{
  "_id": "6a2530874b233be198395c3e",
  "Package": "SSDM",
  "Type": "Package",
  "Title": "Stacked Species Distribution Modelling",
  "Version": "0.2.9",
  "Author": "Sylvain Schmitt, Robin Pouteau, Dimitri Justeau, Florian de\nBoissieu, Lukas Baumbach, Philippe Birnbaum",
  "Maintainer": "Sylvain Schmitt <sylvain.m.schmitt@gmail.com>",
  "URL": "https://github.com/sylvainschmitt/SSDM",
  "BugReports": "https://github.com/sylvainschmitt/SSDM/issues",
  "Description": "Allows to map species richness and endemism based on\nstacked species distribution models (SSDM). Individuals SDMs\ncan be created using a single or multiple algorithms (ensemble\nSDMs). For each species, an SDM can yield a habitat suitability\nmap, a binary map, a between-algorithm variance map, and can\nassess variable importance, algorithm accuracy, and between-\nalgorithm correlation. Methods to stack individual SDMs include\nsumming individual probabilities and thresholding then summing.\nThresholding can be based on a specific evaluation metric or by\ndrawing repeatedly from a Bernoulli distribution. The SSDM\npackage also provides a user-friendly interface.",
  "License": "GPL (>=3) | file LICENSE",
  "LazyData": "TRUE",
  "Collate": "'SDM.R' 'Algorithm.SDM.R' 'Ensemble.SDM.R' 'Env.R'\n'Occurrences.R' 'PA.select.R' 'SSDM.R' 'Stacked.SDM.R'\n'accuracy.R' 'checkargs.R' 'data.values.R' 'ensemble.R'\n'optim.thresh.R' 'evaluate.R' 'modelling.R'\n'ensemble_modelling.R' 'evaluate.axes.R' 'get_PA.R'\n'get_model.R' 'gui.R' 'load_model.R' 'load_occ.R' 'load_var.R'\n'mapDiversity.R' 'plot.model.R' 'project.R' 'save.model.R'\n'stack_modelling.R' 'stacking.R' 'update.stack.R'\n'utils-pipe.R' 'zzz.R'",
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  "Repository": "https://sylvainschmitt.r-universe.dev",
  "Date/Publication": "2025-04-11 08:54:27 UTC",
  "RemoteUrl": "https://github.com/sylvainschmitt/ssdm",
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  "_exports": [
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    "ensemble",
    "ensemble_modelling",
    "evaluate",
    "gui",
    "load_esdm",
    "load_occ",
    "load_stack",
    "load_var",
    "mapDiversity",
    "modelling",
    "plot",
    "project",
    "save.esdm",
    "save.stack",
    "stack_modelling",
    "stacking",
    "update"
  ],
  "_datasets": [
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      "name": "Env",
      "title": "A stack of three environmental variables",
      "object": "Env",
      "class": [
        "RasterStack"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "Occurrences",
      "title": "Plant occurrences data frame",
      "object": "Occurrences",
      "class": [
        "data.frame"
      ],
      "fields": [
        "SPECIES",
        "LONGITUDE",
        "LATITUDE"
      ],
      "rows": 57,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "Algorithm.SDM-class",
      "title": "An S4 class to represent an SDM based on a single algorithm",
      "topics": [
        "Algorithm.SDM-class"
      ]
    },
    {
      "page": "ensemble",
      "title": "Methods to assemble multiple algorithms in an ensemble SDM",
      "topics": [
        "ensemble",
        "ensemble,Algorithm.SDM-method",
        "sum,Algorithm.SDM-method"
      ]
    },
    {
      "page": "ensemble_modelling",
      "title": "Build an ensemble SDM that assembles multiple algorithms",
      "topics": [
        "ensemble_modelling"
      ]
    },
    {
      "page": "Ensemble.SDM-class",
      "title": "An S4 class to represent an ensemble SDM",
      "topics": [
        "Ensemble.SDM-class"
      ]
    },
    {
      "page": "Env",
      "title": "A stack of three environmental variables",
      "topics": [
        "Env"
      ]
    },
    {
      "page": "evaluate",
      "title": "Evaluate",
      "topics": [
        "evaluate",
        "evaluate,Algorithm.SDM-method",
        "evaluate,MAXENT.SDM-method",
        "evaluate,Stacked.SDM-method"
      ]
    },
    {
      "page": "gui",
      "title": "SSDM package Graphic User Interface",
      "topics": [
        "gui"
      ]
    },
    {
      "page": "load_occ",
      "title": "Load occurrence data",
      "topics": [
        "load_occ"
      ]
    },
    {
      "page": "load_var",
      "title": "Load environmental variables",
      "topics": [
        "load_var"
      ]
    },
    {
      "page": "load.model",
      "title": "Load ensemble SDMs and SSDMs.",
      "topics": [
        "load.model",
        "load_esdm",
        "load_stack"
      ]
    },
    {
      "page": "mapDiversity",
      "title": "Map Diversity",
      "topics": [
        "mapDiversity",
        "mapDiversity,Stacked.SDM-method"
      ]
    },
    {
      "page": "modelling",
      "title": "Build an SDM using a single algorithm",
      "topics": [
        "modelling"
      ]
    },
    {
      "page": "Occurrences",
      "title": "Plant occurrences data frame",
      "topics": [
        "Occurrences"
      ]
    },
    {
      "page": "plot.model",
      "title": "Plot SDMs, ensemble SDMs, and SSDMs",
      "topics": [
        "plot,SDM,ANY-method",
        "plot,Stacked.SDM,ANY-method",
        "plot.model"
      ]
    },
    {
      "page": "project",
      "title": "Project model into environment",
      "topics": [
        "project",
        "project,Algorithm.SDM-method",
        "project,Ensemble.SDM-method",
        "project,MAXENT.SDM-method",
        "project,Stacked.SDM-method"
      ]
    },
    {
      "page": "save.model",
      "title": "Save ensemble SDMs and SSDMs",
      "topics": [
        "save.esdm",
        "save.esdm,Ensemble.SDM-method",
        "save.model",
        "save.stack",
        "save.stack,Stacked.SDM-method"
      ]
    },
    {
      "page": "SSDM",
      "title": "SSDM: Stacked species distribution modelling",
      "topics": [
        "SSDM"
      ]
    },
    {
      "page": "stack_modelling",
      "title": "Build an SSDM that assembles multiple algorithms and species.",
      "topics": [
        "stack_modelling"
      ]
    },
    {
      "page": "Stacked.SDM-class",
      "title": "An S4 class to represent SSDMs",
      "topics": [
        "Stacked.SDM-class"
      ]
    },
    {
      "page": "stacking",
      "title": "Stack different ensemble SDMs in an SSDM",
      "topics": [
        "stacking",
        "stacking,Ensemble.SDM-method"
      ]
    },
    {
      "page": "update-Stacked.SDM-method",
      "title": "Update a previous SSDM",
      "topics": [
        "update,Stacked.SDM-method"
      ]
    }
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