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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!

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Version

Install

install.packages('MigConnectivity')

Monthly Downloads

228

Version

0.5.0

License

GPL (>= 3)

Issues

3

Pull Requests

1

Stars

8

Forks

3

Maintainer

Jeffrey A. Hostetler

Last Published

August 27th, 2025

Functions in MigConnectivity (0.5.0)

getIsoMap

Get Isoscape map getIsoMap
estMC

Estimate migratory connectivity
modelCountDataJAGS

Estimates population-level relative abundance from count data
isoAssign

Generate probabilistic isotope assignments
estNMC

Estimate NMC_XY, another type of migratory connectivity strength
estMantel

Estimate Mantel correlation (rM) from geolocator, GPS, and/or raster data.
getCMRexample

Grab (from https://github.com/SMBC-NZP/MigConnectivity) example RMark transition probability estimates obtained from simulated data
estStrength

Estimate MC, migratory connectivity strength
estTransition

Estimate psi (transition probabilities between locations in two phases of the annual cycle)
plot.estMigConnectivity

Basic plot function for estMigConnectivity objects
simGLData

Simulate geolocator (GL) migratory movement data
reverseTransition

Reverse transition probabilities and origin relative abundance
weightAssign

Calculate Weights for Isotope Assignments weightAssign
simCMRData

Simulate capture-mark-reencounter (CMR) migratory movement data
projections

Map projections
samplePsis

Example transition probabilities (psis) between origin and target sites
sampleOriginPos

Example origin and target site positions and distances on a 2-D plane
plot.intrinsicAssign

Basic plot function for the different isoAssign outputs
simMove

Simulates position of birds by individual, season, year, and month.
simCountData

Simulates Breeding Bird Survey-style count data
simProbData

Simulate Dirichlet-based probability table data
sampleOriginN

Example origin site abundances and relative abundances
simTelemetryData

Simulate telemetry/GPS data
diffMC

Pairwise differences between two or more independent MC estimates
MigConnectivity

MigConnectivity: A package for quantifying migratory connectivity pattern and strength for migratory animals
abundExamples

Example relative abundance estimates from simulated data
calcNMC

Calculate NMC_XY, another type of migratory connectivity strength
OVENdata

Ovenbird light-level geolocator and GPS necessary data
distFromPos

Distance matrix from position matrix
calcMC

Migratory connectivity strength function
diffMantel

Pairwise differences between two or more independent Mantel correlation estimates
calcTransition

Calculate psi (transition probabilities between sites in two phases of the annual cycle)
calcMantel

Calculate Mantel correlation (rM) from points and/or distances.