# Estimate Migratory Connectivity for Migratory Animals

## Documentation for package ‘MigConnectivity’ version 0.5.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

abundExamples | Example relative abundance estimates from simulated data
calcMantel | Calculate Mantel correlation (rM) from points and/or distances.
calcMC | Migratory connectivity strength function
calcNMC | Calculate NMC_XY, another type of migratory connectivity strength
calcPsi | Calculate psi (transition probabilities between sites in two phases of the annual cycle)
calcStrength | Migratory connectivity strength function
calcTransition | Calculate psi (transition probabilities between sites in two phases of the annual cycle)
diffCorr | Pairwise differences between two or more independent Mantel correlation estimates
diffMantel | Pairwise differences between two or more independent Mantel correlation estimates
diffMC | Pairwise differences between two or more independent MC estimates
diffStrength | Pairwise differences between two or more independent MC estimates
distFromPos | Distance matrix from position matrix
estCorr | Estimate Mantel correlation (rM) from geolocator, GPS, and/or raster data.
estMantel | Estimate Mantel correlation (rM) from geolocator, GPS, and/or raster data.
estMC | Estimate migratory connectivity
estNMC | Estimate NMC_XY, another type of migratory connectivity strength
estPsi | Estimate psi (transition probabilities between locations in two phases of the annual cycle)
estStrength | Estimate MC, migratory connectivity strength
estTransition | Estimate psi (transition probabilities between locations in two phases of the annual cycle)
getCMRexample | Grab (from https://github.com/SMBC-NZP/MigConnectivity) example RMark transition probability estimates obtained from simulated data
getIsoMap | Get Isoscape map getIsoMap
isoAssign | Generate probabilistic isotope assignments
MigConnectivity | MigConnectivity: A package for quantifying migratory connectivity pattern and strength for migratory animals
modelCountDataJAGS | Estimates population-level relative abundance from count data
OVENdata | Ovenbird light-level geolocator and GPS necessary data
plot.estMigConnectivity | Basic plot function for estMigConnectivity objects
plot.intrinsicAssign | Basic plot function for the different isoAssign outputs
projections | Map projections
reversePi | Reverse transition probabilities and origin relative abundance
reversePsiRelAbund | Reverse transition probabilities and origin relative abundance
reverseTransition | Reverse transition probabilities and origin relative abundance
reverseTransitionRelAbund | Reverse transition probabilities and origin relative abundance
sampleOriginDist | Example origin and target site positions and distances on a 2-D plane
sampleOriginN | Example origin site abundances and relative abundances
sampleOriginPos | Example origin and target site positions and distances on a 2-D plane
sampleOriginRelN | Example origin site abundances and relative abundances
samplePsis | Example transition probabilities (psis) between origin and target sites
sampleTargetDist | Example origin and target site positions and distances on a 2-D plane
sampleTargetPos | Example origin and target site positions and distances on a 2-D plane
simCMRData | Simulate capture-mark-reencounter (CMR) migratory movement data
simCountData | Simulates Breeding Bird Survey-style count data
simGLData | Simulate geolocator (GL) migratory movement data
simMove | Simulates position of birds by individual, season, year, and month.
simProbData | Simulate Dirichlet-based probability table data
simTelemetryData | Simulate telemetry/GPS data
weightAssign | Calculate Weights for Isotope Assignments weightAssign