dir.name can now be provided as project argument so that results may be saved in a custom folder.
predict with CTA algorithm and categorical variables on raster is now possible.
Changed evaluation for EM models merging PA datasets (em.by = "algo" or em.by = "all") so that evaluation uses the union of PA data sets instead of the whole environmental space supplied.
Minor changes
Individual EM models projected as raster are now saved with INT2S data format when on_0_1000 is set to TRUE.
Homogenize the use of load functions (useget_[...],load_stored_objectandBIOMOD_LoadModels, instead ofget(load(...))) and the workflow within get_[...] functions (useload_stored_objectand similar arguments such asas.data.frame,full.name, …).
Adapting predict workflow to properly use S4 class.
Homogenize BIOMOD.ensemble.models.out and BIOMOD.models.out objects
Add slots in BIOMOD.ensemble.models.out object for evaluations, variables importance and predictions.
Moved .Models.save.objects in BIOMOD_modeling to .fill_BIOMOD.models.out in biomod2_internal.R.
Save slots within BIOMOD.ensemble.models.out and use load_stored_object to directly get them within get_[...] functions.
Bug Fix
Validation data can now be properly combined with Pseudo-Absence in BIOMOD_FormatingData, instead of throwing an error linked to data.mask.
Argument on_0_1000 can now be passed without errors so that projection may either be on a range from 0 to 1 or from 0 to 1000. The latter option being more effective memory-wise.
Completed argument check for function BIOMOD_EnsembleModeling so that em.by can not be of length > 1.
Corrected function .get_models_assembling so that it did not confound MAXENT.Phillips2 with MAXENT.Phillips when grouping models by algorithm in BIOMOD_EnsembleModeling.
get_prediction method for BIOMOD.ensemble.models.out now accepts an evaluation arg. Evaluation values, variables' importance and Calibration/Evaluation predictions for ensemble models are now properly saved by BIOMOD_EnsembleModeling().
evaluation metrics are no longer calculated for models prob.ci.inf et prob.ci.sup.
Package now properly pass R CMD check.
BIOMOD_PresenceOnly now properly manage NA.
Corrected bm_PlotResponseCurves to only plot show.variables.
get_predictions.BIOMOD.projection.out now properly works when asked for a subset of model.
add do.progress parameter (to render or not progress bar) and dir.name parameter in BIOMOD_FormatingData and biomod2 objects (Mathieu B. request)
fix BIOMOD_PresenceOnly function by removing ecospat dependency
4.1 (2022-07-12)
fix bugs following major release 4.0
4.0 (2022-03-01)
MAJOR RELEASE
clean all functions, reorganize files, remove old / unused functions
standardize function names and parameter names
update roxygen2 documentation for all functions, including examples
create github website to host documentation, examples, vignettes, news
2021
3.5-3 (2021-11-02)
clean BIOMOD classes definitions and functions (biomod2_classes files)
clean BIOMOD_FormatingData function
clean BIOMOD_ModelingOptions function
fix BIOMOD_FormatingData : test class condition only a first element (to deal with matrix / array objects)
fix BIOMOD_EnsembleForecasting for EMcv model when only one single model was kept
3.5-2 (2021-10-18)
fix BIOMOD_PresenceOnly function (previously BIOMOD_presenceonly)
fix BIOMOD_CrossValidation function (previously BIOMOD_cv)
fix internal function to find MinMax values, when factor included : should get clamping mask to work
2018-2019
3.3-20 (2019-03-05)
Remove maxent Tsurukoa because not maintained anymore (required by CRAN team)
3.3-18 (2018-07-04)
fix the gbm multicore issue
3.3-17 (2018-04-23)
correct the single presence pseudo-absences generation bug (Matthias G.)
2016
3.3-6 (2016-01-14)
add get_predictions function for ensemble models
3.3-5 (2016-01-04)
MARS models are now computed throw earth package (was mda in previous versions)
MARS now supports factorial explanatory variables
MARS now supports formula
2015
3.3-4 (2015-11-04)
update BIOMOD_tuning function (Frank B.)
3.3-3 (2015-10-27)
force sampling of each level of factorial variables
add betamultiplier parameter to tune MAXENT.Phillips (Frank B. request)
3.3-00 (2015-10-05)
MAJOR RELEASE
optimize the memory consumption of projections and ensemble projections procedure
add the possibility to run MAXENT.Phillips with proper background data
classical version of MAXENT has been renamed MAXENT.Phillips
add a new version of MAXENT MAXENT.Tsuruoka
3.2-00 (2015-07-28)
add 3 new functions in biomod2 (Frank B. contribution)
BIOMOD_cv to control models cross validation procedure
BIOMOD_presenceonly to evaluate biomod models using boyce and mpa indices
BIOMOD_tuning to automatically tune BIOMOD_ModelingOptions parameters
2014
3.1-59 (2014-10-23)
add model evaluation scores plotting function
dependence to ggplot2
3.1-53 (2014-08-06)
new ensemble models names to be more coherent with formal models names
3.1-44 (2014-05-20)
possibility to use user defined function to influence the way models are weighted in weighted mean ensemble models (thanks to Frank B.)
3.1-43 (2014-05-20)
add of as.data.frame argument for get_evaluations() function to enable formal and ensemble models evaluation scores merging
3.1-42 (2014-05-19)
enable ensemble forecasting models selection (thanks to Robin E.)
2013
3.1-17 (2013-10-23)
add parameter to control amount of memory reserved for MAXENT calculations (via java) (thanks to Burke G.)
optimization of memory consumption in models projections when do.stack argument is set to FALSE
binary and filtering projections output re-activated
3.1-1 (2013-09-04)
limitation of package dependencies
fairely definition of package namespace
add functions to update biomod2 objects from a version to the current one
3.0.2 (2013-07-23)
new functions to evaluate a-posteriori models quality
remove weights for models scaling and set it FALSE by default
3.0.0 (2013-07-01)
MAJOR RELEASES
ensemble models are now biomod2 models objects (should be predicted, evaluated, and you can do variables importance) the same way than all formal biomod2 models
possibility to produce ensemble models response plot
ensemble forecasting output is now a biomod2_projection object: should be plotted…
ensemble forecasting is now doable without doing previous projections (even if it is still advised). Can work with raw explanatory variables
getter and setter function have been renamed
new variable_importance function
…
2.1.37 (2013-06-12)
change (temporally?) gam default package from mgcv to gam to deal with memory (cache) over-consuming (thanks to Burke G.)
update of response.plot2 function (optimization + deal with factorial variables)
2.1.32 (2013-05-30)
weights for user defined pseudo-absences are now supported (thanks to Rui F.)
deal with unknown factors predictions (thanks to Denis M.)
2.1.13 (2013-03-06)
Add ProbDensFunc() function to package to produce nice plots that show inter-models variability
2.1.12 (2013-03-04)
add rasterVis dependency for nicer biomod2 plots
PA.dist.min and PA.dist.max are now defined in meters when you work with unprojected rasters in disk pseudo absences selection
2.1.9 (2013-02-28)
possibility to indicate manually which data should be used for calibration (resp. for validation) of models within BIOMOD_Modeling
2.1.9 (2013-02-27)
one var modeling supported (thanks Anne O.)
new options for response curves plotting (col, lty, data_species…)
2.1.8 (2013-02-25)
response plot supports now formal models
2.1.0 (2013-02-21)
MAJOR RELEASE
CRAN SUBMISION
add of a modeling.id arg (BIOMOD_Modeling) for prevent from no wanted models overwriting and facilitate models tests and comparisons (thanks Frank B.)
change of biomod2 dataset
vignettes and help files update (thanks Sam P. & Signe N.)
save link between modeling and projection objects
add pROC package dependency
add a modeling cleaner that remove modeling objects from both memory and hard drive: RemoveProperly()
2.0.11 (2013-02-18)
possibility to consider a user.defined pseudo absences selection (thanks to Signe N.)
possibility to switch off stepwise glm selection (**thanks Frank B.*)
2.0.9 (2013-02-15)
automatic save on hard drive of BIOMOD_Projection outputs
2.0.8 (2013-02-14)
BIOMOD_LoadModels supports multiple models input
deal with NA in evaluation table issue (**thanks Frank B.*)
2.0.7 (2013-02-12)
bug on weights corrected (thanks to Lugi M.)
2.0.3 (2013-01-18)
deal with MAXENT categorical variables and categorical raster input
2.0.0 (2013-01-17)
MAJOR RELEASE
CRAN SUBMISION
models built within biomod2 are now defined as “biomod2 models objects” (own scaling models, own predict function, …)
full paths are replaced by relative paths to favor portability
harmonization of names of objects that are saved on hard drive (more coherence between functions)
possibility to save projections directly in raster format (.grd or .img)