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 publication2016-03-01 18:40:06
MaintainerDamien Georges <damien.georges2@gmail.com>
LicenseGPL-2
Version3.3-7

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

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