{
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  "Package": "bamm",
  "Title": "Species Distribution Models as a Function of Biotic, Abiotic and\nMovement Factors (BAM)",
  "Version": "0.7.1",
  "Authors@R": "c(\nperson(\"Luis\", \"Osorio-Olvera\",\nemail = \"luismurao@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-0701-5398\")),\nperson(\"Jorge\", \"Soberón\",\nemail = \"soberon@ku.edu\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-2160-4148\")),\nperson(\"Rusby G.\", \"Contreras-Díaz\",\nemail = \"rusby.contreras.diaz@gmail.com\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-0569-8984\"))\n)",
  "Maintainer": "Luis Osorio-Olvera <luismurao@gmail.com>",
  "Description": "Species Distribution Modeling (SDM) is a practical\nmethodology that aims to estimate the area of distribution of a\nspecies. However, most of the work has focused on estimating\nstatic expressions of the correlation between environmental\nvariables. The outputs of correlative species distribution\nmodels can be interpreted as maps of the suitable environment\nfor a species but not generally as maps of its actual\ndistribution.  Soberón and Peterson (2005)\n<doi:10.17161/bi.v2i0.4> presented the BAM scheme, a heuristic\nframework that states that the occupied area of a species\noccurs on sites that have been accessible through dispersal (M)\nand have both favorable biotic (B) and abiotic conditions (A).\nThe 'bamm' package implements classes and functions to operate\non each element of the BAM and by using a cellular automata\nmodel where the occupied area of a species at time t is\nestimated by the multiplication of three binary matrices: one\nmatrix represents movements (M), another abiotic -niche-\ntolerances (A), and a third, biotic interactions (B).  The\ntheoretical background of the package can be found in Soberón\nand Osorio-Olvera (2023) <doi:10.1111/jbi.14587>.",
  "License": "GPL (>= 3)",
  "URL": "https://luismurao.github.io/bamm/",
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  "Packaged": {
    "Date": "2026-10-13 10:38:18 UTC",
    "User": "root"
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  "Author": "Luis Osorio-Olvera [aut, cre]\n(<https://orcid.org/0000-0003-0701-5398>), Jorge Soberón [aut]\n(<https://orcid.org/0000-0003-2160-4148>), Rusby G.\nContreras-Díaz [ctb] (<https://orcid.org/0000-0002-0569-8984>)",
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  "Repository": "https://luismurao.r-universe.dev",
  "Date/Publication": "2026-04-14 19:15:05 UTC",
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    "bam_sim",
    "bam_ssim",
    "bioindex",
    "bioindex_sparse",
    "community_sim",
    "csd",
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    "diversity_range_analysis",
    "eigen_bam",
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    "model2sparse",
    "models2pam",
    "null_dispersion_field_distribution",
    "occs2sparse",
    "pam",
    "pam2bioindex",
    "pam2richness",
    "permute_pam",
    "plot",
    "pol2pam",
    "predict",
    "sdm_sim",
    "setA",
    "shape2Grid",
    "show",
    "sim2Animation",
    "sim2Raster"
  ],
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    {
      "page": "adj_mat",
      "title": "adj_mat: Function to compute the adjacency matrix of an area.",
      "topics": [
        "adj_mat"
      ]
    },
    {
      "page": "bam_clusters",
      "title": "bam_clusters: Function to estimate the connectivity of suitable areas",
      "topics": [
        "bam_clusters"
      ]
    },
    {
      "page": "bam_sim",
      "title": "bam_sim: Simulate dispersal dynamics using the set B of the BAM framework.",
      "topics": [
        "bam_sim"
      ]
    },
    {
      "page": "bam_ssim",
      "title": "bam_ssim: Simulate dispersal dynamics using the set B of the BAM framework.",
      "topics": [
        "bam_ssim"
      ]
    },
    {
      "page": "bam-class",
      "title": "Class 'bam' digram",
      "topics": [
        "bam",
        "bam-class"
      ]
    },
    {
      "page": "bioindex_sparse-class",
      "title": "Class 'bioindex_sparse'",
      "topics": [
        "biodiversity_index_sparse",
        "bioindex_sparse",
        "bioindex_sparse-class"
      ]
    },
    {
      "page": "bioindex-class",
      "title": "Class 'bioindex'",
      "topics": [
        "biodiversity_index",
        "bioindex",
        "bioindex-class"
      ]
    },
    {
      "page": "community_sim",
      "title": "community_bam: Community 'bamm'",
      "topics": [
        "community_sim"
      ]
    },
    {
      "page": "community_sim-class",
      "title": "Class 'community_sim' digram",
      "topics": [
        "community-class",
        "community_bam",
        "community_sim-class"
      ]
    },
    {
      "page": "csd_estimate",
      "title": "csd_estimate: Estimate the connectivity suitability and dispersal plot",
      "topics": [
        "csd_estimate"
      ]
    },
    {
      "page": "csd-class",
      "title": "Class 'csd'",
      "topics": [
        "csd",
        "csd-class"
      ]
    },
    {
      "page": "csim2pam",
      "title": "csim2pam: Converts community simulation to a Presence Absence Matrix (PAM)",
      "topics": [
        "csim2pam"
      ]
    },
    {
      "page": "diversity_range_analysis",
      "title": "range_diversity_analysis: diversity analysis",
      "topics": [
        "diversity_range_analysis"
      ]
    },
    {
      "page": "diversity_range-class",
      "title": "Class 'diversity_range'",
      "topics": [
        "diversityrange",
        "diversity_range",
        "diversity_range-class"
      ]
    },
    {
      "page": "eigen_bam",
      "title": "eigen_bam: Compute the Eigen system of two bam objects",
      "topics": [
        "eigen_bam"
      ]
    },
    {
      "page": "g_area-class",
      "title": "S4 Class Hierarchy for BAM (Biotic-Abiotic-Movement) Modeling",
      "topics": [
        "g_area",
        "g_area-class"
      ]
    },
    {
      "page": "jaccard",
      "title": "jaccard: Estimates the Jaccard index for comparing two binary maps",
      "topics": [
        "jaccard"
      ]
    },
    {
      "page": "leaflet-class",
      "title": "Class 'leaflet' leaflet",
      "topics": [
        "leaflet",
        "leaflet-class"
      ]
    },
    {
      "page": "model2sparse",
      "title": "model2sparse: Converts a niche model into a diagonal sparse matrix",
      "topics": [
        "model2sparse"
      ]
    },
    {
      "page": "models2pam",
      "title": "models2pam: Converts binary rasters to a PAM",
      "topics": [
        "models2pam"
      ]
    },
    {
      "page": "null_dispersion_field_distribution",
      "title": "null_dispersion_field_distribution: Null distribution of the dispersion field",
      "topics": [
        "null_dispersion_field_distribution"
      ]
    },
    {
      "page": "occs2sparse",
      "title": "occs2sparse: Converts occurrence data into a sparse matrix object",
      "topics": [
        "occs2sparse"
      ]
    },
    {
      "page": "pam-class",
      "title": "Class 'pam' Presence-Absence Matrix",
      "topics": [
        "PAM",
        "pam",
        "pam-class"
      ]
    },
    {
      "page": "pam2bioindex",
      "title": "pam2bioindex: PAM to biodiversity index",
      "topics": [
        "pam2bioindex"
      ]
    },
    {
      "page": "pam2richness",
      "title": "pam2richness: Converts Presence Absence Matrix (pam object) to richness raster",
      "topics": [
        "pam2richness"
      ]
    },
    {
      "page": "permute_pam",
      "title": "permute_pam: Function to permute a Presence-Absence-Matrix.",
      "topics": [
        "permute_pam"
      ]
    },
    {
      "page": "plot",
      "title": "Plot method for objects of class diversity_range 'bamm'.",
      "topics": [
        "plot,diversity_range,ANY-method"
      ]
    },
    {
      "page": "pol2pam",
      "title": "Convert distribution polygons to a presence-absence matrix (PAM)",
      "topics": [
        "pol2pam"
      ]
    },
    {
      "page": "predict",
      "title": "Predict method of the package 'bamm'.",
      "topics": [
        "bam-method",
        "predict",
        "predict,bam-method"
      ]
    },
    {
      "page": "sdm_sim",
      "title": "sdm_sim: Simulate single species dispersal dynamics using the BAM framework.",
      "topics": [
        "sdm_sim"
      ]
    },
    {
      "page": "setA",
      "title": "Class for the A (Abiotic) Set of BAM Diagram",
      "topics": [
        "A-class",
        "setA",
        "setA-class"
      ]
    },
    {
      "page": "setM-class",
      "title": "Class for the M set of the 'bamm' diagram",
      "topics": [
        "M-class",
        "setM",
        "setM-class"
      ]
    },
    {
      "page": "shape2Grid",
      "title": "shape2Grid: Function to create a grid given a spatial polygon",
      "topics": [
        "shape2Grid"
      ]
    },
    {
      "page": "show",
      "title": "Show information in setA class 'bamm'.",
      "topics": [
        "show,bioindex_sparse-method",
        "show,csd-method",
        "show,diversity_range-method",
        "show,pam-method",
        "show,setA-method",
        "show,setM-method"
      ]
    },
    {
      "page": "sim2Animation",
      "title": "sim2Animation: Animate BAM simulation object.",
      "topics": [
        "sim2Animation"
      ]
    },
    {
      "page": "sim2Raster",
      "title": "sim2Raster: Convert a BAM simulation object to RasterStack",
      "topics": [
        "sim2Raster"
      ]
    }
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