Estimate Migratory Connectivity for Migratory Animals

Allows the user to estimate transition probabilities for migratory animals between any two phases of the annual cycle, using a variety of different data types. Also quantifies the strength of migratory connectivity (MC), a standardized metric to quantify the extent to which populations co-occur between two phases of the annual cycle. Includes functions to estimate MC and the more traditional metric of migratory connectivity strength (Mantel correlation) incorporating uncertainty from multiple sources of sampling error. For cross-species comparisons, methods are provided to estimate differences in migratory connectivity strength, incorporating uncertainty. See Cohen et al. (2018) , Cohen et al. (2019) , Roberts et al. (2023) , and Hostetler et al. (2025) for details on some of these methods.

MigConnectivity

The MigConnectivity package quantifies the pattern and strength of migratory connectivity for migratory animals

The pattern of migratory connectivity can be expressed as migratory transition probabilities between sites or regions in any two phases of the annual cycle.

MC is a standardized metric to quantify migratory connectivity strength between two phases of the annual cycle. MC is independent of data type and accounts for the relative abundance of populations distributed across a seasonal range.

See the vignettes for details and examples.

Installation

If you will (or might) use Markov chain Monte Carlo (MCMC) estimation in MigConnectivity, you should first install the program JAGS on your computer, available at https://mcmc-jags.sourceforge.net. Then, now that MigConnectivity is on CRAN:

install.packages("MigConnectivity")

Issues

Find a bug? Want to request an enhancement? Check out our issues page!