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FlywayNet R package

Bird flyway network reconstruction.

Code

Codes are shared using sourcesup.renater.fr forge. See https://sourcesup.renater.fr/scm/?group_id=4720 .

Project members (alphabetic order)

Marie-Josée Cros (INRAE, France) Sam Nicol (CSIRO, Australia) Nathalie Peyrard (INRAE, France) Régis Sabbadin (INRAE France) Ronan Trépos (INRAE France)

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Version

Install

install.packages('FlywayNet')

Monthly Downloads

39

Version

0.1.0

License

GPL-3

Maintainer

Marie-Jos<c3><a9>e Cros

Last Published

March 9th, 2022

Functions in FlywayNet (0.1.0)

generate_modified_migration

Return a modified migration according generative parameters.
FlywayNet-package

FlywayNet package: infer the structure of migratory bird flyway networks given counts
estimate_migration_MCEM

Estimates migration parameters using an MCEM method.
estimate_migration_from_trajectories

Estimates migration parameters using trajectories.
generate_random_migration

Generate a migration structure with a random structure.
estimate_migration_MCEM_C

Internal C function (do not use).
generate_toy_migration

Generate a toy migration structure with 5 sites.
generate_observedcounts

Generate observed counts from the set of bird trajectories.
estimate_migration_ABC

Estimates migration parameters using an ABC method.
estimate_migration_from_trajectories_C

Internal C function (do not use).
get_observation_probability_C

Internal C function (do not use).
plot.migration

Plot a migration network from transition probabilities and mean sojourn time parameters.
write_migration

Write a migration structure in a text file.
new_migration

Initialize a migration structure.
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_paramlikelihood

Computes, by simulation, the log-likelihood of parameters
plot_trajectories

Barplot of birds counts par site and per time step, given bird trajectories.
plot_observedcounts

Barplot observed counts at different sites and time steps.
generate_trajectories_C

Internal C function (do not use).
generate_trajectories

Generate trajectories of birds.
validate_migration

Check a migration structure.
set_freeparametersvalue

Assign free parameter values to a migration structure.
get_counts_C

Internal C function (do not use).
get_counts

Count birds on each site at each time step from given set of trajectories.
read_migration

Read a migration structure in a text file.
reestimate_migration_from_MCEMruns

Estimates migration parameters from multiple MCEM runs