Estimate Migration Birds Flyways Network with HSMM


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Documentation for package ‘FlywayNet’ version 0.1.0

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FlywayNet-package 'FlywayNet' package: infer the structure of migratory bird flyway networks given counts
estimate_migration_ABC Estimates migration parameters using an ABC method.
estimate_migration_from_trajectories Estimates migration parameters using trajectories.
estimate_migration_from_trajectories_C Internal C function (do not use).
estimate_migration_MCEM Estimates migration parameters using an MCEM method.
estimate_migration_MCEM_C Internal C function (do not use).
generate_modified_migration Return a modified migration according generative parameters.
generate_observedcounts Generate observed counts from the set of bird trajectories.
generate_random_migration Generate a migration structure with a random structure.
generate_toy_migration Generate a toy migration structure with 5 sites.
generate_trajectories Generate trajectories of birds.
generate_trajectories_C Internal C function (do not use).
get_counts Count birds on each site at each time step from given set of trajectories.
get_counts_C Internal C function (do not use).
get_freeparametersvalue Extract free parameter values from a migration structure.
get_observation_probability Computes the probability of observations given the birds count from trajectories.
get_observation_probability_C Internal C function (do not use).
get_paramlikelihood Computes, by simulation, the log-likelihood of parameters
new_migration Initialize a migration structure.
plot.migration Plot a migration network from transition probabilities and mean sojourn time parameters.
plot_observedcounts Barplot observed counts at different sites and time steps.
plot_trajectories Barplot of birds counts par site and per time step, given bird trajectories.
read_migration Read a migration structure in a text file.
reestimate_migration_from_MCEMruns Estimates migration parameters from multiple MCEM runs
set_freeparametersvalue Assign free parameter values to a migration structure.
validate_migration Check a migration structure.
write_migration Write a migration structure in a text file.