R/BENS(old)_init_survey.R

In Blevy2/READ-PDB-blevy2-MFS2: Mixed Fishery fleet dynamics simulation tool

#' @title Initialise survey settings
#'
#' @description \code{init_survey} is a function to mimic a
#' fisheries-independent survey to sample catches from the populations.
#'
#' @param sim_init is the general simualtion settings from \link{sim_init}
#' @param design is the survey design used, at the moment only
#' \emph{fixed_station}
#' @param n_stations is a Numeric for the number of stations to be fished each.
#' Note: If using 'fixed_station' design this will be rounded down to maintain
#' a grid shape if not divisble.  
#' @param start_day is a Numeric for the first day of the survey each year
#' @param stations_per_day is a Numeric for the number of stations surveyed per
#' day
#' @param Qs is a named Numeric Vector containing any survey catchabilities, assumed to be time invariant.
#'
#' @return is a list consisting of the survey setting and a a matrix for
#' storing the log of catches from the survey, to be used as an input to
#' \link{run_sim}.

#' @examples
#' init_survey(design = 'fixed_station', n_stations = 50, start_day = 90, stations_per_days = 5, Qs = c("spp1" = 0.1, "spp2" = 0.2)

#' @export

BENS_init_survey <- function (sim_init = NULL, design = 'fixed_station', n_stations = 50, 
			     start_day = 90, stations_per_day = 5, Qs = NULL, strata_coords = NULL) {

	# useful indexes
	idx       <- sim_init[["idx"]]
	n_fleets  <- idx[["nf"]]
	n_vessels <- idx[["nv"]]
	brk.idx   <- sim_init[["brk.idx"]]
	


	### Checks
	if(!start_day %in% sim_init[["brk.idx"]][["day.seq"]]) stop("We don't fish this day, choose another start_day!")

	## determine design

	if(design == 'fixed_station') {

	# Create a grid of stations
	x <- round(seq(1,idx[["ncols"]], length.out = round(sqrt(n_stations),0)),0) # sim_init[["idx"]][["n_rows"]], 1)
	y <- round(seq(1, idx[["nrows"]], length.out = round(sqrt(n_stations),0)),0) # sim_init[["idx"]][["n_cols"]], 1)
	grid <- cbind(x = x, y = rep(y, each = length(x)))

	# update no stations 
	n_stations <- nrow(grid)
	
	
	##########################
	## set up FIXED survey log matrix
	##########################
	
	#create the repeating pattern for the station days
	station_days <- rep(sim_init[["brk.idx"]][["day.seq"]][which(sim_init[["brk.idx"]][["day.seq"]] == 92, arr.ind = T):c(which(sim_init[["brk.idx"]][["day.seq"]] == 92, arr.ind = T) + round(n_stations / stations_per_day, 0) - 1)], each = stations_per_day)[seq_len(n_stations)]
	
	
	log.mat 	       <- matrix(NA, nrow = n_stations * sim_init[["idx"]][["ny"]], 
	                          ncol = 6 + idx[["n.spp"]])
	colnames(log.mat)      <- c("station_no", "x","y","day","tow","year",
	                            paste0("spp",seq(idx[["n.spp"]])))
	log.mat[,'station_no'] <- rep(seq_len(n_stations), sim_init[["idx"]][["ny"]])
	log.mat[,'x']          <- rep(grid[,"x"], times = sim_init[["idx"]][["ny"]])
	log.mat[,'y']          <- rep(grid[,"y"], times = sim_init[["idx"]][["ny"]])
	log.mat[,'day']        <- rep(station_days, times = sim_init[["idx"]][["ny"]])
	log.mat[,'tow']        <- rep(seq_len(n_stations), sim_init[["idx"]][["ny"]]) 
	log.mat[,'year']       <- rep(seq_len(sim_init[["idx"]][["ny"]]), each = n_stations)
	
	
	return(list(survey_settings = c("design" = design, "n_stations" =
	                                  n_stations, "days_fished" = round(n_stations / stations_per_day, 0),
	                                "Qs" = Qs), log.mat = log.mat))
	}

	
	
	
	
	if(design == "random_station") {
	  	#initialize x and y coordinate vectors
	      x <- vector()
	      y <- vector()
    for(j in seq(length(strata_coords))){
	  
	  ##Produce correct number of random x and y locations to sample from

	  #sample as many stations as you need. Output is the matrix positions
	  
      #old version before multiple stations
      #my_sample <- sample(idx[["ncols"]]*idx[["nrows"]],n_stations*sim_init[["idx"]][["ny"]],replace = FALSE)
      
      row_dist <- length(strata_coords[[j]][1]:strata_coords[[j]][2]) #specifies size of given strata
      col_dist <- length(strata_coords[[j]][3]:strata_coords[[j]][4])
      
      x1 <- strata_coords[[j]][1]; x2 <- strata_coords[[j]][2]  #specific coordinates from each strata
      y1 <- strata_coords[[j]][3]; y2 <- strata_coords[[j]][4]
      

      #currently dividing total number of samples evening among each strata
      my_sample <- sample(row_dist*col_dist,n_stations*sim_init[["idx"]][["ny"]]/length(strata_coords),replace = FALSE)
      

	  
	  dim.mat = c(row_dist,col_dist) #dimension of given strata
	  

	  coord <- matrix( NA,nrow=1,ncol=2)
	  
	  #translate each matrix position into an (x,y) index for given strata
	  for(i in my_sample){
	 
	    

        pos <- i	    

	      
	      coord[1,1] <- ((pos-1) %% dim.mat[1]) +1  #xcoordinate
	      coord[1,2] <- ((pos-1) %/% dim.mat[1]) +1 #y coordinate
	   #  show(pos)
	   	      
#	    coords <- pos2coord(pos=i,dim.mat = dim.mat)   #I extracted the above code from this function file 
	      
	      

	    
#tack onto existing coordinates after SHIFT COORDINATES OVER INTO CORRECT STRATA
	    x <- c(x,coord[1,1]+(x1-1))
	    
	    y <- c(y,coord[1,2]+(y1-1)) #subtract 1 because index starts at 1
	    
	    
	  }
    }
	  

	##########################
	## set up RANDOM survey log matrix
	##########################
	
	#create the station days
	station_days <- rep(sim_init[["brk.idx"]][["day.seq"]][which(sim_init[["brk.idx"]][["day.seq"]] == 92, arr.ind = T):c(which(sim_init[["brk.idx"]][["day.seq"]] == 92, arr.ind = T) + round(n_stations / stations_per_day, 0) - 1)], each = stations_per_day)[seq_len(n_stations)]
	
	
	log.mat 	       <- matrix(NA, nrow = n_stations * sim_init[["idx"]][["ny"]], 
	                          ncol = 6 + idx[["n.spp"]])
	colnames(log.mat)      <- c("station_no", "x","y","day","tow","year",
	                            paste0("spp",seq(idx[["n.spp"]])))
	log.mat[,'station_no'] <- rep(seq_len(n_stations), sim_init[["idx"]][["ny"]])
	log.mat[,'x']          <- x  #different than fixed station section
	log.mat[,'y']          <- y  #different than fixed station section
	log.mat[,'day']        <- rep(station_days, times = sim_init[["idx"]][["ny"]])
	log.mat[,'tow']        <- rep(seq_len(n_stations), sim_init[["idx"]][["ny"]]) 
	log.mat[,'year']       <- rep(seq_len(sim_init[["idx"]][["ny"]]), each = n_stations)
	
	
	return(list(survey_settings = c("design" = design, "n_stations" =
	                                  n_stations, "days_fished" = round(n_stations / stations_per_day, 0),
	                                "Qs" = Qs), log.mat = log.mat))
	
	#check for duplicate stations
	
	if(anyDuplicated(log.mat[,2:3])!=0){"There are duplicated sampling stations"}

    
	}

}