biomod2: Ensemble Platform for Species Distribution Modeling

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

Author
Wilfried Thuiller [aut, cre], Damien Georges [aut, cre], Robin Engler [aut], Frank Breiner [aut]
Date of publication
2016-03-01 18:40:06
Maintainer
Damien Georges <damien.georges2@gmail.com>
License
GPL-2
Version
3.3-7

View on CRAN

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

Files in this package

biomod2
biomod2/inst
biomod2/inst/doc
biomod2/inst/doc/index.html
biomod2/inst/doc/Include_MAXENT.pdf
biomod2/inst/doc/Simple_species_modelling.pdf
biomod2/inst/doc/Multi_species_computation.pdf
biomod2/inst/doc/EnsembleModelingAssembly.pdf
biomod2/inst/doc/Available_input_data_combinations.pdf
biomod2/inst/doc/Simple_species_modelling.R
biomod2/inst/doc/html
biomod2/inst/doc/html/R.css
biomod2/inst/doc/html/00Index.html
biomod2/inst/doc/html/vignettes_rds.csv
biomod2/inst/doc/Multi_species_computation.R
biomod2/inst/external
biomod2/inst/external/species
biomod2/inst/external/species/GuloGulo.gri
biomod2/inst/external/species/TenrecEcaudatus.gri
biomod2/inst/external/species/PantheraOnca.grd
biomod2/inst/external/species/ConnochaetesGnou.gri
biomod2/inst/external/species/GuloGulo.grd
biomod2/inst/external/species/mammals_table.csv
biomod2/inst/external/species/PteropusGiganteus.grd
biomod2/inst/external/species/VulpesVulpes.grd
biomod2/inst/external/species/VulpesVulpes.gri
biomod2/inst/external/species/PteropusGiganteus.gri
biomod2/inst/external/species/TenrecEcaudatus.grd
biomod2/inst/external/species/ConnochaetesGnou.grd
biomod2/inst/external/species/mammals_and_bioclim_table.csv
biomod2/inst/external/species/PantheraOnca.gri
biomod2/inst/external/bioclim
biomod2/inst/external/bioclim/future
biomod2/inst/external/bioclim/future/bio7.grd
biomod2/inst/external/bioclim/future/bioclim_table_future.csv
biomod2/inst/external/bioclim/future/bio11.grd
biomod2/inst/external/bioclim/future/bio11.gri
biomod2/inst/external/bioclim/future/bio12.gri
biomod2/inst/external/bioclim/future/bio4.gri
biomod2/inst/external/bioclim/future/bio4.grd
biomod2/inst/external/bioclim/future/bio3.gri
biomod2/inst/external/bioclim/future/bio7.gri
biomod2/inst/external/bioclim/future/bio3.grd
biomod2/inst/external/bioclim/future/bio12.grd
biomod2/inst/external/bioclim/current
biomod2/inst/external/bioclim/current/bio7.grd
biomod2/inst/external/bioclim/current/bio11.grd
biomod2/inst/external/bioclim/current/bio11.gri
biomod2/inst/external/bioclim/current/bio12.gri
biomod2/inst/external/bioclim/current/bioclim_table.csv
biomod2/inst/external/bioclim/current/bio4.gri
biomod2/inst/external/bioclim/current/bio4.grd
biomod2/inst/external/bioclim/current/bio3.gri
biomod2/inst/external/bioclim/current/bio7.gri
biomod2/inst/external/bioclim/current/bio3.grd
biomod2/inst/external/bioclim/current/bio12.grd
biomod2/NAMESPACE
biomod2/NEWS
biomod2/R
biomod2/R/multiple.plot.r
biomod2/R/level.plot.R
biomod2/R/BIOMOD_Projection.R
biomod2/R/functionkeep.R
biomod2/R/response.plot.R
biomod2/R/BIOMOD_Modeling.R
biomod2/R/makeFormula.R
biomod2/R/SampleMat2.R
biomod2/R/Evaluate.models.R
biomod2/R/BIOMOD_RangeSize.R
biomod2/R/FilteringTransformation.R
biomod2/R/BiomodClass.R
biomod2/R/CleverCut.R
biomod2/R/sre.R
biomod2/R/BIOMOD_presenceonly.R
biomod2/R/BIOMOD_LoadModels.R
biomod2/R/CVnnet.R
biomod2/R/transform.outputs.R
biomod2/R/BIOMOD_ConvertOldRun.R
biomod2/R/Prepare.Maxent.WorkDir.R
biomod2/R/deprecated_functions.R
biomod2/R/testnull.R
biomod2/R/BIOMOD_cv.R
biomod2/R/BIOMOD_EnsembleForecasting.R
biomod2/R/BIOMOD_ModelingOptions.R
biomod2/R/update_objects.R
biomod2/R/CustomIndexMaker.R
biomod2/R/scopeExpSyst.R
biomod2/R/BIOMOD_tuning.R
biomod2/R/pseudo.abs.R
biomod2/R/Projection.R
biomod2/R/biomod2_models-class.R
biomod2/R/sample.factor.levels.R
biomod2/R/Rescaler4.R
biomod2/R/ProbDensFunc.R
biomod2/R/variables_importance.R
biomod2/R/BinaryTransformation.R
biomod2/R/models_scores_graph.R
biomod2/R/scope.R
biomod2/R/BIOMOD_FormatingData.R
biomod2/R/Biomod.Models_RE.R
biomod2/R/BIOMOD_EnsembleModeling.R
biomod2/MD5
biomod2/DESCRIPTION
biomod2/man
biomod2/man/BIOMOD.stored.objects-class.Rd
biomod2/man/BIOMOD.models.out-class.Rd
biomod2/man/calculate.stat.Rd
biomod2/man/BIOMOD_FormatingData.Rd
biomod2/man/sample.factor.levels.Rd
biomod2/man/randomise_data.Rd
biomod2/man/FilteringTransformation.Rd
biomod2/man/getStatOptimValue.Rd
biomod2/man/biomod2-package.Rd
biomod2/man/BIOMOD.projection.out-class.Rd
biomod2/man/BIOMOD_presenceonly.Rd
biomod2/man/BIOMOD.projection.out-methods.Rd
biomod2/man/BIOMOD_RangeSize.Rd
biomod2/man/Find.Optim.Stat.Rd
biomod2/man/update_objects.Rd
biomod2/man/evaluate.Rd
biomod2/man/CustomIndexMaker.Rd
biomod2/man/BIOMOD_LoadModels.Rd
biomod2/man/BIOMOD.formated.data-class.Rd
biomod2/man/BIOMOD_EnsembleForecasting.Rd
biomod2/man/makeFormula.Rd
biomod2/man/models_scores_graph.Rd
biomod2/man/sre.Rd
biomod2/man/BinaryTransformation-methods.Rd
biomod2/man/deprecated_functions.Rd
biomod2/man/SampleMat2.Rd
biomod2/man/Print_Default_ModelingOptions.Rd
biomod2/man/ProbDensFunc.Rd
biomod2/man/response.plot.Rd
biomod2/man/BIOMOD.stored.objects-methods.Rd
biomod2/man/full_shuffling.Rd
biomod2/man/response.plot2.Rd
biomod2/man/BIOMOD.models.out-RemoveProperly.Rd
biomod2/man/BIOMOD.Model.Options-class.Rd
biomod2/man/BIOMOD_Projection.Rd
biomod2/man/BIOMOD_tuning.Rd
biomod2/man/multiple.plot.Rd
biomod2/man/BIOMOD.models.out-methods.Rd
biomod2/man/BIOMOD_ModelingOptions.Rd
biomod2/man/BIOMOD.EnsembleModeling.out-methods.Rd
biomod2/man/DF_to_ARRAY.Rd
biomod2/man/biomod2_model-class.Rd
biomod2/man/BIOMOD_EnsembleModeling.Rd
biomod2/man/BIOMOD_ConvertOldRun.Rd
biomod2/man/BIOMOD_cv.Rd
biomod2/man/variables_importance.Rd
biomod2/man/BIOMOD_Modeling.Rd
biomod2/man/biomod2.inner-methods.Rd
biomod2/man/BIOMOD.EnsembleModeling.out-class.Rd
biomod2/man/level.plot.Rd