| Global functions | |
|---|---|
| .BIOMOD.formated.data.PA | Source code |
| .BIOMOD.formated.data.check.args | Source code |
| .BIOMOD.formated.data.check_data | Source code |
| .BIOMOD.options.dataset.check.args | Source code |
| .BIOMOD.options.default.check.args | Source code |
| .BIOMOD.options.default.correct | Source code |
| .BIOMOD_EnsembleForecasting.check.args | Source code |
| .BIOMOD_EnsembleForecasting.prepare.workdir | Source code |
| .BIOMOD_EnsembleModeling.check.args | Source code |
| .BIOMOD_FormatingData.check.args | Source code |
| .BIOMOD_LoadModels.check.args | Source code |
| .BIOMOD_Modeling.check.args | Source code |
| .BIOMOD_Modeling.prepare.workdir | Source code |
| .BIOMOD_Modeling.summary | Source code |
| .BIOMOD_Projection.check.args | Source code |
| .BIOMOD_RangeSize.check.args | Source code |
| .BIOMOD_Report.check.args | Source code |
| .CompteurSp | Source code |
| .add_pa_rownames | Source code |
| .as_ggdat | Source code |
| .automatic_weights_creation | Source code |
| .avail.eval.meth.list | Source code |
| .avail.models.list | Source code |
| .bm_CrossValidation.check.args | Source code |
| .bm_FindOptimStat.check.args | Source code |
| .bm_ModelAnalysis.check.args | Source code |
| .bm_ModelingOptions.check.args | Source code |
| .bm_PlotEvalBoxplot.check.args | Source code |
| .bm_PlotEvalMean.check.args | Source code |
| .bm_PlotRangeSize.check.args | Source code |
| .bm_PlotResponseCurves.check.args | Source code |
| .bm_PlotVarImpBoxplot.check.args | Source code |
| .bm_PseudoAbsences.check.args | Source code |
| .bm_RangeSize.check.args | Source code |
| .bm_RunModel.check.args | Source code |
| .bm_SRE.check.args | Source code |
| .bm_Tuning.check.args | Source code |
| .bm_VariablesImportance.check.args | Source code |
| .bm_cat | Source code |
| .build_clamping_mask | Source code |
| .categorical2numeric | Man page Source code |
| .categorical_stack_to_terra | Source code |
| .check_calib.lines_names | Source code |
| .check_duplicated_cells | Man page Source code |
| .check_env_levels | Source code |
| .check_formating_expl.var | Source code |
| .check_formating_resp.var.abun | Source code |
| .check_formating_resp.var.bin | Source code |
| .check_formating_spatial | Source code |
| .check_formating_table | Source code |
| .check_formating_xy | Source code |
| .contingency_table_check | Source code |
| .contingency_table_ordinal | Source code |
| .convert_bin.array | Source code |
| .convert_bin.array.filt | Source code |
| .convert_bin.matrix | Source code |
| .create.crossing.points | Source code |
| .create.segments | Source code |
| .extract_modelNamesInfo | Source code |
| .extract_projlinkInfo | Source code |
| .extract_selected.layers | Source code |
| .fill_BIOMOD.models.out | Source code |
| .filter_outputs.df | Source code |
| .filter_outputs.vec | Source code |
| .find_freq_mode | Source code |
| .find_mode | Source code |
| .format_proj.df | Source code |
| .full_shuffling | Source code |
| .fun_testIf01 | Source code |
| .fun_testIfIn | Source code |
| .fun_testIfInherits | Source code |
| .fun_testIfPosInt | Source code |
| .fun_testIfPosNum | Source code |
| .fun_testMetric | Source code |
| .getOS | Source code |
| .get_categorical_names | Man page Source code |
| .get_data_mask | Source code |
| .get_env_class | Man page Source code |
| .get_formal_predictions | Source code |
| .get_kept_models | Source code |
| .get_models_assembling | Source code |
| .get_nb_available_pa_cells | Source code |
| .get_nb_true_abs | Source code |
| .get_needed_predictions | Source code |
| .get_var_range | Source code |
| .get_var_type | Source code |
| .guess_scale | Source code |
| .load_gam_namespace | Man page Source code |
| .loss.gain.nonbinary | Source code |
| .maxent.prepare.workdir | Source code |
| .numeric2factor | Source code |
| .onAttach | Source code |
| .plot.BIOMOD.formated.data.abundance | Man page Source code |
| .plot.BIOMOD.formated.data.check.args | Source code |
| .plot.BIOMOD.projection.out.check.args | Source code |
| .randomise_data | Source code |
| .run_pred | Source code |
| .sample_class | Source code |
| .sample_num | Source code |
| .scaling_model | Source code |
| .scope | Source code |
| .set_new_dirname.models | Source code |
| .sre_projection | Source code |
| .summary.BIOMOD.formated.data.check.args | Source code |
| .threshold_ordinal | Source code |
| .transform.outputs.list | Man page Source code |
| .transform.outputs.list-deprecated | Man page |
| .transform_model.as.col | Man page Source code |
| .transform_outputs_list | Source code |
| .which.data.type | Source code |
| .xgb_pred | Source code |
| ANN_biomod2_model-class | Man page |
| BIOMOD.ensemble.models.out | Man page |
| BIOMOD.ensemble.models.out-class | Man page |
| BIOMOD.formated.data | Man page |
| BIOMOD.formated.data,data.frame,ANY-method | Man page |
| BIOMOD.formated.data,numeric,SpatRaster-method | Man page |
| BIOMOD.formated.data,numeric,data.frame-method | Man page |
| BIOMOD.formated.data,numeric,matrix-method | Man page |
| BIOMOD.formated.data-class | Man page |
| BIOMOD.formated.data.PA | Man page |
| BIOMOD.formated.data.PA,numeric,SpatRaster-method | Man page |
| BIOMOD.formated.data.PA,numeric,data.frame-method | Man page |
| BIOMOD.formated.data.PA-class | Man page |
| BIOMOD.models.options | Man page |
| BIOMOD.models.options-class | Man page |
| BIOMOD.models.out | Man page |
| BIOMOD.models.out-class | Man page |
| BIOMOD.options.dataset | Man page |
| BIOMOD.options.dataset,character-method | Man page |
| BIOMOD.options.dataset-class | Man page |
| BIOMOD.options.default | Man page |
| BIOMOD.options.default,character,character-method | Man page |
| BIOMOD.options.default-class | Man page |
| BIOMOD.projection.out | Man page |
| BIOMOD.projection.out-class | Man page |
| BIOMOD.rangesize.out | Man page |
| BIOMOD.rangesize.out-class | Man page |
| BIOMOD.stored.SpatRaster-class | Man page |
| BIOMOD.stored.data | Man page |
| BIOMOD.stored.data-class | Man page |
| BIOMOD.stored.data.frame-class | Man page |
| BIOMOD.stored.files-class | Man page |
| BIOMOD.stored.formated.data-class | Man page |
| BIOMOD.stored.models.out-class | Man page |
| BIOMOD.stored.options-class | Man page |
| BIOMOD_CrossValidation | Man page Source code |
| BIOMOD_CrossValidation-deprecated | Man page |
| BIOMOD_EnsembleForecasting | Man page Source code |
| BIOMOD_EnsembleModeling | Man page Source code |
| BIOMOD_FormatingData | Man page Source code |
| BIOMOD_LoadModels | Man page Source code |
| BIOMOD_Modeling | Man page Source code |
| BIOMOD_ModelingOptions | Man page Source code |
| BIOMOD_ModelingOptions-deprecated | Man page |
| BIOMOD_PresenceOnly | Man page Source code |
| BIOMOD_PresenceOnly-deprecated | Man page |
| BIOMOD_Projection | Man page Source code |
| BIOMOD_RangeSize | Man page Source code |
| BIOMOD_Report | Man page Source code |
| BIOMOD_Report_ODMAP | Source code |
| BIOMOD_Report_code | Source code |
| BIOMOD_Report_summary | Source code |
| BIOMOD_Tuning | Man page Source code |
| BIOMOD_tuning-deprecated | Man page |
| BinaryTransformation | Man page Source code |
| BinaryTransformation-deprecated | Man page |
| CTA_biomod2_model-class | Man page |
| DNN_biomod2_model-class | Man page |
| DataSpecies | Man page |
| EMca_biomod2_model-class | Man page |
| EMci_biomod2_model-class | Man page |
| EMcv_biomod2_model-class | Man page |
| EMfreq_biomod2_model-class | Man page |
| EMmean_biomod2_model-class | Man page |
| EMmedian_biomod2_model-class | Man page |
| EMmode_biomod2_model-class | Man page |
| EMwmean_biomod2_model-class | Man page |
| FDA_biomod2_model-class | Man page |
| Find.Optim.Stat | Man page Source code |
| Find.Optim.Stat-deprecated | Man page |
| GAM_biomod2_model-class | Man page |
| GBM_biomod2_model-class | Man page |
| GLM_biomod2_model-class | Man page |
| MARS_biomod2_model-class | Man page |
| MAXENT_biomod2_model-class | Man page |
| MAXNET_biomod2_model-class | Man page |
| ModelsTable | Man page |
| ODMAP | Man page |
| OptionsBigboss | Man page |
| ProbDensFunc | Man page Source code |
| ProbDensFunc-deprecated | Man page |
| RF_biomod2_model-class | Man page |
| RFd_biomod2_model-class | Man page |
| SRE_biomod2_model-class | Man page |
| XGBOOST_biomod2_model-class | Man page |
| best_point_prg | Source code |
| bioclim_current | Man page |
| bioclim_future | Man page |
| biomod2-deprecated | Man page |
| biomod2_ensemble_model | Man page |
| biomod2_ensemble_model-class | Man page |
| biomod2_model | Man page |
| biomod2_model-class | Man page |
| bm_BinaryTransformation | Man page |
| bm_BinaryTransformation,SpatRaster-method | Man page |
| bm_BinaryTransformation,data.frame-method | Man page |
| bm_BinaryTransformation,matrix-method | Man page |
| bm_BinaryTransformation,numeric-method | Man page |
| bm_CalculateStatAbun | Man page Source code |
| bm_CalculateStatAbund | Man page |
| bm_CalculateStatBin | Man page Source code |
| bm_CrossValidation | Man page Source code |
| bm_CrossValidation_block | Man page |
| bm_CrossValidation_block,BIOMOD.formated.data-method | Man page |
| bm_CrossValidation_block,BIOMOD.formated.data.PA-method | Man page |
| bm_CrossValidation_env | Man page |
| bm_CrossValidation_env,BIOMOD.formated.data-method | Man page |
| bm_CrossValidation_env,BIOMOD.formated.data.PA-method | Man page |
| bm_CrossValidation_kfold | Man page |
| bm_CrossValidation_kfold,BIOMOD.formated.data-method | Man page |
| bm_CrossValidation_kfold,BIOMOD.formated.data.PA-method | Man page |
| bm_CrossValidation_random | Man page |
| bm_CrossValidation_random,BIOMOD.formated.data-method | Man page |
| bm_CrossValidation_random,BIOMOD.formated.data.PA-method | Man page |
| bm_CrossValidation_strat | Man page |
| bm_CrossValidation_strat,BIOMOD.formated.data-method | Man page |
| bm_CrossValidation_strat,BIOMOD.formated.data.PA-method | Man page |
| bm_CrossValidation_user.defined | Man page |
| bm_CrossValidation_user.defined,BIOMOD.formated.data-method | Man page |
| bm_CrossValidation_user.defined,BIOMOD.formated.data.PA-method | Man page |
| bm_FindOptimStat | Man page Source code |
| bm_MakeFormula | Man page Source code |
| bm_ModelAnalysis | Man page Source code |
| bm_ModelingOptions | Man page Source code |
| bm_PlotEvalBoxplot | Man page Source code |
| bm_PlotEvalMean | Man page Source code |
| bm_PlotRangeSize | Man page Source code |
| bm_PlotResponseCurves | Man page Source code |
| bm_PlotVarImpBoxplot | Man page Source code |
| bm_PseudoAbsences | Man page Source code |
| bm_PseudoAbsences_disk | Man page |
| bm_PseudoAbsences_disk,ANY,SpatRaster-method | Man page |
| bm_PseudoAbsences_disk,ANY,SpatVector-method | Man page |
| bm_PseudoAbsences_random | Man page |
| bm_PseudoAbsences_random,ANY,SpatRaster-method | Man page |
| bm_PseudoAbsences_random,ANY,SpatVector-method | Man page |
| bm_PseudoAbsences_sre | Man page |
| bm_PseudoAbsences_sre,ANY,SpatRaster-method | Man page |
| bm_PseudoAbsences_sre,ANY,SpatVector-method | Man page |
| bm_PseudoAbsences_user.defined | Man page |
| bm_PseudoAbsences_user.defined,ANY,SpatRaster-method | Man page |
| bm_PseudoAbsences_user.defined,ANY,SpatVector-method | Man page |
| bm_RangeSize | Man page |
| bm_RangeSize,SpatRaster,SpatRaster-method | Man page |
| bm_RangeSize,data.frame,data.frame-method | Man page |
| bm_RunModel | Man page Source code |
| bm_RunModelsLoop | Man page Source code |
| bm_SRE | Man page Source code |
| bm_SampleBinaryVector | Man page Source code |
| bm_SampleFactorLevels | Man page Source code |
| bm_SampleFactorLevels.SpatRaster | Source code |
| bm_SampleFactorLevels.data.frame | Man page Source code |
| bm_SampleFactorLevels.raster | Man page |
| bm_Tuning | Man page Source code |
| bm_VariablesImportance | Man page Source code |
| calc_auprg | Source code |
| calculate.stat | Man page Source code |
| calculate.stat-deprecated | Man page |
| create_prg_curve | Source code |
| ecospat.boyce | Source code |
| ecospat.mpa | Source code |
| free | Man page |
| free,BIOMOD.projection.out-method | Man page |
| getStatOptimValue | Man page Source code |
| getStatOptimValue-deprecated | Man page |
| get_built_models | Man page |
| get_built_models,BIOMOD.ensemble.models.out-method | Man page |
| get_built_models,BIOMOD.models.out-method | Man page |
| get_calib_lines | Man page |
| get_calib_lines,BIOMOD.models.out-method | Man page |
| get_eval_data | Man page |
| get_eval_data,BIOMOD.formated.data-method | Man page |
| get_evaluations | Man page |
| get_evaluations,BIOMOD.ensemble.models.out-method | Man page |
| get_evaluations,BIOMOD.models.out-method | Man page |
| get_formal_data | Man page |
| get_formal_data,BIOMOD.ensemble.models.out-method | Man page |
| get_formal_data,BIOMOD.models.out-method | Man page |
| get_formal_model | Man page |
| get_formal_model,biomod2_model-method | Man page |
| get_kept_models | Man page |
| get_kept_models,BIOMOD.ensemble.models.out-method | Man page |
| get_optim_value | Man page Source code |
| get_options | Man page |
| get_options,BIOMOD.models.out-method | Man page |
| get_predictions | Man page |
| get_predictions,BIOMOD.ensemble.models.out-method | Man page |
| get_predictions,BIOMOD.models.out-method | Man page |
| get_predictions,BIOMOD.projection.out-method | Man page |
| get_projected_models | Man page |
| get_projected_models,BIOMOD.projection.out-method | Man page |
| get_scaling_model | Man page |
| get_scaling_model,biomod2_model-method | Man page |
| get_species_data | Man page |
| get_species_data,BIOMOD.formated.data-method | Man page |
| get_species_data,BIOMOD.formated.data.PA-method | Man page |
| get_variables_importance | Man page |
| get_variables_importance,BIOMOD.ensemble.models.out-method | Man page |
| get_variables_importance,BIOMOD.models.out-method | Man page |
| getters.bm | Man page |
| getters.out | Man page |
| load_stored_object | Man page |
| load_stored_object,BIOMOD.stored.SpatRaster-method | Man page |
| load_stored_object,BIOMOD.stored.data-method | Man page |
| makeFormula | Man page Source code |
| makeFormula-deprecated | Man page |
| models_scores_graph | Man page Source code |
| models_scores_graph-deprecated | Man page |
| plot,BIOMOD.formated.data,missing-method | Man page |
| plot,BIOMOD.projection.out,missing-method | Man page |
| precision_gain | Source code |
| predict,biomod2_model-method | Man page |
| predict.biomod2_model | Man page |
| predict.bm | Man page |
| predict.em | Man page |
| predict2 | Man page |
| predict2,ANN_biomod2_model,SpatRaster-method | Man page |
| predict2,ANN_biomod2_model,data.frame-method | Man page |
| predict2,CTA_biomod2_model,SpatRaster-method | Man page |
| predict2,CTA_biomod2_model,data.frame-method | Man page |
| predict2,DNN_biomod2_model,SpatRaster-method | Man page |
| predict2,DNN_biomod2_model,data.frame-method | Man page |
| predict2,EMca_biomod2_model,SpatRaster-method | Man page |
| predict2,EMca_biomod2_model,data.frame-method | Man page |
| predict2,EMci_biomod2_model,SpatRaster-method | Man page |
| predict2,EMci_biomod2_model,data.frame-method | Man page |
| predict2,EMcv_biomod2_model,SpatRaster-method | Man page |
| predict2,EMcv_biomod2_model,data.frame-method | Man page |
| predict2,EMfreq_biomod2_model,SpatRaster-method | Man page |
| predict2,EMfreq_biomod2_model,data.frame-method | Man page |
| predict2,EMmean_biomod2_model,SpatRaster-method | Man page |
| predict2,EMmean_biomod2_model,data.frame-method | Man page |
| predict2,EMmedian_biomod2_model,SpatRaster-method | Man page |
| predict2,EMmedian_biomod2_model,data.frame-method | Man page |
| predict2,EMmode_biomod2_model,SpatRaster-method | Man page |
| predict2,EMmode_biomod2_model,data.frame-method | Man page |
| predict2,EMwmean_biomod2_model,SpatRaster-method | Man page |
| predict2,EMwmean_biomod2_model,data.frame-method | Man page |
| predict2,FDA_biomod2_model,SpatRaster-method | Man page |
| predict2,FDA_biomod2_model,data.frame-method | Man page |
| predict2,GAM_biomod2_model,SpatRaster-method | Man page |
| predict2,GAM_biomod2_model,data.frame-method | Man page |
| predict2,GBM_biomod2_model,SpatRaster-method | Man page |
| predict2,GBM_biomod2_model,data.frame-method | Man page |
| predict2,GLM_biomod2_model,SpatRaster-method | Man page |
| predict2,GLM_biomod2_model,data.frame-method | Man page |
| predict2,MARS_biomod2_model,SpatRaster-method | Man page |
| predict2,MARS_biomod2_model,data.frame-method | Man page |
| predict2,MAXENT_biomod2_model,SpatRaster-method | Man page |
| predict2,MAXENT_biomod2_model,data.frame-method | Man page |
| predict2,MAXNET_biomod2_model,SpatRaster-method | Man page |
| predict2,MAXNET_biomod2_model,data.frame-method | Man page |
| predict2,RF_biomod2_model,SpatRaster-method | Man page |
| predict2,RF_biomod2_model,data.frame-method | Man page |
| predict2,RFd_biomod2_model,SpatRaster-method | Man page |
| predict2,RFd_biomod2_model,data.frame-method | Man page |
| predict2,SRE_biomod2_model,SpatRaster-method | Man page |
| predict2,SRE_biomod2_model,data.frame-method | Man page |
| predict2,XGBOOST_biomod2_model,SpatRaster-method | Man page |
| predict2,XGBOOST_biomod2_model,data.frame-method | Man page |
| predict2,biomod2_ensemble_model,SpatRaster-method | Man page |
| predict2,biomod2_ensemble_model,data.frame-method | Man page |
| predict2,biomod2_model,SpatRaster-method | Man page |
| predict2,biomod2_model,data.frame-method | Man page |
| predict2.ANN_biomod2_model.SpatRaster | Man page |
| predict2.ANN_biomod2_model.data.frame | Man page |
| predict2.CTA_biomod2_model.SpatRaster | Man page |
| predict2.CTA_biomod2_model.data.frame | Man page |
| predict2.DNN_biomod2_model.SpatRaster | Man page |
| predict2.DNN_biomod2_model.data.frame | Man page |
| predict2.EMca_biomod2_model.SpatRaster | Man page |
| predict2.EMca_biomod2_model.data.frame | Man page |
| predict2.EMci_biomod2_model.SpatRaster | Man page |
| predict2.EMci_biomod2_model.data.frame | Man page |
| predict2.EMcv_biomod2_model.SpatRaster | Man page |
| predict2.EMcv_biomod2_model.data.frame | Man page |
| predict2.EMfreq_biomod2_model.SpatRaster | Man page |
| predict2.EMfreq_biomod2_model.data.frame | Man page |
| predict2.EMmean_biomod2_model.SpatRaster | Man page |
| predict2.EMmean_biomod2_model.data.frame | Man page |
| predict2.EMmedian_biomod2_model.SpatRaster | Man page |
| predict2.EMmedian_biomod2_model.data.frame | Man page |
| predict2.EMmode_biomod2_model.SpatRaster | Man page |
| predict2.EMmode_biomod2_model.data.frame | Man page |
| predict2.EMwmean_biomod2_model.SpatRaster | Man page |
| predict2.EMwmean_biomod2_model.data.frame | Man page |
| predict2.FDA_biomod2_model.SpatRaster | Man page |
| predict2.FDA_biomod2_model.data.frame | Man page |
| predict2.GAM_biomod2_model.SpatRaster | Man page |
| predict2.GAM_biomod2_model.data.frame | Man page |
| predict2.GBM_biomod2_model.SpatRaster | Man page |
| predict2.GBM_biomod2_model.data.frame | Man page |
| predict2.GLM_biomod2_model.SpatRaster | Man page |
| predict2.GLM_biomod2_model.data.frame | Man page |
| predict2.MARS_biomod2_model.SpatRaster | Man page |
| predict2.MARS_biomod2_model.data.frame | Man page |
| predict2.MAXENT_biomod2_model.data.frame | Man page |
| predict2.MAXNET_biomod2_model.SpatRaster | Man page |
| predict2.MAXNET_biomod2_model.data.frame | Man page |
| predict2.RF_biomod2_model.SpatRaster | Man page |
| predict2.RF_biomod2_model.data.frame | Man page |
| predict2.RFd_biomod2_model.SpatRaster | Man page |
| predict2.RFd_biomod2_model.data.frame | Man page |
| predict2.SRE_biomod2_model.SpatRaster | Man page |
| predict2.SRE_biomod2_model.data.frame | Man page |
| predict2.biomod2_ensemble_model.SpatRaster | Man page |
| predict2.biomod2_ensemble_model.data.frame | Man page |
| predict2.biomod2_model.SpatRaster | Man page |
| predict2.biomod2_model.data.frame | Man page |
| predict2.bm | Man page |
| predict2.em | Man page |
| print,BIOMOD.models.options-method | Man page |
| print,BIOMOD.options.dataset-method | Man page |
| rast.has.values | Man page Source code |
| recall_gain | Source code |
| response.plot2 | Man page Source code |
| response.plot2-deprecated | Man page |
| sample.factor.levels | Man page Source code |
| sample.factor.levels-deprecated | Man page |
| set_new_dirname | Man page |
| set_new_dirname,BIOMOD.ensemble.models.out-method | Man page |
| set_new_dirname,BIOMOD.models.out-method | Man page |
| set_new_dirname,BIOMOD.projection.out-method | Man page |
| setters | Man page |
| show,BIOMOD.ensemble.models.out-method | Man page |
| show,BIOMOD.formated.data-method | Man page |
| show,BIOMOD.models.options-method | Man page |
| show,BIOMOD.models.out-method | Man page |
| show,BIOMOD.options.dataset-method | Man page |
| show,BIOMOD.projection.out-method | Man page |
| show,biomod2_ensemble_model-method | Man page |
| show,biomod2_model-method | Man page |
| sre | Man page Source code |
| sre-deprecated | Man page |
| summary,BIOMOD.formated.data-method | Man page |
| variables_importance | Man page Source code |
| variables_importance-deprecated | Man page |
| zzz_bm | Man page Source code |
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