R/get_counts.R

In FlywayNet: Estimate Migration Birds Flyways Network with HSMM

#' Count birds on each site at each time step from given set of trajectories.
#'
#' @description  Count birds on each site at each time step from given set of trajectories. 
#'               The number of flying and dead birds are also computed.
#'
#' @param migr A migration structure (attributes horizon, initial_state are used).
#' @param traj A trajectory matrix N x (horizon+1) with a trajectory for each bird.
#'  For each bird, at each time step (from 0 to horizon), state of the bird is specified:
#'  site number, 0 for flying, -1 for dead.
#'
#' @return Counts of birds on sites, matrix (S+2) x (horizon+1).
#'  At each time step (from 1 to horizon), count of birds in each site.
#'  The first column (time step 0) and the two last rows (state flying and dead)
#'  are set to NA.
#'  
#' @export
#'
#' @examples
#' migr <- generate_toy_migration()
#' traj <- generate_trajectories( migr )
#' get_counts( migr, traj )
 
get_counts <- function ( migr, traj ) {
 
   stopifnot( class(migr) == "migration" )
   stopifnot( all(dim(traj) == c(sum(migr$initial_state), migr$horizon + 1)) )
 
   counts <- get_counts_C(migr, traj)
 
   return(counts)
 }