{
  "_id": "6a16c2a2acfb0bcc41d87ee2",
  "Package": "MetaLandSim",
  "Type": "Package",
  "Title": "Landscape and Range Expansion Simulation",
  "Version": "2.0.0",
  "Date": "2023-01-12",
  "Author": "Frederico Mestre, Fernando Canovas, Benjamin Risk, Ricardo\nPita, Antonio Mira, Pedro Beja.",
  "Maintainer": "Frederico Mestre <mestre.frederico@gmail.com>",
  "Description": "Tools to generate random landscape graphs, evaluate\nspecies occurrence in dynamic landscapes, simulate future\nlandscape occupation and evaluate range expansion when new\nempty patches are available (e.g. as a result of climate\nchange). References: Mestre, F., Canovas, F., Pita, R., Mira,\nA., Beja, P. (2016) <doi:10.1016/j.envsoft.2016.03.007>;\nMestre, F., Risk, B., Mira, A., Beja, P., Pita, R. (2017)\n<doi:10.1016/j.ecolmodel.2017.06.013>; Mestre, F., Pita, R.,\nMira, A., Beja, P. (2020) <doi:10.1186/s12898-019-0273-5>.",
  "License": "GPL (>= 2)",
  "Config/pak/sysreqs": "libgdal-dev gdal-bin libgeos-dev libglpk-dev\nlibxml2-dev libproj-dev libsqlite3-dev",
  "Repository": "https://fmestre1.r-universe.dev",
  "Date/Publication": "2025-05-02 12:15:10 UTC",
  "RemoteUrl": "https://github.com/fmestre1/metalandsim",
  "RemoteRef": "HEAD",
  "RemoteSha": "78b5d8ab6c9c325a1f1fe0c7b52d52016334acce",
  "NeedsCompilation": "no",
  "Packaged": {
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    "User": "root"
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  "_user": "fmestre1",
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  "_created": "2026-05-27T10:02:49.000Z",
  "_published": "2026-05-27T10:08:34.143Z",
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    "committer": "FMestre1 <mestre.frederico@gmail.com>",
    "message": "update readme\n",
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  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_topics": [
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    "ecology",
    "metapopulation",
    "species"
  ],
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    "accept.calculate",
    "addpoints",
    "calcmode",
    "cluster.graph",
    "cluster.id",
    "coda.create",
    "combine.chains",
    "components.graph",
    "convert.graph",
    "create.parameter.df",
    "edge.graph",
    "extract.graph",
    "ifm.missing.MCMC",
    "ifm.naive.MCMC",
    "ifm.robust.MCMC",
    "import.shape",
    "iterate.graph",
    "list.stats",
    "manage_expansion_sim",
    "manage_landscape_sim",
    "matrix.graph",
    "merge_order",
    "metrics.graph",
    "min_distance",
    "parameter.estimate",
    "plot_expansion",
    "plot_graph",
    "plotL.graph",
    "range_expansion",
    "range_raster",
    "remove.species",
    "removepoints",
    "rland.graph",
    "simulate_graph",
    "span.graph",
    "species.graph",
    "spom",
    "summary_landscape",
    "summary_metapopulation"
  ],
  "_datasets": [
    {
      "name": "cabrera",
      "title": "Modified patch occupancy data of Cabrera vole",
      "object": "cabrera",
      "file": "cabrera.rda",
      "class": [
        "metapopulation"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "landscape_change",
      "title": "Landscape loosing 5% of patches per time step",
      "object": "landscape_change",
      "file": "landscape_change.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "mc_df",
      "title": "Modified patch occupancy data of Cabrera vole as a data frame",
      "object": "mc_df",
      "file": "mc_df.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "x",
        "y",
        "area",
        "mc"
      ],
      "rows": 685,
      "table": true,
      "tojson": true
    },
    {
      "name": "occ.landscape",
      "title": "Sample landscape with one simulated occupancy snapshot",
      "object": "occ.landscape",
      "file": "occ.landscape.rda",
      "class": [
        "metapopulation"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "occ.landscape2",
      "title": "Sample landscape with 10 simulated occupancy snapshots",
      "object": "occ.landscape2",
      "file": "occ.landscape2.rda",
      "class": [
        "metapopulation"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "param1",
      "title": "Sample parameter data frame number 1",
      "object": "param1",
      "file": "param1.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "par_output"
      ],
      "rows": 4,
      "table": true,
      "tojson": true
    },
    {
      "name": "param2",
      "title": "Sample parameter data frame number 2",
      "object": "param2",
      "file": "param2.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "par_output"
      ],
      "rows": 4,
      "table": true,
      "tojson": true
    },
    {
      "name": "rg_exp",
      "title": "List with range.expansion output",
      "object": "rg_exp",
      "file": "rg_exp.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "DISTANCE",
        "OCCUPATION",
        "PROPORTION",
        "TIME STEP"
      ],
      "rows": 100,
      "table": true,
      "tojson": true
    },
    {
      "name": "rland",
      "title": "Random landscape",
      "object": "rland",
      "file": "rland.rda",
      "class": [
        "landscape"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sim.area",
      "title": "Vector of the areas for each site; here, 100 sites",
      "object": "simulatedifm",
      "file": "simulatedifm.rda",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "sim.det.20",
      "title": "Array corresponding to nsites x nyears x nvisits",
      "object": "simulatedifm",
      "file": "simulatedifm.rda",
      "class": [
        "array"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "sim.distance",
      "title": "Distance matrix between sampling sites (nsite x nsite).",
      "object": "simulatedifm",
      "file": "simulatedifm.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": {},
      "rows": 100,
      "table": true,
      "tojson": true
    },
    {
      "name": "z.sim",
      "title": "Occupancy data generated with perfect detection.",
      "object": "simulatedifm",
      "file": "simulatedifm.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": {},
      "rows": 100,
      "table": true,
      "tojson": true
    },
    {
      "name": "z.sim.20",
      "title": "Occupancy data generated with perfect detection with approximately 20% of data missing at random.",
      "object": "simulatedifm",
      "file": "simulatedifm.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": {},
      "rows": 100,
      "table": true,
      "tojson": true
    },
    {
      "name": "z.sim.20.fa",
      "title": "Occupancy data containing false absences",
      "object": "simulatedifm",
      "file": "simulatedifm.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": {},
      "rows": 100,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "MetaLandSim-package",
      "title": "Landscape And Range Expansion Simulation",
      "topics": [
        "MetaLandSim-package",
        "MetaLandSim"
      ]
    },
    {
      "page": "accept.calculate",
      "title": "Calculate acceptance rates in MCMC chains",
      "topics": [
        "accept.calculate"
      ]
    },
    {
      "page": "addpoints",
      "title": "Add a given number of patches to a landscape",
      "topics": [
        "addpoints"
      ]
    },
    {
      "page": "cabrera",
      "title": "Modified patch occupancy data of Cabrera vole",
      "topics": [
        "cabrera"
      ]
    },
    {
      "page": "calcmode",
      "title": "Function for mode estimation of a continuous variable",
      "topics": [
        "calcmode"
      ]
    },
    {
      "page": "cluster.graph",
      "title": "Delivers the number of patches per cluster",
      "topics": [
        "cluster.graph"
      ]
    },
    {
      "page": "cluster.id",
      "title": "Classify patches in clusters",
      "topics": [
        "cluster.id"
      ]
    },
    {
      "page": "coda.create",
      "title": "Create files for use with R-package coda.",
      "topics": [
        "coda.create"
      ]
    },
    {
      "page": "combine.chains",
      "title": "Combines two chains into a single chain.",
      "topics": [
        "combine.chains"
      ]
    },
    {
      "page": "components.graph",
      "title": "Number of components of a landscape",
      "topics": [
        "components.graph"
      ]
    },
    {
      "page": "convert.graph",
      "title": "Convert data frame to landscape",
      "topics": [
        "convert.graph"
      ]
    },
    {
      "page": "create.parameter.df",
      "title": "Create parameter data frame",
      "topics": [
        "create.parameter.df"
      ]
    },
    {
      "page": "edge.graph",
      "title": "Produce an edge (links) data frame",
      "topics": [
        "edge.graph"
      ]
    },
    {
      "page": "expansion",
      "title": "Class 'expansion'",
      "topics": [
        "expansion"
      ]
    },
    {
      "page": "extract.graph",
      "title": "Extract landscape from span.graph generated list",
      "topics": [
        "extract.graph"
      ]
    },
    {
      "page": "ifm.missing.MCMC",
      "title": "Estimate the 'missing' design incidence function model",
      "topics": [
        "ifm.missing.MCMC"
      ]
    },
    {
      "page": "ifm.naive.MCMC",
      "title": "Estimate the naive design incidence function model",
      "topics": [
        "ifm.naive.MCMC"
      ]
    },
    {
      "page": "ifm.robust.MCMC",
      "title": "Estimate the robust design incidence function model",
      "topics": [
        "ifm.robust.MCMC"
      ]
    },
    {
      "page": "import.shape",
      "title": "Import a shapefile",
      "topics": [
        "import.shape"
      ]
    },
    {
      "page": "iterate.graph",
      "title": "Simulate landscape series occupation",
      "topics": [
        "iterate.graph"
      ]
    },
    {
      "page": "landscape",
      "title": "Class 'landscape'",
      "topics": [
        "landscape"
      ]
    },
    {
      "page": "landscape_change",
      "title": "Landscape loosing 5% of patches per time step",
      "topics": [
        "landscape_change"
      ]
    },
    {
      "page": "list.stats",
      "title": "Returning information on a dynamic landscape list",
      "topics": [
        "list.stats"
      ]
    },
    {
      "page": "manage_expansion_sim",
      "title": "Simulate range expansion simulation",
      "topics": [
        "manage_expansion_sim"
      ]
    },
    {
      "page": "manage_landscape_sim",
      "title": "Batch landscape simulation",
      "topics": [
        "manage_landscape_sim"
      ]
    },
    {
      "page": "matrix.graph",
      "title": "Returning a matrix with information on connections between patches",
      "topics": [
        "matrix.graph"
      ]
    },
    {
      "page": "mc_df",
      "title": "Modified patch occupancy data of Cabrera vole as a data frame",
      "topics": [
        "mc_df"
      ]
    },
    {
      "page": "merge_order",
      "title": "Internal functions for the MetaLandSim package.",
      "topics": [
        "merge_order"
      ]
    },
    {
      "page": "metapopulation",
      "title": "Class 'metapopulation'",
      "topics": [
        "metapopulation"
      ]
    },
    {
      "page": "metrics.graph",
      "title": "Computes landscape connectivity metrics",
      "topics": [
        "metrics.graph"
      ]
    },
    {
      "page": "min_distance",
      "title": "Computes topological distance",
      "topics": [
        "min_distance"
      ]
    },
    {
      "page": "occ.landscape",
      "title": "Sample landscape with one simulated occupancy snapshot",
      "topics": [
        "occ.landscape"
      ]
    },
    {
      "page": "occ.landscape2",
      "title": "Sample landscape with 10 simulated occupancy snapshots",
      "topics": [
        "occ.landscape2"
      ]
    },
    {
      "page": "param1",
      "title": "Sample parameter data frame number 1",
      "topics": [
        "param1"
      ]
    },
    {
      "page": "param2",
      "title": "Sample parameter data frame number 2",
      "topics": [
        "param2"
      ]
    },
    {
      "page": "parameter.estimate",
      "title": "Estimate parameters",
      "topics": [
        "parameter.estimate"
      ]
    },
    {
      "page": "plot_expansion",
      "title": "Graphical display of the expansion simulations",
      "topics": [
        "plot_expansion"
      ]
    },
    {
      "page": "plot_graph",
      "title": "Graphical display of the landscape",
      "topics": [
        "plot_graph"
      ]
    },
    {
      "page": "plotL.graph",
      "title": "Plot one landscape of the list created by span.graph",
      "topics": [
        "plotL.graph"
      ]
    },
    {
      "page": "range_expansion",
      "title": "Computes a range expansion model",
      "topics": [
        "range_expansion"
      ]
    },
    {
      "page": "range_raster",
      "title": "Probability of occupancy, dispersal model",
      "topics": [
        "range_raster"
      ]
    },
    {
      "page": "remove.species",
      "title": "Remove the species occupancy from the landscape",
      "topics": [
        "remove.species"
      ]
    },
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