Man pages for biomodhub/biomod2
Ensemble Platform for Species Distribution Modeling
| BinaryTransformation-deprecated | BinaryTransformation |
| bioclim_current | Bioclimatic variables for SDM based on current condition |
| bioclim_future | Bioclimatic variables for SDM based on future condition |
| biomod2-deprecated | Deprecated functions in package 'biomod2'. |
| biomod2_ensemble_model | Ensemble model output object class (when running... |
| biomod2_model | Single model output object class (when running... |
| BIOMOD_CrossValidation-deprecated | BIOMOD_CrossValidation |
| BIOMOD_EnsembleForecasting | Project ensemble species distribution models onto new... |
| BIOMOD_EnsembleModeling | Create and evaluate an ensemble set of models and predictions |
| BIOMOD.ensemble.models.out | 'BIOMOD_EnsembleModeling()' output object class |
| BIOMOD.formated.data | 'BIOMOD_FormatingData()' output object class |
| BIOMOD.formated.data.PA | 'BIOMOD_FormatingData()' output object class (with... |
| BIOMOD_FormatingData | Format input data, and select pseudo-absences if wanted, for... |
| BIOMOD_LoadModels | Load species distribution models built with 'biomod2' |
| BIOMOD_Modeling | Run a range of species distribution models |
| BIOMOD_ModelingOptions-deprecated | BIOMOD_ModelingOptions |
| BIOMOD.models.options | 'bm_ModelingOptions' output object class |
| BIOMOD.models.out | 'BIOMOD_Modeling()' output object class |
| BIOMOD.options.dataset | 'bm_ModelingOptions' output object class |
| BIOMOD.options.default | 'bm_ModelingOptions' output object class |
| BIOMOD_PresenceOnly-deprecated | BIOMOD_PresenceOnly |
| BIOMOD_Projection | Project a range of calibrated species distribution models... |
| BIOMOD.projection.out | 'BIOMOD_Projection()' output object class |
| BIOMOD_RangeSize | Analyze the range size differences between projections of... |
| BIOMOD.rangesize.out | 'BIOMOD_RangeSize()' output object class |
| BIOMOD_Report | Produce summary outputs from a simulation folder |
| BIOMOD.stored.data | 'BIOMOD_Modeling' and 'BIOMOD_EnsembleModeling' output object... |
| BIOMOD_tuning-deprecated | BIOMOD_Tuning |
| bm_BinaryTransformation | Convert probability values into binary values using a... |
| bm_CrossValidation | Build cross-validation table |
| bm_FindOptimStat | Calculate the best score according to a given evaluation... |
| bm_MakeFormula | Standardized formula maker |
| bm_ModelAnalysis | Analyze the residuals of the single models |
| bm_ModelingOptions | Configure the modeling options for each selected model |
| bm_PlotEvalBoxplot | Plot boxplot of evaluation scores |
| bm_PlotEvalMean | Plot mean evaluation scores |
| bm_PlotRangeSize | Plot species range change |
| bm_PlotResponseCurves | Plot response curves |
| bm_PlotVarImpBoxplot | Plot boxplot of variables importance |
| bm_PseudoAbsences | Select pseudo-absences |
| bm_RangeSize | Analyze the range size differences between projections of... |
| bm_RunModelsLoop | Loop to compute all single species distribution models |
| bm_SampleBinaryVector | Sample binary vector |
| bm_SampleFactorLevels | Sample all levels of a factorial variable |
| bm_SRE | Surface Range Envelope |
| bm_Tuning | Tune models parameters |
| bm_VariablesImportance | Variables' importance calculation |
| calculate.stat-deprecated | calculate.stat |
| DataSpecies | Presence-Absence data to build test SDM |
| dot-categorical2numeric | Transform categorical into numeric variables |
| dot-check_duplicated_cells | Check duplicated cells |
| dot-get_categorical_names | Get categorical variable names |
| dot-get_env_class | Get class of environmental data provided |
| dot-load_gam_namespace | Load library for GAM models |
| dot-transform_model.as.col | Transform predictions data.frame from long to wide with... |
| dot-transform.outputs.list-deprecated | .transform.outputs.list |
| Find.Optim.Stat-deprecated | Find.Optim.Stat |
| getStatOptimValue-deprecated | getStatOptimValue |
| getters.bm | Functions to extract informations from 'biomod2_model'... |
| getters.out | Functions to extract informations from 'BIOMOD.models.out',... |
| load_stored_object | Functions to load 'BIOMOD.stored.data' objects |
| makeFormula-deprecated | makeFormula |
| models_scores_graph-deprecated | models_scores_graph |
| ModelsTable | Single models package and functions |
| ODMAP | ODMAP empty table |
| OptionsBigboss | Bigboss pre-defined parameter values for single models |
| plot | 'plot' method for 'BIOMOD.formated.data' object class |
| predict2.bm | Functions to get predictions from 'biomod2_model' objects |
| predict2.em | Functions to get predictions from 'biomod2_ensemble_model'... |
| predict.bm | Functions to get predictions from 'biomod2_model' objects |
| predict.em | Functions to get predictions from 'biomod2_ensemble_model'... |
| ProbDensFunc-deprecated | ProbDensFunc |
| rast.has.values | Check whether SpatRaster is an empty 'rast()' |
| response.plot2-deprecated | response.plot2 |
| sample.factor.levels-deprecated | sample.factor.levels |
| setters | Functions to change the place of the different biomod2... |
| sre-deprecated | sre |
| summary | 'summary' method for 'BIOMOD.formated.data' object class |
| variables_importance-deprecated | variables_importance |
| zzz_bm | Dummy function to clean working directory after package... |
