqn{FP = Landings_{FG}/Biomass_{FG}} where
#'  \eqn{Landings_{FG}} is the landed catch of the fished group and
#'  \eqn{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 \eqn{Landings_{FG}}, \eqn{Biomass_{FG}} or both. If
#'  \eqn{Landings_{FG}} and \eqn{Biomass_{FG}} change in the same direction,
#'  exploitation rate may not change.
#'@inheritParams landings
#'@param X A dataframe of fishery independent data derived from research vessel
#'  survey data or model output, with columns \code{YEAR}, \code{ID},
#'  \code{SPECIES}, and \code{BIOMASS}. \code{YEAR} indicates the year the
#'  observation was recorded, \code{ID} is an area code indicating where the
#'  observation was recorded, \code{SPECIES} is a numeric code indicating the
#'  species sampled, and \code{BIOMASS} is the corresponding biomass (stratified
#'  and corrected for catchability as required).
#'@param land A dataframe of commercial landings data with columns \code{YEAR},
#'  \code{ID}, \code{SPECIES} and \code{CATCH}. \code{YEAR} indicates the year
#'  the landing was recorded, \code{ID} is an area code indicating where the
#'  landing was recorded, \code{SPECIES} is a numeric code indicating the
#'  species landed, and \code{CATCH} is the corresponding landed weight (in the
#'  same  units as \code{BIOMASS} in \code{X}).
#'@param FP.groups A dataframe with two columns, which must be named
#'  \code{group.land} and \code{group.X}. Each row holds the group names to
#'  calculate the fishing pressure on a target group, with the numerator in
#'  column \code{group.land} and the denominator in column \code{group.X}. Each
#'  entry must be a character string matching the name of a column in
#'  \code{species.table}.
#'@param species.table A table with column names that match the entries of
#'  \code{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 \code{SPECIES} column of \code{land} (for groups in \code{group.land})
#'  or \code{X} (for groups in \code{group.X}). \code{species.table} may also
#'  include columns for other species groups; these will be ignored. Note that
#'  an entry in \code{FP.groups} could be \code{"ALL"}. In this case, a column
#'  in \code{species.table} named \code{"ALL"} is not required; the function
#'  will automatically include all species in \code{land} and/or \code{X}.
#'@return Returns a dataframe with columns: \code{ID} and \code{YEAR}, and a
#'  column for each target group, named \code{FP_group.X}.
#'
#'  If biomass of \code{group.X} is \code{NA} and landings of \code{group.land}
#'  are zero, fishing pressure is set to zero. Otherwise, if biomass of
#'  \code{group.X} is \code{NA}, fishing pressure is set to \code{NA}.
#'
#'@family fishing pressure indicators
#'@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, 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
#'@author  Danielle Dempsey, Adam Cook \email{Adam.Cook@@dfo-mpo.gc.ca},
#'  Catalina Gomez, Alida Bundy
#'@examples
#'# 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))
#'@export

fishingPressure <- function(X, land, FP.groups, species.table, years){
  
  for (k in 1:nrow(FP.groups)){
    
    B.k <- resourcePotential(X = X, metric = "BIOMASS", groups = FP.groups[k, "group.X"], 
                         species.table = species.table, years = years)                                              # calculate the biomass of "group.X" in the community
    Y.k <- landings(land = land, groups = FP.groups[k, "group.land"], species.table = species.table, years = years) # calculate the landings of "group.land"
    
    ind.k <- merge(Y.k, B.k, by = c("ID", "YEAR"), all.x = T)
    
    ind.k$FP <- ind.k[,3]/ind.k[,4]                        # calculate fishing pressure
    index_zero <- which(ind.k[,3] == 0)                    # index of where landings is zero
    ind.k$FP[index_zero] <- 0                              # set fishing pressure to zero wherever there are no landings (even if biomass = NA)
    ind.k[,3] <- NULL                                      # remove landings column
    ind.k[,3] <- NULL                                      # remove biomass column
    
    ind.name <- paste("FP", "_", FP.groups[k, "group.X"], sep ="")         # name indicator: FP_group
    names(ind.k) <- c("ID", "YEAR", ind.name)
    ind.k <- ind.k[order(ind.k$ID), ]                          # order by ID to be consistent with other functions
    
    if(k == 1) ind = ind.k
    ind <- merge(ind, ind.k)
  }
  ind                                                  # return indicator dataframe
  
}