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  "Title": "Species Distribution Modelling",
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  "Date": "2025-09-24",
  "Authors@R": "c(person(given = \"Babak\",\nfamily = \"Naimi\",\nrole = c(\"aut\", \"cre\"),\nemail = \"naimi.b@gmail.com\",\ncomment = c(ORCID = \"0000-0001-5431-2729\")),\nperson(given = c(\"Miguel\", \"B.\"),\nfamily = \"Araujo\",\nrole = \"aut\"))",
  "Description": "An extensible framework for developing species\ndistribution models using individual and community-based\napproaches, generate ensembles of models, evaluate the models,\nand predict species potential distributions in space and time.\nFor more information, please check the following paper: Naimi,\nB., Araujo, M.B. (2016) <doi:10.1111/ecog.01881>.",
  "License": "GPL (>= 3)",
  "URL": "https://www.biogeoinformatics.org",
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  "Repository": "https://babaknaimi.r-universe.dev",
  "Date/Publication": "2025-09-24 16:34:08 UTC",
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  "Author": "Babak Naimi [aut, cre] (ORCID: <https://orcid.org/0000-0001-5431-2729>),\nMiguel B. Araujo [aut]",
  "Maintainer": "Babak Naimi <naimi.b@gmail.com>",
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    "getmethod",
    "getmethodNames",
    "getModelId",
    "getModelInfo",
    "getModelObject",
    "getReplication",
    "getResponseCurve",
    "getRoc",
    "getThreshold",
    "getVarImp",
    "gui",
    "installAll",
    "niche",
    "nicheSimilarity",
    "pa",
    "pca",
    "rcurve",
    "read.sdm",
    "roc",
    "sdm",
    "sdmAdapt",
    "sdmData",
    "sdmSetting",
    "threshold",
    "write.sdm"
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      "page": "add",
      "title": "Add a new method to the package",
      "topics": [
        "add",
        "add,list,character-method",
        "getmethod",
        "getmethod,character-method",
        "getmethodNames",
        "getmethodNames,ANY-method"
      ]
    },
    {
      "page": "aoa",
      "title": "Area of Applicability",
      "topics": [
        "aoa",
        "aoa,SpatRaster,sdmdata-method",
        "aoa,SpatRaster,sdmModels-method"
      ]
    },
    {
      "page": "arithm",
      "title": "Combine (merge) two sdmModels into a single object",
      "topics": [
        "+,sdmModels,sdmModels-method",
        "Arith-methods"
      ]
    },
    {
      "page": "as.data.frame",
      "title": "Get a data.frame with record id values (rID)",
      "topics": [
        "as.data.frame",
        "as.data.frame,sdmdata-method"
      ]
    },
    {
      "page": "background",
      "title": "Generates background (pseudo-absence) records",
      "topics": [
        "background",
        "background,Raster-method",
        "background,SpatRaster-method"
      ]
    },
    {
      "page": "boxplot",
      "title": "boxplot",
      "topics": [
        "boxplot",
        "boxplot,sdmEvaluate-method"
      ]
    },
    {
      "page": "calibration",
      "title": "Calibration",
      "topics": [
        "calibration",
        "calibration,sdmEvaluate,missing-method",
        "calibration,vector,vector-method"
      ]
    },
    {
      "page": "coordinates",
      "title": "Get or set spatial coordinates of species data",
      "topics": [
        "coords",
        "coords,sdmdata-method",
        "coords,sdmModels-method",
        "coords<-",
        "coords<-,sdmdata-method"
      ]
    },
    {
      "page": "density",
      "title": "density",
      "topics": [
        "density",
        "density,sdmEvaluate-method"
      ]
    },
    {
      "page": "ensemble",
      "title": "Ensemble Forecasting of SDMs",
      "topics": [
        "ensemble",
        "ensemble,sdmModels,data.frame-method",
        "ensemble,sdmModels,Raster-method",
        "ensemble,sdmModels,SpatRaster-method",
        "ensemble,sdmModels-method"
      ]
    },
    {
      "page": "evaluates",
      "title": "evaluate for accuracy",
      "topics": [
        "evaluates",
        "evaluates,sdmdata,RasterLayer-method",
        "evaluates,sdmdata,SpatRaster-method",
        "evaluates,sdmModels,missing-method",
        "evaluates,sdmModels,SpatRaster-method",
        "evaluates,vector,vector-method",
        "getEvaluation",
        "getEvaluation,sdmModels-method",
        "getReplication",
        "getReplication,sdmModels-method",
        "show,sdmEvaluate-method"
      ]
    },
    {
      "page": "extractIndex",
      "title": "Indexing to extract records of a sdmdata object",
      "topics": [
        "[,sdmdata,ANY,ANY-method",
        "[,sdmdata,missing,missing-method"
      ]
    },
    {
      "page": "featuresFrame-class",
      "title": "featureFrame class",
      "topics": [
        "featuresFrame-class"
      ]
    },
    {
      "page": "getModelInfo",
      "title": "Get information/modelIDs relevant to fitted models in a sdmModels object",
      "topics": [
        "getModelId",
        "getModelId,sdmModels-method",
        "getModelInfo",
        "getModelInfo,sdmModels-method",
        "getModelObject",
        "getModelObject,sdmModels-method"
      ]
    },
    {
      "page": "varImportance",
      "title": "variable importance",
      "topics": [
        "getVarImp",
        "getVarImp,sdmModels-method"
      ]
    },
    {
      "page": "gui",
      "title": "Graphical User Interface",
      "topics": [
        "gui",
        "gui,sdmModels-method"
      ]
    },
    {
      "page": "installAll",
      "title": "Install all packages that may be required by the package",
      "topics": [
        "installAll",
        "installAll,ANY-method"
      ]
    },
    {
      "page": "names",
      "title": "Names of species",
      "topics": [
        "names",
        "names,sdmdata-method",
        "names<-",
        "names<-,sdmdata-method"
      ]
    },
    {
      "page": "niche",
      "title": "Generate and plot Ecological Niche",
      "topics": [
        "niche",
        "niche,RasterStackBrick,RasterLayer-method",
        "niche,RasterStackBrick,sdmdata-method",
        "niche,RasterStackBrick,SpatialPoints-method",
        "niche,sdmdata,ANY-method",
        "niche,SpatRaster,sdmdata-method",
        "niche,SpatRaster,SpatRaster-method",
        "niche,SpatRaster,SpatVector-method",
        "plot,.nicheRaster-method",
        "plot,.nicheSpatRaster-method"
      ]
    },
    {
      "page": "nicheSimilarity",
      "title": "Niche Similarity",
      "topics": [
        "nicheSimilarity",
        "nicheSimilarity,.nicheSpatRaster,.nicheSpatRaster-method",
        "nicheSimilarity,SpatRaster,missing-method",
        "nicheSimilarity,SpatRaster,SpatRaster-method"
      ]
    },
    {
      "page": "pa",
      "title": "Converting probability of occurrence to presence-absence",
      "topics": [
        "pa",
        "pa,SpatRaster,numeric-method",
        "pa,SpatRaster,sdmdata-method",
        "pa,SpatRaster,sdmModels-method"
      ]
    },
    {
      "page": "pca",
      "title": "Principle Components Analysis",
      "topics": [
        "pca",
        "pca,data.frame-method",
        "pca,RasterStackBrick-method",
        "pca,sdmdata-method",
        "pca,SpatRaster-method",
        "princomp-class"
      ]
    },
    {
      "page": "predict",
      "title": "sdm model prediction",
      "topics": [
        "predict",
        "predict,.maxlikeModel-method",
        "predict,sdmModels-method"
      ]
    },
    {
      "page": "response",
      "title": "Generate and plot response curves",
      "topics": [
        "getResponseCurve",
        "getResponseCurve,sdmModels-method",
        "plot,.responseCurve-method",
        "rcurve",
        "rcurve,.responseCurve-method",
        "rcurve,sdmModels-method"
      ]
    },
    {
      "page": "read.sdm",
      "title": "read/write sdm* object from/to a file",
      "topics": [
        "read.sdm",
        "read.sdm,character-method",
        "write.sdm",
        "write.sdm,.sdmCorSetting,character-method",
        "write.sdm,sdmdata,character-method",
        "write.sdm,sdmModels,character-method"
      ]
    },
    {
      "page": "roc",
      "title": "plot ROC curves",
      "topics": [
        "getRoc",
        "getRoc,sdmModels,ANY-method",
        "getRoc,vector,vector-method",
        "roc",
        "roc,sdmModels,ANY-method",
        "roc,sdmModels-method",
        "roc,vector,vector-method"
      ]
    },
    {
      "page": "sdm",
      "title": "Fit and evaluate species distribution models",
      "topics": [
        "sdm",
        "sdm,ANY,sdmdata,.sdmCorSetting-method",
        "sdm,ANY,sdmdata,character-method",
        "sdm,sdmdata,.sdmCorSetting,ANY-method"
      ]
    },
    {
      "page": "adapt",
      "title": "Adapting sdm* objects in the new version",
      "topics": [
        "sdmAdapt",
        "sdmAdapt,sdmdata-method",
        "sdmAdapt,sdmModels-method"
      ]
    },
    {
      "page": "sdmCorrelativeMethod-class",
      "title": "sdmCorrelativeMethod class",
      "topics": [
        "sdmCorrelativeMethod-class"
      ]
    },
    {
      "page": "sdmData",
      "title": "Creating sdmdata object",
      "topics": [
        "sdmData",
        "sdmData,ANY,data.frame,missing,missing-method",
        "sdmData,ANY,data.frame,missing-method",
        "sdmData,ANY,data.frame,SpatRaster-method",
        "sdmData,ANY,SpatialPoints,missing-method",
        "sdmData,ANY,SpatialPoints,Raster-method",
        "sdmData,ANY,SpatVector,SpatRaster-method",
        "sdmData,data.frame,formula,missing-method",
        "sdmData,data.frame,missing,missing-method"
      ]
    },
    {
      "page": "sdmdata-class",
      "title": "An S4 class representing sdm dataset",
      "topics": [
        "sdmdata-class",
        "show,sdmdata-method"
      ]
    },
    {
      "page": "sdmModel-class",
      "title": "sdmModels classes",
      "topics": [
        ".pcaObject-class",
        "characterORmissing-class",
        "characterORnull-class",
        "CRSorNULL-class",
        "data.frameORmatrix-class",
        "data.frameORnull-class",
        "environmentORnull-class",
        "expressionORnull-class",
        "formulaORnull-class",
        "functionORcharacter-class",
        "functionORnull-class",
        "integerORnull-class",
        "listORcharacter-class",
        "listORnull-class",
        "matrixORnull-class",
        "numericORnull-class",
        "sdmEvaluate-class",
        "sdmFormula-class",
        "sdmModels-class",
        "show,sdmModels-method"
      ]
    },
    {
      "page": "sdmSetting",
      "title": "creating sdmSetting object",
      "topics": [
        "sdmSetting",
        "sdmSetting,ANY,sdmdata,character-method",
        "show,sdmSetting-method"
      ]
    },
    {
      "page": "subset",
      "title": "Subset models in a sdmModels object",
      "topics": [
        "subset",
        "subset,sdmModels-method",
        "[[,sdmModels,ANY,ANY-method"
      ]
    },
    {
      "page": "threshold",
      "title": "Identifying/extracting the best threshold to convert probabilities to presence-absence",
      "topics": [
        "getThreshold",
        "getThreshold,sdmModels,character-method",
        "getThreshold,sdmModels,numeric-method",
        "threshold",
        "threshold,sdmModels,character-method",
        "threshold,sdmModels,numeric-method"
      ]
    }
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  "_readme": "https://github.com/babaknaimi/sdm/raw/HEAD/README.md",
  "_rundeps": [
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      "source": "quick_sdm.pdf.asis",
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        "Installing sdm and all the required packages",
        "A brief overview:",
        "Example Dataset:",
        "Data preparation",
        "Model Fitting and Evaluation",
        "Prediction",
        "Ensemble forecasting",
        "Reference"
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      "modified": "2018-04-05 16:12:15",
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