biomod2: Ensemble Platform for Species Distribution Modeling

Functions for species distribution modeling, calibration and evaluation, ensemble of models.

AuthorWilfried Thuiller [aut, cre], Damien Georges [aut, cre], Robin Engler [aut], Frank Breiner [aut]
Date of publication2017-03-13 13:33:33
MaintainerDamien Georges <damien.georges2@gmail.com>
LicenseGPL-2
Version3.3-15

View on R-Forge

Man pages

BinaryTransformation-methods: Convert species' probability of occurrence into binary...

biomod2.inner-methods: biomod2 internal functions

biomod2_model-class: biomod2 models objects class and functions

biomod2-package: Species Distribution Modeling within an Ensemble Forecasting...

BIOMOD_ConvertOldRun: Convert objects and outputs from BIOMOD.xx into biomod2.xx...

BIOMOD_cv: Custom models cross-validation procedure

BIOMOD_EnsembleForecasting: Ensemble projections of species over space and time

BIOMOD_EnsembleModeling: Create and evaluate an ensemble set of models and predictions

BIOMOD.EnsembleModeling.out-class: BIOMOD_EnsembleModeling() outputs objects class

BIOMOD.EnsembleModeling.out-methods: BIOMOD.EnsembleModeling.out getters

BIOMOD.formated.data-class: BIOMOD_FormatingData() outputs objects class

BIOMOD_FormatingData: Initialise the datasets for usage in 'biomod2'

BIOMOD_LoadModels: Load models built within BIOMOD_Modeling function

BIOMOD_Modeling: Run a range of species distribution models

BIOMOD_ModelingOptions: Configure the modeling options for each selected model

BIOMOD.Model.Options-class: BIOMOD_ModelingOptions() outputs objects class

BIOMOD.models.out-class: BIOMOD_modelling() outputs objects class

BIOMOD.models.out-methods: BIOMOD.models.out getters

BIOMOD.models.out-RemoveProperly: remove properly BIOMOD_Modeling outputs

BIOMOD_presenceonly: evaluate models with presences only metrics

BIOMOD_Projection: Project the calibrated models within 'biomod2' into new space...

BIOMOD.projection.out-class: BIOMOD_Projection() outputs objects class

BIOMOD.projection.out-methods: BIOMOD.projection.out getters

BIOMOD_RangeSize: Analysis of the range size changes

BIOMOD.stored.objects-class: BIOMOD.stored.xxx objects class

BIOMOD.stored.objects-methods: BIOMOD.stored.objects functions

BIOMOD_tuning: Tune models parameters

calculate.stat: Calculate evaluation metrics based on a misclassification...

CustomIndexMaker: Replace default package Index help file by a custom one.

deprecated_functions: biomod2 deprecated functions

DF_to_ARRAY: Convert a biomod2 data.frame (or list) into array

evaluate: biomod2 modelling outputs evaluation

FilteringTransformation: Convert species' probability of occurrence into binary...

Find.Optim.Stat: Calculate the best score according to a given evaluation...

full_shuffling: data set shuffling tool

getStatOptimValue: get the optimal score of evaluation statistical metrics

level.plot: Plot 2-dimensional data for visualizing distribution of...

makeFormula: Standardized formula maker

models_scores_graph: Produce models evaluation bi-dimensional graph

multiple.plot: Plot and compare prediction maps within BIOMOD

Print_Default_ModelingOptions: Get default values of BIOMOD inner models' options

ProbDensFunc: Probability Density Function

randomise_data: data set shuffling tool

response.plot: Analysis of the response curves of a model within Biomod

response.plot2: Function for for plotting predicted responses from species...

sample.factor.levels: Tool to ensure the sampling of all levels of a factorial...

SampleMat2: Sample binary vector

sre: Surface Range Envelope

update_objects: update biomod2 objects

variables_importance: Variables importance calculation

Functions

ANN_biomod2_model Man page
ANN_biomod2_model-class Man page
array-method Man page
BinaryTransformation Man page
BinaryTransformation, Man page
BinaryTransformation,array-method Man page
BinaryTransformation,data.frame-method Man page
BinaryTransformation,matrix-method Man page
BinaryTransformation,numeric-method Man page
BinaryTransformation,RasterBrick-method Man page
BinaryTransformation,RasterLayer-method Man page
BinaryTransformation,RasterStack-method Man page
biomod2 Man page
biomod2_ensemble_model Man page
biomod2_ensemble_model-class Man page
biomod2_model Man page
biomod2_model-class Man page
biomod2-package Man page
BIOMOD_ConvertOldRun Man page
BIOMOD_cv Man page
BIOMOD_EnsembleForecasting Man page
BIOMOD_EnsembleModeling Man page
BIOMOD.EnsembleModeling.out Man page
BIOMOD.EnsembleModeling.out-class Man page
BIOMOD.formated.data Man page
BIOMOD.formated.data-class Man page
BIOMOD.formated.data,data.frame,ANY-method Man page
BIOMOD.formated.data,numeric,data.frame-method Man page
BIOMOD.formated.data,numeric,matrix-method Man page
BIOMOD.formated.data,numeric,RasterStack-method Man page
BIOMOD.formated.data.PA Man page
BIOMOD.formated.data.PA-class Man page
BIOMOD_FormatingData Man page
BIOMOD_LoadModels Man page
BIOMOD_Modeling Man page
BIOMOD_ModelingOptions Man page
BIOMOD.Model.Options-class Man page
BIOMOD.models.out-class Man page
BIOMOD_presenceonly Man page
BIOMOD_Projection Man page
BIOMOD.projection.out Man page
BIOMOD.projection.out-class Man page
BIOMOD_RangeSize Man page
BIOMOD_RangeSize,array,array-method Man page
BIOMOD_RangeSize,data.frame,data.frame-method Man page
BIOMOD_RangeSize-methods Man page
BIOMOD_RangeSize,RasterLayer,RasterLayer-method Man page
BIOMOD_RangeSize,RasterLayer,RasterStack-method Man page
BIOMOD_RangeSize,RasterStack,RasterStack-method Man page
BIOMOD.stored.array Man page
BIOMOD.stored.array-class Man page
BIOMOD.stored.data Man page
BIOMOD.stored.data-class Man page
BIOMOD.stored.data.frame Man page
BIOMOD.stored.data.frame-class Man page
BIOMOD.stored.files Man page
BIOMOD.stored.files-class Man page
BIOMOD.stored.formated.data Man page
BIOMOD.stored.formated.data-class Man page
BIOMOD.stored.models.options Man page
BIOMOD.stored.models.options-class Man page
BIOMOD.stored.models.out Man page
BIOMOD.stored.models.out-class Man page
BIOMOD.stored.raster.stack Man page
BIOMOD.stored.raster.stack-class Man page
BIOMOD_tuning Man page
calculate.stat Man page
check_data_range Man page
CTA_biomod2_model Man page
CTA_biomod2_model-class Man page
CustomIndexMaker Man page
data.frame-method Man page
DF_to_ARRAY Man page
disk.pseudo.abs.selection Man page
disk.pseudo.abs.selection,ANY,RasterStack-method Man page
disk.pseudo.abs.selection,ANY,SpatialPointsDataFrame-method Man page
EMca_biomod2_model Man page
EMca_biomod2_model-class Man page
EMci_biomod2_model Man page
EMci_biomod2_model-class Man page
EMcv_biomod2_model Man page
EMcv_biomod2_model-class Man page
EMmean_biomod2_model Man page
EMmean_biomod2_model-class Man page
EMmedian_biomod2_model Man page
EMmedian_biomod2_model-class Man page
EMwmean_biomod2_model Man page
EMwmean_biomod2_model-class Man page
evaluate Man page
FDA_biomod2_model Man page
FDA_biomod2_model-class Man page
FilteringTransformation Man page
FilteringTransformation,array-method Man page
FilteringTransformation,data.frame-method Man page
FilteringTransformation,matrix-method Man page
FilteringTransformation-methods Man page
FilteringTransformation,numeric-method Man page
FilteringTransformation,RasterBrick-method Man page
FilteringTransformation,RasterLayer-method Man page
FilteringTransformation,RasterStack-method Man page
Find.Optim.Stat Man page
free Man page
free,BIOMOD.projection.out-method Man page
full_suffling Man page
GAM_biomod2_model Man page
GAM_biomod2_model-class Man page
GBM_biomod2_model Man page
GBM_biomod2_model-class Man page
get_built_models Man page
get_built_models Man page
get_built_models,BIOMOD.EnsembleModeling.out-method Man page
get_built_models,BIOMOD.EnsembleModeling.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
getEMalgos Man page
getEMalgos,BIOMOD.EnsembleModeling.out-method Man page
getEMbuiltModels Man page
getEMbuiltModels,BIOMOD.EnsembleModeling.out-method Man page
getEMeval Man page
getEMeval,BIOMOD.EnsembleModeling.out-method Man page
getEMkeptModels Man page
getEMkeptModels,BIOMOD.EnsembleModeling.out-method Man page
getEM_needed_models Man page
getEM_needed_models,BIOMOD.EnsembleModeling.out-method Man page
get_evaluations Man page
get_evaluations Man page
get_evaluations,BIOMOD.EnsembleModeling.out-method Man page
get_evaluations,BIOMOD.EnsembleModeling.out-method Man page
get_evaluations,BIOMOD.models.out-method Man page
get_formal_data Man page
get_formal_data,BIOMOD.models.out-method Man page
get_formal_model Man page
getFormalModel Man page
get_formal_model,biomod2_model-method Man page
getFormalModel,biomod2_model-method Man page
get_kept_models Man page
get_kept_models,BIOMOD.EnsembleModeling.out-method Man page
getModelsBuiltModels Man page
getModelsBuiltModels,BIOMOD.models.out-method Man page
getModelsEvaluations Man page
getModelsEvaluations,BIOMOD.models.out-method Man page
getModelsInputData Man page
getModelsInputData,BIOMOD.models.out-method Man page
getModelsOptions Man page
getModelsOptions,BIOMOD.models.out-method Man page
getModelsPrediction Man page
getModelsPrediction,BIOMOD.models.out-method Man page
getModelsPredictionEval Man page
getModelsPredictionEval,BIOMOD.models.out-method Man page
getModelsVarImport Man page
getModelsVarImport,BIOMOD.models.out-method Man page
get_needed_models Man page
get_needed_models,BIOMOD.EnsembleModeling.out-method Man page
get_options Man page
get_options,BIOMOD.models.out-method Man page
get_predictions Man page
get_predictions Man page
get_predictions Man page
get_predictions,BIOMOD.EnsembleModeling.out-method Man page
get_predictions,BIOMOD.models.out-method Man page
get_predictions,BIOMOD.models.out-method Man page
get_predictions,BIOMOD.projection.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
getProjection Man page
getProjection,BIOMOD.projection.out-method Man page
get_scaling_model Man page
getScalingModel Man page
get_scaling_model,biomod2_model-method Man page
getScalingModel,biomod2_model-method Man page
getStatOptimValue Man page
get_variables_importance Man page
get_variables_importance,BIOMOD.EnsembleModeling.out-method Man page
get_variables_importance,BIOMOD.models.out-method Man page
get_var_range Man page
get_var_type Man page
GLM_biomod2_model Man page
GLM_biomod2_model-class Man page
level.plot Man page
LIST_to_ARRAY Man page
load_stored_object Man page
load_stored_object,BIOMOD.stored.data-method Man page
makeFormula Man page
MARS_biomod2_model Man page
MARS_biomod2_model-class Man page
matrix-method Man page
MAXENT.Phillips_biomod2_model Man page
MAXENT.Phillips_biomod2_model-class Man page
MAXENT.Tsuruoka_biomod2_model Man page
MAXENT.Tsuruoka_biomod2_model-class Man page
.Models.prepare.data Man page
.Models.prepare.data,BIOMOD.formated.data-method Man page
.Models.prepare.data,BIOMOD.formated.data.PA-method Man page
models_scores_graph Man page
multiple.plot Man page
numeric-method Man page
plot,BIOMOD.formated.data,missing-method Man page
plot,BIOMOD.formated.data.PA,missing-method Man page
plot,BIOMOD.projection.out,missing-method Man page
predict,ANN_biomod2_model-method Man page
predict,CTA_biomod2_model-method Man page
predict,EMca_biomod2_model-method Man page
predict,EMci_biomod2_model-method Man page
predict,EMcv_biomod2_model-method Man page
predict,EMmean_biomod2_model-method Man page
predict,EMmedian_biomod2_model-method Man page
predict,EMwmean_biomod2_model-method Man page
predict,FDA_biomod2_model-method Man page
predict,GAM_biomod2_model-method Man page
predict,GBM_biomod2_model-method Man page
predict,GLM_biomod2_model-method Man page
predict,MARS_biomod2_model-method Man page
predict,MAXENT.Phillips_biomod2_model-method Man page
predict,MAXENT.Tsuruoka_biomod2_model-method Man page
predict,RF_biomod2_model-method Man page
predict,SRE_biomod2_model-method Man page
Print_Default_ModelingOptions Man page
ProbDensFunc Man page
Projection Man page
Projection,ANY,ANY,data.frame-method Man page
Projection,ANY,ANY,RasterStack-method Man page
.Projection.do.proj Man page
.Projection.do.proj,ANY,data.frame-method Man page
.Projection.do.proj,ANY,RasterStack-method Man page
randomise_data Man page
random.pseudo.abs.selection Man page
random.pseudo.abs.selection,ANY,RasterStack-method Man page
random.pseudo.abs.selection,ANY,SpatialPointsDataFrame-method Man page
RasterBrick-method Man page
RasterLayer-method Man page
RasterStack-method Man page
RemoveProperly Man page
RemoveProperly,BIOMOD.models.out-method Man page
response.plot Man page
response.plot2 Man page
RF_biomod2_model Man page
RF_biomod2_model-class Man page
sample.factor.levels Man page
SampleMat2 Man page
show,biomod2_model-method Man page
show,BIOMOD.EnsembleModeling.out-method Man page
show,BIOMOD.formated.data-method Man page
show,BIOMOD.formated.data.PA-method Man page
show,BIOMOD.Model.Options-method Man page
show,BIOMOD.models.out-method Man page
show,BIOMOD.projection.out-method Man page
sre Man page
SRE_biomod2_model Man page
SRE_biomod2_model-class Man page
sre.pseudo.abs.selection Man page
sre.pseudo.abs.selection,ANY,RasterStack-method Man page
sre.pseudo.abs.selection,ANY,SpatialPointsDataFrame-method Man page
.transform.outputs Man page
.transform.outputs,array-method Man page
.transform.outputs,list-method Man page
update_objects Man page
user.defined.pseudo.abs.selection Man page
user.defined.pseudo.abs.selection,ANY,RasterStack-method Man page
user.defined.pseudo.abs.selection,ANY,SpatialPointsDataFrame-met Man page
variables_importance Man page

Files

biomod2/DESCRIPTION
biomod2/NAMESPACE
biomod2/NEWS
biomod2/R
biomod2/R/BIOMOD_ConvertOldRun.R biomod2/R/BIOMOD_EnsembleForecasting.R biomod2/R/BIOMOD_EnsembleModeling.R biomod2/R/BIOMOD_FormatingData.R biomod2/R/BIOMOD_LoadModels.R biomod2/R/BIOMOD_Modeling.R biomod2/R/BIOMOD_ModelingOptions.R biomod2/R/BIOMOD_Projection.R biomod2/R/BIOMOD_RangeSize.R biomod2/R/BIOMOD_cv.R biomod2/R/BIOMOD_presenceonly.R biomod2/R/BIOMOD_tuning.R biomod2/R/BinaryTransformation.R biomod2/R/Biomod.Models_RE.R biomod2/R/BiomodClass.R biomod2/R/CVnnet.R biomod2/R/CleverCut.R biomod2/R/CustomIndexMaker.R biomod2/R/Evaluate.models.R biomod2/R/FilteringTransformation.R biomod2/R/Prepare.Maxent.WorkDir.R biomod2/R/ProbDensFunc.R biomod2/R/Projection.R biomod2/R/Rescaler4.R biomod2/R/SampleMat2.R biomod2/R/biomod2_models-class.R biomod2/R/deprecated_functions.R biomod2/R/functionkeep.R biomod2/R/level.plot.R biomod2/R/makeFormula.R biomod2/R/models_scores_graph.R
biomod2/R/multiple.plot.r
biomod2/R/pseudo.abs.R biomod2/R/response.plot.R biomod2/R/sample.factor.levels.R biomod2/R/scope.R biomod2/R/scopeExpSyst.R biomod2/R/sre.R biomod2/R/testnull.R biomod2/R/transform.outputs.R biomod2/R/update_objects.R biomod2/R/variables_importance.R
biomod2/inst
biomod2/inst/doc
biomod2/inst/doc/Available_input_data_combinations.pdf
biomod2/inst/doc/EnsembleModelingAssembly.pdf
biomod2/inst/doc/Include_MAXENT.pdf
biomod2/inst/doc/Multi_species_computation.R
biomod2/inst/doc/Multi_species_computation.pdf
biomod2/inst/doc/Simple_species_modelling.R
biomod2/inst/doc/Simple_species_modelling.pdf
biomod2/inst/doc/html
biomod2/inst/doc/html/00Index.html
biomod2/inst/doc/html/R.css
biomod2/inst/doc/html/vignettes_rds.csv
biomod2/inst/doc/index.html
biomod2/inst/external
biomod2/inst/external/bioclim
biomod2/inst/external/bioclim/current
biomod2/inst/external/bioclim/current/bio11.grd
biomod2/inst/external/bioclim/current/bio11.gri
biomod2/inst/external/bioclim/current/bio12.grd
biomod2/inst/external/bioclim/current/bio12.gri
biomod2/inst/external/bioclim/current/bio3.grd
biomod2/inst/external/bioclim/current/bio3.gri
biomod2/inst/external/bioclim/current/bio4.grd
biomod2/inst/external/bioclim/current/bio4.gri
biomod2/inst/external/bioclim/current/bio7.grd
biomod2/inst/external/bioclim/current/bio7.gri
biomod2/inst/external/bioclim/current/bioclim_table.csv
biomod2/inst/external/bioclim/future
biomod2/inst/external/bioclim/future/bio11.grd
biomod2/inst/external/bioclim/future/bio11.gri
biomod2/inst/external/bioclim/future/bio12.grd
biomod2/inst/external/bioclim/future/bio12.gri
biomod2/inst/external/bioclim/future/bio3.grd
biomod2/inst/external/bioclim/future/bio3.gri
biomod2/inst/external/bioclim/future/bio4.grd
biomod2/inst/external/bioclim/future/bio4.gri
biomod2/inst/external/bioclim/future/bio7.grd
biomod2/inst/external/bioclim/future/bio7.gri
biomod2/inst/external/bioclim/future/bioclim_table_future.csv
biomod2/inst/external/higher_resolution
biomod2/inst/external/higher_resolution/data.zip
biomod2/inst/external/species
biomod2/inst/external/species/ConnochaetesGnou.grd
biomod2/inst/external/species/ConnochaetesGnou.gri
biomod2/inst/external/species/GuloGulo.grd
biomod2/inst/external/species/GuloGulo.gri
biomod2/inst/external/species/PantheraOnca.grd
biomod2/inst/external/species/PantheraOnca.gri
biomod2/inst/external/species/PteropusGiganteus.grd
biomod2/inst/external/species/PteropusGiganteus.gri
biomod2/inst/external/species/TenrecEcaudatus.grd
biomod2/inst/external/species/TenrecEcaudatus.gri
biomod2/inst/external/species/VulpesVulpes.grd
biomod2/inst/external/species/VulpesVulpes.gri
biomod2/inst/external/species/mammals_and_bioclim_table.csv
biomod2/inst/external/species/mammals_table.csv
biomod2/man
biomod2/man/BIOMOD.EnsembleModeling.out-class.Rd biomod2/man/BIOMOD.EnsembleModeling.out-methods.Rd biomod2/man/BIOMOD.Model.Options-class.Rd biomod2/man/BIOMOD.formated.data-class.Rd biomod2/man/BIOMOD.models.out-RemoveProperly.Rd biomod2/man/BIOMOD.models.out-class.Rd biomod2/man/BIOMOD.models.out-methods.Rd biomod2/man/BIOMOD.projection.out-class.Rd biomod2/man/BIOMOD.projection.out-methods.Rd biomod2/man/BIOMOD.stored.objects-class.Rd biomod2/man/BIOMOD.stored.objects-methods.Rd biomod2/man/BIOMOD_ConvertOldRun.Rd biomod2/man/BIOMOD_EnsembleForecasting.Rd biomod2/man/BIOMOD_EnsembleModeling.Rd biomod2/man/BIOMOD_FormatingData.Rd biomod2/man/BIOMOD_LoadModels.Rd biomod2/man/BIOMOD_Modeling.Rd biomod2/man/BIOMOD_ModelingOptions.Rd biomod2/man/BIOMOD_Projection.Rd biomod2/man/BIOMOD_RangeSize.Rd biomod2/man/BIOMOD_cv.Rd biomod2/man/BIOMOD_presenceonly.Rd biomod2/man/BIOMOD_tuning.Rd biomod2/man/BinaryTransformation-methods.Rd biomod2/man/CustomIndexMaker.Rd biomod2/man/DF_to_ARRAY.Rd biomod2/man/FilteringTransformation.Rd biomod2/man/Find.Optim.Stat.Rd biomod2/man/Print_Default_ModelingOptions.Rd biomod2/man/ProbDensFunc.Rd biomod2/man/SampleMat2.Rd biomod2/man/biomod2-package.Rd biomod2/man/biomod2.inner-methods.Rd biomod2/man/biomod2_model-class.Rd biomod2/man/calculate.stat.Rd biomod2/man/deprecated_functions.Rd biomod2/man/evaluate.Rd biomod2/man/full_shuffling.Rd biomod2/man/getStatOptimValue.Rd biomod2/man/level.plot.Rd biomod2/man/makeFormula.Rd biomod2/man/models_scores_graph.Rd biomod2/man/multiple.plot.Rd biomod2/man/randomise_data.Rd biomod2/man/response.plot.Rd biomod2/man/response.plot2.Rd biomod2/man/sample.factor.levels.Rd biomod2/man/sre.Rd biomod2/man/update_objects.Rd biomod2/man/variables_importance.Rd

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