Package: MigConnectivity 0.4.7

Jeffrey A. Hostetler

MigConnectivity: 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) <doi:10.1111/2041-210X.12916>, Cohen et al. (2019) <doi:10.1111/ecog.03974>, and Roberts et al. (2023) <doi:10.1002/eap.2788> for details on some of these methods.

Authors:Jeffrey A. Hostetler [cre, aut], Michael T. Hallworth [aut], Clark S. Rushing [ctb], Emily B. Cohen [ctb], Valentine Herrmann [ctb]

MigConnectivity_0.4.7.tar.gz
MigConnectivity_0.4.7.tar.gz(r-4.5-noble)MigConnectivity_0.4.7.tar.gz(r-4.4-noble)
MigConnectivity_0.4.7.tgz(r-4.4-emscripten)MigConnectivity_0.4.7.tgz(r-4.3-emscripten)
MigConnectivity.pdf |MigConnectivity.html✨
MigConnectivity/json (API)
NEWS

# Install 'MigConnectivity' in R:
install.packages('MigConnectivity', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/smbc-nzp/migconnectivity/issues

Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3
Datasets:
  • OVENdata - Ovenbird light-level geolocator and GPS necessary data
  • abundExamples - Example relative abundance estimates from simulated data
  • projections - Map projections
  • 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

jagscpp

4.27 score 41 scripts 197 downloads 31 exports 49 dependencies

Last updated 9 months agofrom:d0574dcc99. Checks:OK: 1 NOTE: 1. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 22 2024
R-4.5-linuxNOTEDec 22 2024

Exports:calcMantelcalcMCcalcPsicalcStrengthcalcTransitiondiffCorrdiffManteldiffMCdiffStrengthdistFromPosestCorrestMantelestMCestPsiestStrengthestTransitiongetCMRexamplegetIsoMapisoAssignmodelCountDataJAGSreversePireversePsiRelAbundreverseTransitionreverseTransitionRelAbundsimCMRDatasimCountDatasimGLDatasimMovesimProbDatasimTelemetryDataweightAssign

Dependencies:abindbitopsbootcaToolsclassclassIntclicodaDBIe1071expmfansigenericsgeodistgluegplotsgtoolsKernSmoothlatticelifecyclemagrittrMASSMatrixmatrixcalcmsmmvtnormncfpillarpkgconfigproxyR2jagsR2WinBUGSRcpprjagsrlangRMarks2sfshapestringistringrsurvivalterratibbleunitsutf8vctrsVGAMwk

'MigConnectivity' package: isotope simulation

Michael T. Hallworth, Jeffrey A. Hostetler

Rendered fromsimulateIsoMC.Rmdusingknitr::rmarkdownon Dec 22 2024.

Last update: 2024-01-17
Started: 2024-01-17

MigConnectivity package

Jeffrey A. Hostetler, Michael T. Hallworth

Rendered fromMigConnectivity.Rmdusingknitr::rmarkdownon Dec 22 2024.

Last update: 2024-01-17
Started: 2024-01-17

MigConnectivity package (older functionality)

Jeffrey A. Hostetler, Michael T. Hallworth

Rendered fromolderFunctionality.Rmdusingknitr::rmarkdownon Dec 22 2024.

Last update: 2024-01-17
Started: 2024-01-17

Readme and manuals

Help Manual

Help pageTopics
Example relative abundance estimates from simulated dataabundExamples
Calculate Mantel correlation (rM) from points and/or distances.calcMantel
Migratory connectivity strength functioncalcMC calcStrength
Calculate psi (transition probabilities between sites in two phases of the annual cycle)calcPsi calcTransition
Pairwise differences between two or more independent Mantel correlation estimatesdiffCorr diffMantel
Pairwise differences between two or more independent MC estimatesdiffMC diffStrength
Distance matrix from position matrixdistFromPos
Estimate Mantel correlation (rM) from geolocator, GPS, and/or raster data.estCorr estMantel
Estimate migratory connectivityestMC
Estimate MC, migratory connectivity strengthestStrength
Estimate psi (transition probabilities between locations in two phases of the annual cycle)estPsi estTransition
Grab (from https://github.com/SMBC-NZP/MigConnectivity) example RMark transition probability estimates obtained from simulated datagetCMRexample
Get Isoscape map getIsoMapgetIsoMap
Generate probabilistic isotope assignmentsisoAssign
MigConnectivity: A package for quantifying migratory connectivity pattern and strength for migratory animalsMigConnectivity
Estimates population-level relative abundance from count datamodelCountDataJAGS
Ovenbird light-level geolocator and GPS necessary dataOVENdata
Basic plot function for estMigConnectivity objectsplot.estMigConnectivity
Basic plot function for the different isoAssign outputsplot.intrinsicAssign
Map projectionsprojections
Reverse transition probabilities and origin relative abundancereversePi reversePsiRelAbund reverseTransition reverseTransitionRelAbund
Example origin site abundances and relative abundancessampleOriginN sampleOriginRelN
Example origin and target site positions and distances on a 2-D planesampleOriginDist sampleOriginPos sampleTargetDist sampleTargetPos
Example transition probabilities (psis) between origin and target sitessamplePsis
Simulate capture-mark-reencounter (CMR) migratory movement datasimCMRData
Simulates Breeding Bird Survey-style count datasimCountData
Simulate geolocator (GL) migratory movement datasimGLData
Simulates position of birds by individual, season, year, and month.simMove
Simulate Dirichlet-based probability table datasimProbData
Simulate telemetry/GPS datasimTelemetryData
Calculate Weights for Isotope Assignments weightAssignweightAssign