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"bm_CrossValidation_random,BIOMOD.formated.data.PA-method", "bm_CrossValidation_strat", "bm_CrossValidation_strat,BIOMOD.formated.data-method", "bm_CrossValidation_strat,BIOMOD.formated.data.PA-method", "bm_CrossValidation_user.defined", "bm_CrossValidation_user.defined,BIOMOD.formated.data-method", "bm_CrossValidation_user.defined,BIOMOD.formated.data.PA-method" ] }, { "page": "bm_FindOptimStat", "title": "Calculate the best score according to a given evaluation method", "concept": [ "Secondary functions" ], "topics": [ "bm_CalculateStatAbun", "bm_CalculateStatAbund", "bm_CalculateStatBin", "bm_FindOptimStat", "get_optim_value" ] }, { "page": "bm_MakeFormula", "title": "Standardized formula maker", "concept": [ "Secondary functions" ], "topics": [ "bm_MakeFormula" ] }, { "page": "bm_ModelAnalysis", "title": "Analyze the residuals of the single models", "concept": [ "Plot functions", "Secondary functions" ], "topics": [ "bm_ModelAnalysis" ] }, { "page": "bm_ModelingOptions", "title": "Configure the modeling options for each selected model", "concept": [ "Secondary functions" ], "topics": [ "bm_ModelingOptions" ] }, { "page": "bm_PlotEvalBoxplot", "title": "Plot boxplot of evaluation scores", "concept": [ "Plot functions", "Secondary functions" ], "topics": [ "bm_PlotEvalBoxplot" ] }, { "page": "bm_PlotEvalMean", "title": "Plot mean evaluation scores", "concept": [ "Plot functions", "Secondary functions" ], "topics": [ "bm_PlotEvalMean" ] }, { "page": "bm_PlotRangeSize", "title": "Plot species range change", "concept": [ "Plot functions", "Secondary functions" ], "topics": [ "bm_PlotRangeSize" ] }, { "page": "bm_PlotResponseCurves", "title": "Plot response curves", "concept": [ "Plot functions", "Secondary functions" ], "topics": [ "bm_PlotResponseCurves" ] }, { "page": "bm_PlotVarImpBoxplot", "title": "Plot boxplot of variables importance", "concept": [ "Plot functions", "Secondary functions" ], "topics": [ "bm_PlotVarImpBoxplot" ] }, { "page": "bm_PseudoAbsences", "title": "Select pseudo-absences", "concept": [ "Secondary functions" ], "topics": [ "bm_PseudoAbsences", "bm_PseudoAbsences_disk", "bm_PseudoAbsences_disk,ANY,SpatRaster-method", "bm_PseudoAbsences_disk,ANY,SpatVector-method", "bm_PseudoAbsences_random", "bm_PseudoAbsences_random,ANY,SpatRaster-method", "bm_PseudoAbsences_random,ANY,SpatVector-method", "bm_PseudoAbsences_sre", "bm_PseudoAbsences_sre,ANY,SpatRaster-method", "bm_PseudoAbsences_sre,ANY,SpatVector-method", "bm_PseudoAbsences_user.defined", "bm_PseudoAbsences_user.defined,ANY,SpatRaster-method", "bm_PseudoAbsences_user.defined,ANY,SpatVector-method" ] }, { "page": "bm_RangeSize", "title": "Analyze the range size differences between projections of species distribution models", "concept": [ "Secondary functions" ], "topics": [ "bm_RangeSize", "bm_RangeSize,data.frame,data.frame-method", "bm_RangeSize,SpatRaster,SpatRaster-method" ] }, { "page": "bm_RunModelsLoop", "title": "Loop to compute all single species distribution models", "concept": [ "Secondary functions" ], "topics": [ "bm_RunModel", "bm_RunModelsLoop" ] }, { "page": "bm_SampleBinaryVector", "title": "Sample binary vector", "concept": [ "Secondary functions" ], "topics": [ "bm_SampleBinaryVector" ] }, { "page": "bm_SampleFactorLevels", "title": "Sample all levels of a factorial variable", "concept": [ "Secondary functions" ], "topics": [ "bm_SampleFactorLevels", "bm_SampleFactorLevels.data.frame", "bm_SampleFactorLevels.raster" ] }, { "page": "bm_SRE", "title": "Surface Range Envelope", "concept": [ "Secondary functions" ], "topics": [ "bm_SRE" ] }, { "page": "bm_Tuning", "title": "Tune models parameters", "concept": [ "Secondary functions" ], "topics": [ "bm_Tuning" ] }, { "page": "bm_VariablesImportance", "title": "Variables' importance calculation", "concept": [ "Secondary functions" ], "topics": [ "bm_VariablesImportance" ] }, { "page": "DataSpecies", "title": "Presence-Absence data to build test SDM", "topics": [ "DataSpecies" ] }, { "page": "DataSTOC", "title": "Abundance to build test SDM", "topics": [ "DataSTOC" ] }, { "page": "getters.bm", "title": "Functions to extract informations from 'biomod2_model' objects", "concept": [ "Toolbox functions" ], "topics": [ "getters.bm", "get_formal_model", "get_formal_model,biomod2_model-method", "get_scaling_model", "get_scaling_model,biomod2_model-method" ] }, { "page": "getters.out", "title": "Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects", "concept": [ "Toolbox functions" ], "topics": [ "free", "free,BIOMOD.projection.out-method", "getters.out", "get_built_models", "get_built_models,BIOMOD.ensemble.models.out-method", "get_built_models,BIOMOD.models.out-method", "get_calib_lines", "get_calib_lines,BIOMOD.models.out-method", "get_evaluations", "get_evaluations,BIOMOD.ensemble.models.out-method", "get_evaluations,BIOMOD.models.out-method", "get_eval_data", "get_eval_data,BIOMOD.formated.data-method", "get_formal_data", "get_formal_data,BIOMOD.ensemble.models.out-method", "get_formal_data,BIOMOD.models.out-method", "get_kept_models", "get_kept_models,BIOMOD.ensemble.models.out-method", "get_options", "get_options,BIOMOD.models.out-method", "get_predictions", "get_predictions,BIOMOD.ensemble.models.out-method", "get_predictions,BIOMOD.models.out-method", "get_predictions,BIOMOD.projection.out-method", "get_projected_models", "get_projected_models,BIOMOD.projection.out-method", "get_species_data", "get_species_data,BIOMOD.formated.data-method", "get_species_data,BIOMOD.formated.data.PA-method", "get_variables_importance", "get_variables_importance,BIOMOD.ensemble.models.out-method", "get_variables_importance,BIOMOD.models.out-method" ] }, { "page": "load_stored_object", "title": "Functions to load 'BIOMOD.stored.data' objects", "concept": [ "Toolbox functions" ], "topics": [ "load_stored_object", "load_stored_object,BIOMOD.stored.data-method", "load_stored_object,BIOMOD.stored.SpatRaster-method" ] }, { "page": "ModelsTable", "title": "Single models package and functions", "topics": [ "ModelsTable" ] }, { "page": "ODMAP", "title": "ODMAP empty table", "topics": [ "ODMAP" ] }, { "page": "OptionsBigboss", "title": "Bigboss pre-defined parameter values for single models", "topics": [ "OptionsBigboss" ] }, { "page": "plot", "title": "'plot' method for 'BIOMOD.formated.data' and 'BIOMOD.formated.data.PA' object class", "topics": [ "plot,BIOMOD.formated.data,missing-method" ] }, { "page": "predict.bm", "title": "Functions to get predictions from 'biomod2_model' objects", "concept": [ "Toolbox functions" ], "topics": [ "predict,biomod2_model-method", "predict.biomod2_model", "predict.bm" ] }, { "page": "predict.em", "title": "Functions to get predictions from 'biomod2_ensemble_model' objects", "concept": [ "Toolbox functions" ], "topics": [ "predict.em" ] }, { "page": "setters", "title": "Functions to change the place of the different biomod2 objects", "concept": [ "Toolbox functions" ], "topics": [ "setters", "set_new_dirname", "set_new_dirname,BIOMOD.ensemble.models.out-method", "set_new_dirname,BIOMOD.models.out-method", "set_new_dirname,BIOMOD.projection.out-method" ] }, { "page": "summary", "title": "'summary' method for 'BIOMOD.formated.data' object class", "topics": [ "summary,BIOMOD.formated.data-method" ] } ], "_readme": "https://github.com/biomodhub/biomod2/raw/HEAD/README.md", "_rundeps": [ "abind", "cli", "codetools", "cpp11", "dplyr", "farver", "foreach", "gbm", "generics", "ggplot2", "glue", "gtable", "isoband", "iterators", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "pillar", "pkgconfig", "plyr", "PresenceAbsence", "pROC", "R6", "RColorBrewer", "Rcpp", "reshape", "reshape2", "rlang", "rpart", "S7", "scales", "sp", "stringi", "stringr", "survival", "terra", "tibble", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], 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