R/group_data_gen.R

In R2ucare: Goodness-of-Fit Tests for Capture-Recapture Models

#' Group individual capture-recapture data in encounter histories along specific column(s)
#'
#' This function pools together individuals with the same encounter capture-recapture history along specified directions given by columns.
#' @param X matrix of capture-recapture histories
#' @param effX vector with numbers of individuals with that particular capture-recapture history
#' @param s scalar or vector of columns along which the grouping should be done
#' @return matrix with grouped capture-recapture histories and counts in the last column
#' @author Olivier Gimenez <olivier.gimenez@cefe.cnrs.fr>, Roger Pradel, Rémi Choquet
#' @keywords package
#' @export

group_data_gen <- function(X,effX, s){

# sort data
if (length(effX) == 1) {
  Y <- t(matrix(c(X,effX)))
} else {
Y <- cbind(X,effX)
}

s = rev(s)
for (i in s){
  if (nrow(Y) == 1) {
    Y <- Y
  } else {
    Y <- Y[order(Y[,i]),]
  }
            }

# pool data
if (nrow(Y)==1){
  res <- Y
  return(res)
}


if (nrow(Y)>1){
compteur = 0
effY = Y[,ncol(Y)]
Y = Y[,-ncol(Y)]
i = 1
while (i <= dim(Y)[1]){
	j = i
	## while ((j <= dim(Y)[1])&&(sum(Y[i,]==Y[j,])==s)){
	## 2022-07-05 compare only first element of s
	while ((j <= dim(Y)[1])&&(sum(Y[i,]==Y[j,])==s[1])){
	    j = j+1
	}
   tot1 = sum((effY[i:(j-1)]>0) * effY[i:(j-1)])
   tot2 = sum((effY[i:(j-1)]<0) * effY[i:(j-1)])
   if (any(as.logical(tot1))){
   	compteur = compteur + 1
   	Y[compteur,] = Y[i,]
   	effY[compteur] = tot1
   	}
   if (any(as.logical(tot2))){
   	compteur = compteur + 1
    effY[compteur] = tot2
    Y[compteur,]=Y[i,]
   }
   i = j
}
Y = Y[1:compteur,]
effY = effY[1:compteur]
res = cbind(Y,effY)
return(res)
}
}