biomod2 v3.3-7.1

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Ensemble Platform for Species Distribution Modeling

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

Functions in biomod2

Name Description
BIOMOD.Model.Options-class BIOMOD_ModelingOptions() outputs objects class
BIOMOD.models.out-class BIOMOD_modelling() outputs objects class
calculate.stat Calculate evaluation metrics based on a misclassification table
BIOMOD_Modeling Run a range of species distribution models
Find.Optim.Stat Calculate the best score according to a given evaluation method
FilteringTransformation Convert species' probability of occurrence into binary presence-absence data using a predefined threshold
multiple.plot Plot and compare prediction maps within BIOMOD
biomod2.deprecated.functions biomod2 deprecated functions
BIOMOD_ModelingOptions Configure the modeling options for each selected model
getStatOptimValue get the optimal score of evaluation statistical metrics
randomise_data data set shuffling tool
BIOMOD.stored.objects-methods BIOMOD.stored.objects functions
BIOMOD_FormatingData Initialise the datasets for usage in biomod2
BIOMOD_ConvertOldRun Convert objects and outputs from BIOMOD.xx into biomod2.xx objects and outputs
biomod2-package Species Distribution Modeling within an Ensemble Forecasting framework
SampleMat2 Sample binary vector
BIOMOD_LoadModels Load models built within BIOMOD_Modeling function
makeFormula Standardized formula maker
Print_Default_ModelingOptions Get default values of BIOMOD inner models' options
BIOMOD.projection.out-method BIOMOD.projection.out getters
ProbDensFunc Probability Density Function
models_scores_graph Produce models evaluation bi-dimensional graph
BIOMOD_Projection Project the calibrated models within biomod2 into new space or time
BIOMOD.stored.objects-class BIOMOD.stored.xxx objects class
level.plot Plot 2-dimensional data for visualizing distribution of species or environment
BIOMOD_EnsembleForecasting Ensemble projections of species over space and time
response.plot Analysis of the response curves of a model within Biomod
response.plot2 Function for for plotting predicted responses from species distribution models in 2 or 3 dimensions
evaluate biomod2 modelling outputs evaluation
BIOMOD_EnsembleModeling Create and evaluate an ensemble set of models and predictions
full_suffling data set shuffling tool
update_objects update biomod2 objects
CustomIndexMaker Replace default package Index help file by a custom one.
DF_to_ARRAY Convert a biomod2 data.frame (or list) into array
BIOMOD_cv Custom models cross-validation procedure
BIOMOD_RangeSize Analysis of the range size changes
BIOMOD_presenceonly evaluate models with presences only metrics
variables_importance Variables importance calculation
biomod2.inner-method biomod2 internal functions
sample.factor.levels Tool to ensure the sampling of all levels of a factorial variable
biomod2_model-class biomod2 models objects class and functions
sre Surface Range Envelope
BIOMOD.projection.out-class BIOMOD_Projection() outputs objects class
BIOMOD.models.out-methods BIOMOD.models.out getters
BIOMOD.EnsembleModeling.out-class BIOMOD_EnsembleModeling() outputs objects class
BIOMOD.models.out-RemoveProperly remove properly BIOMOD_Modeling outputs
BIOMOD.formated.data-class BIOMOD_FormatingData() outputs objects class
BIOMOD.EnsembleModeling.out-method BIOMOD.EnsembleModeling.out getters
BIOMOD_tuning Tune models parameters
BinaryTransformation Convert species' probability of occurrence into binary presence-absence data using a predefined threshold
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Details

Type Package
Date 2016-03-01
Contact Wilfried Thuiller , Damien Georges
BugReports https://r-forge.r-project.org/R/?group_id=302
License GPL-2
RoxygenNote 5.0.1
Repository CRAN
Repository/R-Forge/Project biomod
Repository/R-Forge/Revision 716
Repository/R-Forge/DateTimeStamp 2016-03-01 10:01:06
Date/Publication 2019-03-08 09:25:30 UTC
NeedsCompilation no
Packaged 2019-03-08 09:14:08 UTC; ripley

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