generate_observedcounts: Generate observed counts from the set of bird trajectories.

In FlywayNet: Estimate Migration Birds Flyways Network with HSMM

Generate observed counts from the set of bird trajectories.

Description

Generate observed counts from the set of bird trajectories.

Usage

generate_observedcounts(migr, traj, mask)

Arguments

migr	A migration structure (attributes site_name, horizon, initial_state are used).
traj	A trajectory matrix with a trajectory for each bird. For each bird, at each time step (from 0 to horizon), position of the bird. positions: sites, 0 for flying, -1 for dead. matrix N x (horizon + 1)
mask	Boolean matrix (horizon x S) indicating the available observations, (mask(t,i)=TRUE if site i is observed at time t).

Value

Counts of observed birds on sites for time steps from 1 to horizon, from the provided set of bird trajectories, matrix (S + 2) x (horizon + 1). At each time step, count of birds observed on each site. NA correspond to non observation. For compatibility with trajectory, the first column (time step 0) and the 2 last rows ( S+1 and S+2) are kept and filled with NA.

Examples

migr <- generate_toy_migration()
traj <- generate_trajectories( migr )
obs <- generate_observedcounts( migr, traj )

FlywayNet documentation built on March 18, 2022, 7:21 p.m.