R/write_functions.R

In NOAA-EDAB/Rpath: R implementation of Ecopath with Ecosim

#'Write function for Ecopath object
#'
#'Outputs basic parameters or mortalities to a .csv file.
#'
#'@family Rpath functions
#'
#'@param x Rpath model created by the ecopath() function.
#'@param file file name for resultant file.  Need to specify ".csv" or ".RData".
#'@param morts Logical value whether to output basic parameters or mortalities.  
#'
#'@return Writes a .csv file with the basic parameters or mortalities from an Rpath object.
#'@import utils
#'@export
#Write -- note, not a generic function
write.Rpath <- function(x, file = NA, morts = F){
  #Check extention for output type - if not supplied a .csv or .RData the output
  #will be saved as a list object
  ext <- 'list'
  if(grepl('.csv', file) == T) ext <- 'csv'
  if(grepl('.RData', file, ignore.case = T) == T) ext <- 'RData'
  
  if(morts == F){
    removals <- rowSums(x$Landings) + rowSums(x$Discard)
    out <- data.frame(Group    = x$Group,
                      type     = x$type,
                      TL       = x$TL,
                      Biomass  = x$Biomass,
                      PB       = x$PB,
                      QB       = x$QB,
                      EE       = x$EE,
                      GE       = x$GE,
                      Removals = removals)
  }
  if(morts == T){
    ngroup <- x$NUM_LIVING + x$NUM_DEAD
    out <- data.frame(Group    = x$Group[1:ngroup],
                      type     = x$type [1:ngroup],
                      PB       = x$PB   [1:ngroup])
    #Calculate M0
    M0  <- c(x$PB[1:x$NUM_LIVING] * (1 - x$EE[1:x$NUM_LIVING]), 
             x$EE[(x$NUM_LIVING + 1):ngroup])
    out <- cbind(out, M0)
    #Calculate F mortality
    totcatch <- x$Landings + x$Discards
    Fmort    <- as.data.frame(totcatch / x$Biomass[row(as.matrix(totcatch))])
    #setnames(Fmort, paste('V',  1:x$NUM_GEARS,                     sep = ''), 
    #         paste('F.', x$Group[(ngroup +1):x$NUM_GROUPS], sep = ''))
    out  <- cbind(out, Fmort[1:ngroup, ])
    #Calculate M2
    bio  <- x$Biomass[1:x$NUM_LIVING]
    BQB  <- bio * x$QB[1:x$NUM_LIVING]
    diet <- as.data.frame(x$DC)
    nodetrdiet <- diet[1:x$NUM_LIVING, ]
    detrdiet   <- diet[(x$NUM_LIVING +1):ngroup, ]
    newcons    <- nodetrdiet * BQB[col(as.matrix(nodetrdiet))]
    predM      <- newcons / bio[row(as.matrix(newcons))]
    detcons    <- detrdiet * BQB[col(as.matrix(detrdiet))]
    predM      <- rbind(predM, detcons)
    setnames(predM, names(predM), paste0('M2.', names(predM)))
    out <- cbind(out, predM)
  }
  if(ext == 'csv')   write.csv(out, file = file)
  if(ext == 'RData') save(out, file = file)
  if(ext == 'list')  return(out)
}


#'Write function for Ecosim object
#'
#'Outputs start/end biomass and catch to a .csv file.
#'
#'@family Rpath functions
#'
#'@param Rsim.output object created by the rsim.run() function.
#'@param file file name for resultant .csv file.  Be sure to include ".csv".  
#'
#'@return Writes a .csv file with the start and end biomass and catch per group
#' from an Rpath.sim object.
#'@import utils
#'@export
#Write -- note, not a generic function
write.Rsim <- function(Rsim.output, file = NA){
  #Check extention for output type - if not supplied a .csv or .RData the output
  #will be saved as a list object
  ext <- 'list'
  if(grepl('.csv', file) == T) ext <- 'csv'
  if(grepl('.RData', file, ignore.case = T) == T) ext <- 'RData'
  
  gear.zero <- rep(0, Rsim.output$params$NUM_GEARS)
  start_Catch <- c(Rsim.output$out_Catch[2, ], gear.zero)
  end_Catch   <- c(Rsim.output$out_Catch[nrow(Rsim.output$out_Catch) - 1, ], gear.zero)
  out <- data.frame(Group      = Rsim.output$params$spname,
                    StartBio   = Rsim.output$start_state$Biomass,
                    EndBio     = Rsim.output$end_state$Biomass,
                    BioES      = Rsim.output$end_state$Biomass / 
                                 Rsim.output$start_state$Biomass,
                    StartCatch = start_Catch * 12,
                    EndCatch   = end_Catch * 12,
                    CatchES    = (end_Catch * 12) / (start_Catch * 12))
  if(ext == 'csv')   write.csv(out, file = file)
  if(ext == 'RData') save(out, file = file)
  if(ext == 'list')  return(out)
}