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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

172

Version

0.4.7

License

GPL (>= 3)

Issues

3

Pull Requests

1

Stars

8

Forks

3

Maintainer

Jeffrey A. Hostetler

Last Published

March 26th, 2024

Functions in MigConnectivity (0.4.7)

diffMantel

Pairwise differences between two or more independent Mantel correlation estimates
estMC

Estimate migratory connectivity
OVENdata

Ovenbird light-level geolocator and GPS necessary data
calcMantel

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

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

Distance matrix from position matrix
MigConnectivity

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

Pairwise differences between two or more independent MC estimates
abundExamples

Example relative abundance estimates from simulated data
calcMC

Migratory connectivity strength function
getCMRexample

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

Generate probabilistic isotope assignments
getIsoMap

Get Isoscape map getIsoMap
estMantel

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

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

Basic plot function for the different isoAssign outputs
modelCountDataJAGS

Estimates population-level relative abundance from count data
plot.estMigConnectivity

Basic plot function for estMigConnectivity objects
projections

Map projections
simProbData

Simulate Dirichlet-based probability table data
simTelemetryData

Simulate telemetry/GPS data
estStrength

Estimate MC, migratory connectivity strength
simCountData

Simulates Breeding Bird Survey-style count data
simCMRData

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

Simulate geolocator (GL) migratory movement data
simMove

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

Reverse transition probabilities and origin relative abundance
weightAssign

Calculate Weights for Isotope Assignments weightAssign
sampleOriginPos

Example origin and target site positions and distances on a 2-D plane
sampleOriginN

Example origin site abundances and relative abundances
samplePsis

Example transition probabilities (psis) between origin and target sites