{
  "_id": "6a1f1d90b401979e7341fc0d",
  "Package": "samc",
  "Type": "Package",
  "Title": "Spatial Absorbing Markov Chains",
  "Version": "4.0.0",
  "Authors@R": "c(\nperson(\"Andrew\", \"Marx\", , \"ajm.rpackages@gmail.com\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-7456-1631\")\n),\nperson(\"Robert\", \"Fletcher\", , , role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0003-1717-5707\")\n),\nperson(\"Miguel\", \"Acevedo\", , , role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-8289-1497\")\n),\nperson(\"Jorge\", \"Sefair\", , , role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-5887-8938\")\n),\nperson(\"Chao\", \"Wang\", , , role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0003-2706-5122\")\n),\nperson(\"Hughes\", \"Josie\", , , role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0001-7875-9015\")\n),\nperson(\"Barrett\", \"Griffin\", , , role = c(\"ctb\"))\n)",
  "Description": "Implements functions for working with absorbing Markov\nchains. The implementation is based on the framework described\nin \"Toward a unified framework for connectivity that\ndisentangles movement and mortality in space and time\" by\nFletcher et al. (2019) <doi:10.1111/ele.13333>, which applies\nthem to spatial ecology. This framework incorporates both\nresistance and absorption with spatial absorbing Markov chains\n(SAMC) to provide several short-term and long-term predictions\nfor metrics related to connectivity in landscapes. Despite the\necological context of the framework, this package can be used\nin any application of absorbing Markov chains.",
  "License": "AGPL (>= 3)",
  "URL": "https://andrewmarx.github.io/samc/",
  "BugReports": "https://github.com/andrewmarx/samc/issues/",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "Collate": "'RcppExports.R' 'location-class.R' 'internal-classes.R'\n'samc-class.R' 'absorption.R' 'check.R' 'cond_passage.R'\n'data.R' 'visitation.R' 'dispersal.R' 'distribution.R'\n'generics.R' 'internal-data.R' 'internal-functions.R'\n'internal-utils.R' 'internal-validation.R' 'locate.R' 'map.R'\n'mortality.R' 'pairwise.R' 'rasterize.R' 'samc.R' 'survival.R'\n'zzz.R'",
  "Config/pak/sysreqs": "libgdal-dev gdal-bin libgeos-dev libproj-dev\nlibsqlite3-dev",
  "Repository": "https://andrewmarx.r-universe.dev",
  "Date/Publication": "2026-01-16 22:31:24 UTC",
  "RemoteUrl": "https://github.com/andrewmarx/samc",
  "RemoteRef": "HEAD",
  "RemoteSha": "d0903701503215b8a694ab557866e6acdb5b8ecd",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-16 08:29:49 UTC",
    "User": "root"
  },
  "Author": "Andrew Marx [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0002-7456-1631>),\nRobert Fletcher [ctb] (ORCID: <https://orcid.org/0000-0003-1717-5707>),\nMiguel Acevedo [ctb] (ORCID: <https://orcid.org/0000-0002-8289-1497>),\nJorge Sefair [ctb] (ORCID: <https://orcid.org/0000-0002-5887-8938>),\nChao Wang [ctb] (ORCID: <https://orcid.org/0000-0003-2706-5122>),\nHughes Josie [ctb] (ORCID: <https://orcid.org/0000-0001-7875-9015>),\nBarrett Griffin [ctb]",
  "Maintainer": "Andrew Marx <ajm.rpackages@gmail.com>",
  "MD5sum": "857ad217afb8f542e654676ba86eff8c",
  "_user": "andrewmarx",
  "_type": "src",
  "_file": "samc_4.0.0.tar.gz",
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  "_created": "2026-05-16T08:29:49.000Z",
  "_published": "2026-06-02T18:14:40.488Z",
  "_distro": "noble",
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  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/andrewmarx/samc",
  "_commit": {
    "id": "d0903701503215b8a694ab557866e6acdb5b8ecd",
    "author": "Andrew Marx <andrewjmarx@gmail.com>",
    "committer": "Andrew Marx <andrewjmarx@gmail.com>",
    "message": "Merge branch 'develop'\n",
    "time": 1768602684
  },
  "_maintainer": {
    "name": "Andrew Marx",
    "email": "ajm.rpackages@gmail.com",
    "orcid": "0000-0002-7456-1631"
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  "_dependencies": [
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      "role": "Depends"
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      "package": "Rcpp",
      "version": ">= 1.0.10",
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      "package": "methods",
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    {
      "package": "Matrix",
      "version": ">= 1.5-3",
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  "_owner": "andrewmarx",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-03",
      "n": 3
    }
  ],
  "_tags": [],
  "_topics": [
    "absorbing-markov-chains",
    "connectivity",
    "landscape-ecology",
    "landscape-metrics",
    "markov-chain",
    "cpp"
  ],
  "_stars": 15,
  "_contributors": [
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      "user": "andrewmarx",
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      "uuid": 13956617
    }
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    "type": "user",
    "name": "Andrew Marx"
  },
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/samc"
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  "_devurl": "https://github.com/andrewmarx/samc",
  "_pkgdown": "https://andrewmarx.github.io/samc/",
  "_searchresults": 15,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/samc.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/andrewmarx/samc",
  "_realowner": "andrewmarx",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.3",
      "date": "2019-08-21"
    },
    {
      "version": "1.0.4",
      "date": "2020-01-08"
    },
    {
      "version": "1.1.0",
      "date": "2020-05-19"
    },
    {
      "version": "1.2.0",
      "date": "2020-10-14"
    },
    {
      "version": "1.2.1",
      "date": "2020-11-03"
    },
    {
      "version": "1.3.0",
      "date": "2021-04-01"
    },
    {
      "version": "1.4.0",
      "date": "2021-06-27"
    },
    {
      "version": "1.4.1",
      "date": "2021-09-02"
    },
    {
      "version": "2.0.0",
      "date": "2021-10-23"
    },
    {
      "version": "2.0.1",
      "date": "2022-06-11"
    },
    {
      "version": "3.0.2",
      "date": "2023-02-01"
    },
    {
      "version": "3.1.0",
      "date": "2023-04-07"
    },
    {
      "version": "3.2.0",
      "date": "2023-05-04"
    },
    {
      "version": "3.2.1",
      "date": "2023-05-09"
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    {
      "version": "3.3.0",
      "date": "2024-07-11"
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    {
      "version": "4.0.0",
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    },
    {
      "version": "4.1.0",
      "date": "2026-02-05"
    },
    {
      "version": "4.2.1",
      "date": "2026-03-13"
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  ],
  "_exports": [
    "absorption",
    "check",
    "cond_passage",
    "dispersal",
    "distribution",
    "locate",
    "map",
    "mortality",
    "pairwise",
    "rasterize",
    "samc",
    "survival",
    "visitation",
    "visitation_net"
  ],
  "_datasets": [
    {
      "name": "example_maze",
      "title": "Simple maze example",
      "object": "example_maze",
      "class": [
        "matrix",
        "array"
      ],
      "fields": {},
      "rows": 20,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_split_corridor",
      "title": "Simple split corridor example",
      "object": "example_split_corridor",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "example_toy_res",
      "title": "Toy resistance data",
      "object": "example_toy_res",
      "class": [
        "matrix",
        "array"
      ],
      "fields": {},
      "rows": 10,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "absorption",
      "title": "Calculate absorption metrics",
      "topics": [
        "absorption",
        "absorption,samc,ANY,missing-method",
        "absorption,samc,missing,location-method",
        "absorption,samc,missing,missing-method"
      ]
    },
    {
      "page": "check",
      "title": "Check landscape data",
      "topics": [
        "check",
        "check,matrix,matrix-method",
        "check,matrix,missing-method",
        "check,Raster,missing-method",
        "check,Raster,Raster-method",
        "check,samc,matrix-method",
        "check,samc,numeric-method",
        "check,samc,Raster-method",
        "check,samc,SpatRaster-method",
        "check,SpatRaster,missing-method",
        "check,SpatRaster,SpatRaster-method"
      ]
    },
    {
      "page": "cond_passage",
      "title": "Conditional Mean First Passage Time",
      "topics": [
        "cond_passage",
        "cond_passage,samc,ANY,missing,location-method",
        "cond_passage,samc,missing,location,location-method",
        "cond_passage,samc,missing,missing,location-method"
      ]
    },
    {
      "page": "dispersal",
      "title": "Calculate dispersal metrics",
      "topics": [
        "dispersal",
        "dispersal,samc,ANY,missing,location,missing-method",
        "dispersal,samc,ANY,missing,location,numeric-method",
        "dispersal,samc,ANY,missing,missing,missing-method",
        "dispersal,samc,missing,location,location,missing-method",
        "dispersal,samc,missing,location,location,numeric-method",
        "dispersal,samc,missing,location,missing,missing-method",
        "dispersal,samc,missing,missing,location,missing-method",
        "dispersal,samc,missing,missing,location,numeric-method",
        "dispersal,samc,missing,missing,missing,missing-method"
      ]
    },
    {
      "page": "distribution",
      "title": "Calculate distribution metrics",
      "topics": [
        "distribution",
        "distribution,samc,ANY,missing,location,numeric-method",
        "distribution,samc,ANY,missing,missing,numeric-method",
        "distribution,samc,missing,location,location,numeric-method",
        "distribution,samc,missing,location,missing,numeric-method",
        "distribution,samc,missing,missing,location,numeric-method",
        "distribution,samc,missing,missing,missing,numeric-method"
      ]
    },
    {
      "page": "example_maze",
      "title": "Simple maze example",
      "topics": [
        "example_maze"
      ]
    },
    {
      "page": "example_split_corridor",
      "title": "Simple split corridor example",
      "topics": [
        "example_split_corridor"
      ]
    },
    {
      "page": "example_toy_res",
      "title": "Toy resistance data",
      "topics": [
        "example_toy_res"
      ]
    },
    {
      "page": "locate",
      "title": "Get cell numbers",
      "topics": [
        "locate",
        "locate,samc,ANY-method",
        "locate,samc,missing-method"
      ]
    },
    {
      "page": "location-class",
      "title": "location class",
      "topics": [
        "location-class"
      ]
    },
    {
      "page": "map",
      "title": "Map vector data",
      "topics": [
        "map",
        "map,samc,list-method",
        "map,samc,numeric-method"
      ]
    },
    {
      "page": "mortality",
      "title": "Calculate mortality metrics",
      "topics": [
        "mortality",
        "mortality,samc,ANY,missing,location,missing-method",
        "mortality,samc,ANY,missing,location,numeric-method",
        "mortality,samc,ANY,missing,missing,missing-method",
        "mortality,samc,ANY,missing,missing,numeric-method",
        "mortality,samc,missing,location,location,missing-method",
        "mortality,samc,missing,location,location,numeric-method",
        "mortality,samc,missing,location,missing,missing-method",
        "mortality,samc,missing,location,missing,numeric-method",
        "mortality,samc,missing,missing,location,missing-method",
        "mortality,samc,missing,missing,location,numeric-method",
        "mortality,samc,missing,missing,missing,missing-method",
        "mortality,samc,missing,missing,missing,numeric-method"
      ]
    },
    {
      "page": "pairwise",
      "title": "Pairwise analyses",
      "topics": [
        "pairwise",
        "pairwise,function,samc,location,location-method",
        "pairwise,function,samc,location,missing-method"
      ]
    },
    {
      "page": "rasterize",
      "title": "Rasterize input",
      "topics": [
        "rasterize",
        "rasterize,matrix-method",
        "rasterize,RasterLayer-method",
        "rasterize,SpatRaster-method"
      ]
    },
    {
      "page": "samc",
      "title": "Create an samc object",
      "topics": [
        "samc",
        "samc,dgCMatrix,missing,missing,missing-method",
        "samc,matrix,matrix,matrix,list-method",
        "samc,matrix,matrix,missing,list-method",
        "samc,matrix,missing,missing,missing-method",
        "samc,RasterLayer,RasterLayer,missing,list-method",
        "samc,RasterLayer,RasterLayer,RasterLayer,list-method",
        "samc,SpatRaster,SpatRaster,missing,list-method",
        "samc,SpatRaster,SpatRaster,SpatRaster,list-method"
      ]
    },
    {
      "page": "samc-class",
      "title": "samc class",
      "topics": [
        "samc-class"
      ]
    },
    {
      "page": "survival",
      "title": "Calculate survival metrics",
      "topics": [
        "survival",
        "survival,samc,ANY,missing-method",
        "survival,samc,missing,location-method",
        "survival,samc,missing,missing-method"
      ]
    },
    {
      "page": "visitation",
      "title": "Calculate visitation metrics",
      "topics": [
        "visitation",
        "visitation,samc,ANY,missing,location,missing-method",
        "visitation,samc,ANY,missing,missing,missing-method",
        "visitation,samc,ANY,missing,missing,numeric-method",
        "visitation,samc,missing,location,location,missing-method",
        "visitation,samc,missing,location,location,numeric-method",
        "visitation,samc,missing,location,missing,missing-method",
        "visitation,samc,missing,location,missing,numeric-method",
        "visitation,samc,missing,missing,location,missing-method",
        "visitation,samc,missing,missing,location,numeric-method",
        "visitation,samc,missing,missing,missing,missing-method",
        "visitation,samc,missing,missing,missing,numeric-method"
      ]
    },
    {
      "page": "visitation_net",
      "title": "Calculate net visitation",
      "topics": [
        "visitation_net",
        "visitation_net,samc,ANY,missing,location-method",
        "visitation_net,samc,ANY,missing,missing-method",
        "visitation_net,samc,missing,location,location-method",
        "visitation_net,samc,missing,location,missing-method"
      ]
    }
  ],
  "_readme": "https://github.com/andrewmarx/samc/raw/HEAD/README.md",
  "_rundeps": [
    "boot",
    "circular",
    "lattice",
    "Matrix",
    "mvtnorm",
    "raster",
    "Rcpp",
    "RcppEigen",
    "RcppThread",
    "sp",
    "terra"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "overview.Rmd",
      "filename": "overview.html",
      "title": "Overview",
      "author": "Andrew Marx",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Background",
        "The samc-class",
        "Option 1: Maps",
        "Option 2: P Matrix",
        "Option 3: igraph",
        "Utility Functions",
        "Analytical Functions",
        "Initial State Data",
        "Built-in Example Data"
      ],
      "created": "2019-08-12 17:58:07",
      "modified": "2024-10-31 02:29:35",
      "commits": 10
    }
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  "_indexed": true,
  "_nocasepkg": "samc",
  "_universes": [
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