Type: Package
Package: MigConnectivity
Title: Estimate Migratory Connectivity for Migratory Animals
Version: 0.5.0
Date: 2025-08-01
Authors@R: c(
    person("Jeffrey A.", "Hostetler", , "jhostetler@usgs.gov", role = c("cre", "aut")),
    person("Michael T.", "Hallworth", role = "aut"),
    person("Clark S.", "Rushing", role = "ctb"),
    person("Emily B.", "Cohen", role = "ctb"),
    person("Valentine", "Herrmann", role = "ctb"),
    person("Henry", "Stevens", role = "ctb")
  )
Description: 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>, Roberts et al. (2023)
        <doi:10.1002/eap.2788>, and Hostetler et al. (2025)
        <doi:10.1111/2041-210X.14467> for details on some of these
        methods.
License: GPL (>=3)
URL: https://github.com/SMBC-NZP/MigConnectivity
Depends: R (>= 3.5.0)
Imports: coda, geodist, gplots, graphics, grDevices, MASS, methods,
        ncf, R2jags, RMark (>= 2.1.14), sf, shape, stats, terra, utils,
        VGAM
Suggests: knitr, maps, rmarkdown, testthat
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
RoxygenNote: 7.3.2
SystemRequirements: JAGS (https://mcmc-jags.sourceforge.net)
Config/pak/sysreqs: libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev
        jags libicu-dev libssl-dev libproj-dev libsqlite3-dev
        libudunits2-dev
Repository: https://smbc-nzp.r-universe.dev
Date/Publication: 2025-08-01 14:28:56 UTC
RemoteUrl: https://github.com/smbc-nzp/migconnectivity
RemoteRef: HEAD
RemoteSha: 9b2b1c76f2a41b7b93a64d9a5bcc1df4618ea05d
NeedsCompilation: no
Packaged: 2026-07-05 13:51:53 UTC; root
Author: Jeffrey A. Hostetler [cre, aut],
  Michael T. Hallworth [aut],
  Clark S. Rushing [ctb],
  Emily B. Cohen [ctb],
  Valentine Herrmann [ctb],
  Henry Stevens [ctb]
Maintainer: Jeffrey A. Hostetler <jhostetler@usgs.gov>