R/06.00.combine.R

In y-yasutomo/malia:

#04.05.combine
#'Combine natural and artificial individuals into same category
#'@description density ...
#'
#'@param leg.table
#'@param Voyage.name
#'@param Ar character vector of artificial product
#'@param Nt character vector of natural product
#'
#'@author Tomoki Yasuhara
#'@export
#'
#'@examples
#'


ls.<-function (leg.table, Ar = c("FGN", "FGF", 
                                              "FGO", "EPS", "PBA", "PBO", "FP", 
                                              "PC", "G", "M", "W", "UO"), 
               Nt = c("SW", "DW", "NO")) 
{
  
  d.colmn <- grep("Density", names(leg.table))
  n.colmn <- grep("Detected.Number", names(leg.table))
  d. <- leg.table[, d.colmn]
  n. <- leg.table[, n.colmn]
  NAME <- sapply(strsplit(names(d.), split = "_"), "[")[1, 
                                                        ]
  n.NAME <- sapply(strsplit(names(n.), split = "_"), 
                   "[")[1, ]
  D.Ar.ind <- which(NAME %in% Ar)
  D.Nt.ind <- which(NAME %in% Nt)
  D.Ar.tmp <- as.numeric(apply(d.[, D.Ar.ind], 1, sum))
  D.Nt.tmp <- as.numeric(apply(d.[, D.Nt.ind], 1, sum))
  n.Ar.ind <- which(n.NAME %in% Ar)
  n.Nt.ind <- which(n.NAME %in% Nt)
  n.Ar <- as.numeric(apply(n.[, n.Ar.ind], 1, sum))
  n.Nt <- as.numeric(apply(n.[, n.Nt.ind], 1, sum))
  tmp <- cbind(n.Ar, n.Nt)
  sp <- apply(tmp, 1, sum)
  r.mat <- matrix(NA, nrow(tmp), ncol(tmp))
  for (i in 1:nrow(r.mat)) {
    r.mat[i, ] <- tmp[i, ]/sp[i]
  }
  D.uk.ind <- which(!NAME %in% c(Ar, Nt))
  if (0 != length(D.uk.ind)) {
    sp.mat <- matrix(NA, nrow(tmp), ncol(tmp))
    for (i in 1:nrow(sp.mat)) {
      sp.mat[i, ] <- ifelse(is.nan(r.mat[i, ] * d.[, D.uk.ind][i]), 
                            0, r.mat[i, ] * d.[, D.uk.ind][i])
    }
  }
  D.Ar <- D.Ar.tmp + ifelse(0 == length(D.uk.ind), 0, sp.mat[, 
                                                             1])
  D.Nt <- D.Nt.tmp + ifelse(0 == length(D.uk.ind), 0, sp.mat[, 
                                                             2])
  ttmp <- cbind(n.Ar, D.Ar, n.Nt, D.Nt)
  colnames(ttmp) <- c("Artificial_Number", "Artificial_Density", 
                      "Natural_Number", "Natural_Density")
  cbind(leg.table[, c("Voyage_name","Leg.No.", "Leg.Length", 
                      "Lat.Start", "Lon.Start", "Lat.End", 
                      "Lon.End")], ttmp)
}