---
title: "News"
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vignette: >
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---

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## <i class="fas fa-code"></i> Development updates


### <i class="fa-solid fa-chess-rook"></i> 2026

##### Bugfix

- 4.3-4-6 : 
    + update user related messages : 
        * remove _test_ argument from `.fun_test[...]` functions and use them whenever possible
        * add `.fun_testIfNULL`, `.fun_testIfLength`, `.fun_testIfInOnlyOne`, `.fun_testIfSameSize` functions, and change `.fun_testIf01` and `.fun_testMetric` to `.fun_testIf0X` and `.fun_testIfSize`
        * add `.bm_cat2` function and update all _cat_ messages
        * add distinction between _cat_ and _message_, and switch most _warning_ to _message_
        * standardize / uniformize all _cat_, _message_, _stop_ and _warning_ messages
    + update default parameters in functions (set to NULL if possible)
    + add `seed.val` parameter in `bm_CrossValidation`
    + add check in `BIOMOD_Projection` and `BIOMOD_EnsembleForecasting` to deal with single model projection failing
    + remove `.BIOMOD_EnsembleForecasting.prepare.workdir` function 
    + fix `kfold` selection for non-binary data in `bm_CrossValidation`
    + add check in `bm_PseudoAbsences` to select presences in `PA.user.table` when `user.defined` strategy
    + fix `bm_Tuning` for DNN : multiple sets (PA x RUN), hidden `width` and `depth` parameters
    + fix `EMwmean` for abundance models using `RMSE`, `MSE`, `MAE` or `Max_error` as selection metrics
    + add new video tutorial on YouTube
- 4.3-4-5 : pass CRAN check

#### 4.3-4-4 Clean version (2026-01-22) 

- Upgrade `xgboost` package from 1.7.10.1 to 3.1.3.1 :
    + change modelling function from _xgboost_ to _xgb\_train_ in `ModelsTable`
    + update default parameters with `xgb.params` (for _objective_ and _verbosity_)
    + update `OptionsBigboss` data
    + deactivate tuning for XGBOOST until bug is fixed
    + authorize categorical variables for XGBOOST
    + change from _reshape_ to _type_ (_"response"_ or _"class"_ value) parameter in `xgboost::predict` function
    + give data to `xgb.train` function through `xgb.DMatrix`
- New `ModelsTable` and `OptionsBigBoss`

##### Bugfix

- Remove obsolete parameter (_transpose_) in `pROC::coords` function in `bm_FindOptimStat`
- Fix `bm_PseudoAbsences` with `strategy = 'user.defined'` and true absences in `resp.var`
- Update vignettes


### <i class="fas fa-pen-alt"></i> 2025

##### Bugfix

- 4.3-4-3 :
  + split *Main functions* example in 2 : *binary* and *abund*
  + add `DataSTOC` data set
  + fix tuning function for DNN
  + fix `biomod2_template_report.Rmd` to adapt to last plot changes and abundance data
  + fix `plot` function for `BIOMOD.formated.data` with `plot.type == "raster" & plot.valid` for `_allData_allRun` case
  + fix `metric.eval` in `plot.Rscore` in `bm_ModelAnalysis` function
- 4.3-4-2 :
  + merge `BIOMOD.formated.data` `plot` functions to deal with all data types, add `plot.valid` parameter
  + reformat `bm_ModelAnalysis` function
- 4.3-4-1 : change `color` to `fill`, and add `filtered.by` in `bm_Plot[...]Boxplot` functions (*Eval* and *VarImp*)

#### 4.3-4 DNN model (2025-06-04) 

- Add `DNN` : Deep Neural Network with `cito` package
- New `ModelsTable` and `OptionsBigBoss` 
- Tuning made with the `tune` function of `cito` package

##### Bugfix

- Fix `EMwmean` when only one model selected
- Fix `bm_RunModelsLoop` output list
- Fix plot function of `BIOMOD.projection.out` object

#### 4.3-3 Multiclass datatype (2025-05-20) 

##### Major Changes

- In _biomod2_classes_0_ file :
  + add new data type : _"multiclass"_
  + adaptation of `.BIOMOD.options.default.correct` function 
- In _biomod2_classes_1_ file :
  + adaptation of `plot` method for `BIOMOD.projection.out` object 
- In _biomod2_classes_3_ file :
  + adaptation of `.BIOMOD.formated.data.check_data`, `.plot.BIOMOD.formated.data.abundance`, `summary` and `show` function 
- In _biomod2_classes_4_ file :
  + `factor_levels` slot for `biomod2_model` class
  + update all `predict2` functions for single models to deal with the different data types
- In `bm_RunModelsLoop`, `BIOMOD_Projection`, `BIOMOD_EnsembleModeling` and `BIOMOD_EnsembleForecasting` functions :
  + management of model predictions format, in particular for _"ordinal"_ and _"multiclass"_ cases
- In _biomod2_classes_5_ file :
  + definition of `EMmode` and `EMfreq` with `predict` methods

##### Bugfix

- 4.3-2-3 : fix `data.type` in `bm_ModelingOptions`
- 4.3-2-2 : 
  + change the name of the metric `ROC` to `AUCroc`. It will switch automatically if you use `ROC`
  + add the metric `AUCprg` : Area Under Curve of the Precision-Recall-Gain curve

- 4.3-2-1 :
  + add `togglelayerselected`, `maximumbackground`, `maximumiterations`, `convergencethreshold`, `autofeature`, `jackknife`, `writeclampgrid`, `writemess`, `logfile` and `verbose` parameters in `MAXENT` parameters
  + fix `.check_calib.lines_names` for `BIOMOD.formated.data.PA` object in `bm_CrossValidation_user.defined`
  + merge `binary` and `nonbinary` models into `OptionsBigboss`
  + set `data.type = 'binary'` by default in `bm_ModelingOptions`
  + correct `.BIOMOD_Modeling.summary` 
  + remove `gam::` in `bm_MakeFormula`


#### 4.3-2 Report (2025-03-11)

- Add `call` slot for `BIOMOD.formated.data` and `BIOMOD.formated.data.PA`, `BIOMOD.models.out`, `BIOMOD.projection.out`, and `BIOMOD.ensemble.models.out` classes
- Add `BIOMOD_Report` function
- Add `.Rmd` templates in `inst/rmd/` folder (for _report_, _ODMAP_ and _code_)

#### 4.3-1 RangeSize (2025-03-03)

- Change `BIOMOD_RangeSize` to `bm_RangeSize`
- Change `BIOMOD_RangeSize` inputs to `BIOMOD.projection.out` objects
- Add new class `BIOMOD.rangesize.out`
- Change `bm_PlotRangeSize` input to `BIOMOD.rangesize.out` objects, and project maps with coordinates of `BIOMOD.projection.out` object
- Fix `show` outputs of `BIOMOD.[...].out` objects


#### 4.3-0 Abundance (2025-01-30)

##### Major Changes

- In _biomod2_classes_0_ file :
  + add new data types : _"binary"_, _"abundance"_, _"count"_, _"ordinal"_, _"relative"_, _"nonbinary"_
  + add `data.type`, `has.filter.raster` and `biomod2.version` slot for `BIOMOD.formated.data` and `BIOMOD.formated.data.PA` classes
  + add `.BIOMOD.options.default.correct` function (default changes and corrections depending on the data type (mainly for `type`, `method`, `family` and `distribution` options) to `BIOMOD.options.dataset`)
- In _biomod2_classes_1_ file :
  + add `.BIOMOD.formated.data.check_data` function (routine that can be applied to both original and evaluation datasets)
  + add `.plot.BIOMOD.formated.data.abundance` function (to plot formated data when data type is not binary)
  + update `BIOMOD.formated.data` summary to the different data types
- In _biomod2_classes_3_ file :
  + add `data.type` slot for `BIOMOD.models.out` class
  + add `set_new_dirname` and `set_new_dirname.models` functions (to recursively modify the `dir.name` slot in all biomod2 objects of an existing simulation directory)
- In _biomod2_classes_4_ file :
  + add `model_type` and `thresholds_ordinal` slot for `biomod2_model` class
  + update all `predict2` functions for single models to deal with the different data types (mainly between _binary_, _ordinal_ and the others)

- In `bm_CrossValidation` function :
  + split `.sample_mat` function into `.sample_num` and `.sample_class` functions
  + update all functions to deal with the different data types (mainly between _ordinal_ and the others)
- In `bm_FindOptimStat` function :
  + add new evaluation metrics : _"RMSE"_, _"MAE"_, _"MSE"_, _"Rsquared"_, _"Rsquared_aj"_, _"Max_error"_ (for abundance/count/relative data) and _"Accuracy"_, _"Recall"_, _"Precision"_, _"F1"_ (for ordinal data)
  + add `k` parameter
  + add `.contingency_table_ordinal` function
  + split `bm_CalculateStat` function into `bm_CalculateStatBin` and `bm_CalculateStatAbun` functions
- In `bm_VariablesImportance` function :
  + use _Spearman_ correlation for _ordinal_, _Pearson_ otherwise
- Use either `on_0_1000` or `on_1_1000` when making projections
- Correct and adapt tuning
- Add `bm_ModelAnalysis` function (_to analyse the residuals of single models_)

##### Minor Changes

- Update `ModelsTable` data with `nonbinary` data type
- Update `OptionsBigboss` data with all _nonbinary_ single models options
- Change `dir.name` slot within `BIOMOD.formated.data` into absolute one instead of relative by default
- Change `aes_string` to [`aes` + `.data`] in `bm_Plot[...]` functions
- Add `digits` and `overwrite` parameters in `BIOMOD_Projection` function
- Change `get_var_type` and `get_var_range` to internal functions (`.get_var_type` and `.get_var_range`)
<!-- - Remove `raster` dependency -->
- Remove deprecated functions and corresponding documentation
- Add vignette for abundance (_to help you navigate through the new datatypes available_)
- Update examples and documentation

##### Bugfix

- Fix stratified cross-validation strategy in `bm_CrossValidation` (partitions not being balanced correctly)
- Fix selection of metrics in `bm_PlotEvalMean`
- Fix formula when given by user in `bm_Tuning` (to be able to run the step AIC with the user formula)
- Change `scale.models = FALSE` by default in `BIOMOD_Modeling` and `bm_RunModelsLoop`


### <i class="fas fa-pencil-alt"></i> 2024

##### Bugfix

- 4.2-6-2 :
  + fix `get_evaluations` and `get_variables_importance` message when data is not available (extended to `bm_Plot[...]` functions)
  + ~~add cluster management code through `parallel::stopCluster` and `foreach:::.foreachGlobals`~~ <br/>
  finally rather through `.errorhandling` in `foreach` loop in `bm_RunModelsLoop` (_for MAXENT on Windows_)
  + merge request improving balanced partitions for stratification strategy in `bm_CrossValidation`
  + fix metric selection in `bm_PlotEvalMean`
  + add new tutorial video (_for version 4.2-6_)
  + add `MAXENT.partitions`, `MAXENT.kfolds`, `MAXENT.user.grp` and `MAXENT.tune.args` parameters in `bm_Tuning` function
- 4.2-6-1 : fixed path failure within species name (e.g. data format like `tif`)


#### 4.2-6 RFd and some tuning (2024-07-22)

- Warning ! Some options for `OptionsBigboss` have been modified (concerns only ANN, CTA and RF models)
- Some changes for the tuning ranges.
- Add `RFd` : Random Forest with a down-sampling method.
- Add `seed.val` for `bm_pseudoAbsences` and `BIOMOD_FormatingData`.
- Add `fact.aggr` argument for pseudo-absence selection with the random and disk methods. It allows to reduce the resolution of the environment.
- Possibility to give the same options to all datasets with _"for_all_datasets"_ in `bm_ModelingOptions`.

##### Bugfix

- 4.2-5-2 :
  + fixed `BIOMOD_EnsembleModeling` when multiple PA datasets (`obs` and `fit` not matching when calling `bm_FindOptimStat`)
  + always keep same order for variable names for `new.env` in `BIOMOD_Projection` and `BIOMOD_EnsembleForecasting`
- 4.2-5-1 :
  + removed `tests/` folder (unused)
  + fixed check for variable names for `new.env` in `BIOMOD_Projection` and `BIOMOD_EnsembleForecasting`
  + fixed connection issue with `MAXENT` tuning


#### 4.2-5 Modeling options and Tuning (2024-05-02)

##### Major Changes

- Add print function for `BIOMOD.options.dataset` and `BIOMOD.models.options` classes
- Add `GAM.binary.gam.gam` and `GAM.binary.mgcv.bam` in `OptionsBigboss` dataset
- Add checks for `obs` and `fit` parameters in `bm_FindOptimStat`
- In `bm_Tuning` function :
    + add `MAXENT.algorithm` and `MAXENT.parallel` parameters
    + be sure to update default tuning parameters if not all provided
    + fix tuning for `XGBOOST` and `SRE`
    + fix optimization of formula
    + switch from `gamSpline` to `gamLoess` method to tune `GAM.gam.gam` model, and add `GAM.span` and `GAM.degree` parameters
- Fix multiple cases when using different settings of PA / cross-validation / modeling options through all the different secundary functions and `BIOMOD_Modeling`


##### Minor Changes

- Add vignette for cross-validation (_to prepare your own calibration / validation datasets_)
- Add vignette for modeling options (_to help you navigate through the new way of parameterizing single models_)
- Update examples and documentation

##### Bugfix

- Add `try` and error message in call for models in `bm_RunModelsLoop`
- Check for predictions `>1000`
- Correct `BIOMOD_EnsembleForecasting` when using `data.frame`
- Correct predictions for `EMci` (removing round)



### <i class="fas fa-feather"></i> 2023 

#### 4.2-5 Modeling options and Tuning (2023-09-12)

##### Major Changes

- Reformat modeling options, how they are created and how they are given to models : 
     + Create `BIOMOD.options.default` and `BIOMOD.options.dataset` classes, retrieving default parameters and values with `formalArgs` function
     + Modeling options can now be different for PA x cross-validation datasets x models
     + Add `ModelsTable` and `OptionsBigboss` datasets containing single models informations and pre-defined modeling options
     + Move `BIOMOD_ModelingOptions` to `bm_ModelingOptions`
     + Call `bm_ModelingOptions` directly in `BIOMOD_Modeling` and add related `OPT.[...]` parameters
- Move `BIOMOD_Tuning` to `bm_Tuning` and adapt it to match with new modeling options
- Modify the call to single models in `bm_RunModelsLoop` in a more generalized way dealing with new modeling options

##### Minor Changes

- Remove `BIOMOD_PresenceOnly` function and add `BOYCE` and `MPA` indices into `bm_FindOptimStat` function
- Save ensemble projections with `FLT4S` datatype only when EMcv is activated, otherwise use `INT2S`
- Add vignette for data preparation (_questions you should ask yourself before modeling_)
- Correct getters (variable importance, built models)
- Update examples and documentation

##### Bugfix

- 4.2-4-10 : fixed `wrap` applied to a `data.frame` in `BIOMOD_Projection`
- 4.2-4-9 : fixed `predict` method for `RF` with `do.classif = FALSE`
- 4.2-4-8 : improved tests in `bm_PlotEvalMean`
- 4.2-4-7 : fixed `do.classif` ignored in `BIOMOD_ModelingOptions`
- 4.2-4-6 : fixed parallelization in `BIOMOD_Projection`
- 4.2-4-5 : fixed summary method for `BIOMOD.formated.data` and `BIOMOD.formated.data.PA`
- 4.2-4-4 : fixed `bm_PlotResponseCurves` for ensemble models merged by algo (for Maxent)
- 4.2-4-3 :
  + added `point.size` argument to `plot.BIOMOD.Formated.data`
  + added `maxcell` argument to `plot.BIOMOD.projected.out`
- 4.2-4-2  : set XGBOOST `verbose = 0` (from `verbose = 1`)
- 4.2-4-1 : fixed `BIOMOD_FormatingData` checks for `resp.xy`


#### 4.2-4 XGBOOST (2023-06-21)

##### Major Changes

* added XGBOOST as a possible algorithm in `BIOMOD_Modeling`

##### Minor Changes

* changed `CV.do.full.models` default value to `FALSE`

##### Bugfix

- 4.2-3-5 :
  * fixed some more issues related to categorical variables badly interacting with missing values. Projection and Ensemble Forecasting are now only calculated on cells without any missing values.
  * removed obsolete code for SRE pseudo absences sampling with categorical variables, as SRE do not work with categorical variables
  * added internal function to get mask of data `.get_data_mask`
- 4.2-3-4 : fixed bug in `BIOMOD_Modeling` when using `sampsize` as a vector. argument `strata` was badly formatted
- 4.2-3-3 : fixed bug in `BIOMOD_EnsembleModeling` for additional projection with only one environmental variables
- 4.2-3-2 : fixed bugs in `BIOMOD_EnsembleForecasting` when several projection are running simultaneously and using the same temporary directory
- 4.2-3-1 : fixed bugs in `bm_CrossValidation` with `user.defined` tables badly formatted (TRUE/FALSE for data not in the given PA dataset are now properly transformed into NA)


#### 4.2-3 Cross-Validation and Pseudo-Absences (2023-05-09)

##### Major Changes

* Improved pseudo-absence management: it is now possible to have pseudo-absence dataset of different size and algorithm can be setup to run on different pseudo-absence dataset (with `models.pa` argument in `BIOMOD_Modeling`).
* Rework and harmonization of cross-validation function. `BIOMOD_CrossValidation` have been renamed `bm_CrossValidation` and cross-validation with k-fold, stratified and environmental strategy now work properly with pseudo-absence dataset. All cross-validation strategy can now be called directly through `BIOMOD_Modeling`.

##### Minor Changes

* improved Documentation (`get_evaluations`, `BIOMOD_EnsembleModeling`, `bm_RunModelsLoop`, `bm_RunModel`)
* updated website tutorial to use current biomod2 version
* removed unused parameter `save.output`. output are now automatically saved.
* improved management of categorical raster for both `terra` and `raster`
* `CV.perc` (formerly `data.split.perc`) now uses a 0-1 range (instead of 0-100)
* deprecated arguments for `BIOMOD_EnsembleModeling` now gives an error. 
* added argument `metric.select.dataset` to `BIOMOD_EnsembleModeling` to choose the dataset which evaluation metric should be used to filter and/or weigh the ensemble models. Default value is now 'validation' instead of 'evaluation'.
* added argument `na.rm` to `BIOMOD_EnsembleModeling` to harmonize the management of `NA` among individual model predictions. 

##### Bugfix

* validation metric calculation now properly use the calibration threshold (i.e a threshold optimized on calibration data instead of validation data). This can lead to less optimistic threshold-dependent validation metric.
* fixed SRE projection assuming the same variables ordering in calibration and projection data
* ensemble model can again be calculated over models without validation
* correct print for multiple values in `RF$sampsize` parameter in `BIOMOD_ModelingOptions`
* fixed layer name in `BIOMOD_Projection` and `BIOMOD_EnsembleForecasting` when `terraOption(todisk = TRUE)` is activated (for large or numerous raster).
* fixed Ensemble Models based on models without cross-validation ("allRun")
* model is now robust to using `data.table` object (that are converted into standard `data.frame`).
* fixed projection raster name when using `do.stack = FALSE` and `resp.name` with `.` inside.
* fixed using user-defined pseudo-absences along with `filter.raster = TRUE` in `bm_PseudoAbsence`.
* fixed weights calculation when using only one pseudo-absence dataset
* fixed summary and show method for `BIOMOD.formated.data.PA`

##### Internal 

* add internal function `get_species_data` and `get_eval_data`
* removed `.BIOMOD_Modeling.prepare.data`
* reorganised `bm_RunModelsLoop` to do the PA loop within the function
* `calib.lines` and `eval.lines` variable names are standardised (no more `calibLines` or `eval_lines`)
* removed dependency to `data.table` (removed use of `rbindlist`)
* added `.get_env_class` to reduce code redundancy
* renamed `categorical_stack_to_terra` into `.categorical_stack_to_terra`
* dispatched some of `BIOMOD_FormatingData` checks into `bm_PseudoAbsences`

#### 4.2-2 Improvement patch (2023-01-13)

##### Major Changes

* `'.tif'` is available as an output format for raster projection
* `'.tif'` is the new default output format for raster projection
* Improved `plot` and `summary` methods for `BIOMOD_FormatingData` output. These method now support the use of `calib.lines` to explore how the cross-validation dataset are structured.
* Updated `plot` methods for `BIOMOD.projection.out` objects so that it uses `ggplot2` for nicer plots.
* Binary and Filtered transformation are now properly stored in `BIOMOD.projection.out` objects. They can be loaded from the disk with `get_predictions` or represented through `BIOMOD.projection.out` plot method.
* `get_predictions` now return a proper `data.frame` (unless projection on spatial data) with many additional information available. Old behavior can be reproduced by using `get_predictions(x, model.as.col = TRUE)`.
* `get_evaluations` now return a cleaner `data.frame` with more consistent information available.

##### Minor Changes

* Simplified maxent model names:  'MAXENT.Phillips' -> 'MAXENT' (based on `maxent.jar`); 'MAXENT.Phillips.2' -> 'MAXNET' (based on `maxnet` package).
* `BIOMOD_FormatingData` now gives warning when several input data points are located in the same raster cells
* Added options `filter.raster` in `BIOMOD_FormatingData` to filter data points so that none are located in the same raster cells.
* `BIOMOD_EnsembleModeling` now have an argument `em.algo` to select the ensemble algorithm to be computed. Separate arguments are now deprecated (`prob.mean`, `prob.median`, `prob.cv`, `prob.ci`, `committee.averaging`, `prob.mean.weight`). Building all possible ensemble models can now be done with `em.algo = c('EMmean','EMmedian','EMcv','EMci','EMca','EMwmean')`.
* Some possible values for `em.by` have slightly changed: 'PA_dataset' -> 'PA', 'PA_dataset+repet' -> 'PA+run' and 'PA_dataset+algo' -> 'PA+algo'
* Added an appropriate message when all models fail for `BIOMOD_Modeling` and `BIOMOD_EnsembleModeling`.

##### Bugfix

* Fixed `MAXENT.Phillips.2` and single variable models.
* Fixed ensemble models when several filtering metrics were asked and some combination of ensemble/metrics had no models
* Bugfix for projection for ensemble models to ensure that the proper set of models was selected
* Bugfix for `BIOMOD_CrossValidation` for block-stratified sampling
* Bugfix for `BIOMOD_CrossValidation` for pseudo-absences 

##### Internal Changes

* Array have disappeared from most internal functions
* Removed `rasterVis` from `Suggests`
* Added `tidyterra` and `ggtext` to `Suggests`
* Added checks to `get_evaluation` when models have no evaluations.

### <i class="fas fa-chess-pawn"></i> 2022

#### 4.2-1 Bugfix patch

##### Major Changes

* Package `sp` is back into `Imports` due to the need to use `sp::read.asciigrid`
* Added control for `terra` version number (>= 1.6-33) as `terra` 1.6-41 was released on CRAN.
* With `do.stack = TRUE`, only stacked projection are now saved to the disk.

##### Minor Changes

* Added `initial_heap_size` and `max_heap_size` in `MAXENT.Phillips` modeling options
* Improved projection efficiency for raster with `MAXENT.Phillips`.

##### Bugfix

* Fixed `MAXENT.Phillips` predict method for large dataset (require `sp::read.asciigrid`). 
* Fixed ensemble models using a single PA dataset with `em.by = 'all'` or `'algo'`.
* Models using repetition dataset cannot be merged anymore with models using Full dataset in `BIOMOD_EnsembleModeling`.
* Fixed error in `BIOMOD_EnsembleForecasting` when a single evaluation metric was available and binary/filtered transformation were asked for.
* Bugfix for plot method for `BIOMOD.formated.data.PA` object.
* Fixed `MAXENT.Phillips` for Windows.
* Fixed using `do.stack = FALSE` with `BIOMOD_Projection`.
* Fixed `EMcv` ensemble modeling for `data.frame` by removing dependency to `raster::cv`.
* Fixed `free` method with `PackedSpatRaster`
* Fixed `BIOMOD_FormatingData` in case where no coordinates are given

##### Internal

* Updated github workflow : removed obsolete ubuntu 18.04 ; added test on r-devel ; added cache for R packages.
* Updated `MAXENT.Phillips` `predict2` method for `SpatRaster` so that it saves environmental data as `.asc` and do not use the `data.frame` method.
* Fixed some automatic boolean conversion
* Cleaned up `BIOMOD.formated.data@data.mask` slot. `data.mask` can now be safely saved and re-opened ; `data.mask` can now store a different extent for evaluation dataset

####  4.2-0 Terra Update

##### Major Changes

* Package now rely only on `terra` (`> 1.6.33`) and do not automatically import `raster` and `sp`.
* Moved `raster` and `sp` package into `SUGGESTS` rather than `DEPENDS`.
* `raster` and `sp` input data type are still supported.
* Package dataset now are now documented and loaded with `data()` .

##### Minor Changes

* `bm_BinaryTransformation` now always returns `0`/`1` and never `TRUE`/`FALSE`
* Added a check to `bm_PlotResponseCurves` for `new.env` possible data types.
* `BIOMOD_Projection` and `BIOMOD_EnsembleForecasting` now properly support matrix as `new.env`
* `get_prediction` on `biomod.projection.out` generated from `BIOMOD_Projection` based on `SpatRaster` with arg `as.data.frame = TRUE` are now possible.
* `bm_BinaryTransformation` now return same type of object as its input
* Improved communication for `BIOMOD_RangeSize`, indicating how comparison are done depending on the number of models in current vs future.
* Added argument check for `BIOMOD_CrossValidation`

##### Bugfix

* MAXENT.Phillips models can now properly fail
* bugfix for `bm_BinaryTransformation` with `data.frame`/`matrix` and `do.filtering = TRUE`
* Removed obsolete warning about CTA and categorical variables when using raster
* `bm_PlotResponseCurves` now work with factors in univariate representation
* `bm_PlotResponseCurves` properly handles `SpatRaster` and `Raster` as `new.env`
* Bugfix for predictions with `MAXENT.Phillips` and a single environmental variable
* Bugfix for `BIOMOD_EnsembleForecasting` so that it properly accounts for `new.env.xy` when projecting on `matrix` or `data.frame`.
* `BIOMOD_EnsembleModeling` now works when called for a single ensemble model
* Improved argument check for `BIOMOD_RangeSize`. Comparisons with non-binary values throw errors.
* bugfix for `BIOMOD_RangeSize` and data.frame method
* `BIOMOD_RangeSize` `data.frame` method now handles 1 current vs n future projection
* bugfix for `BIOMOD_PresenceOnly` that can now work when evaluation data are provided
* bugfix for `BIOMOD_PresenceOnly` that can now work when only the EM have been provided
* expanded support for `BIOMOD_PresenceOnly` to `SpatRaster` and `SpatVector`.
* `build_clamping_mask` now support categorical variables
* fixed ensemble model EMcv based on a single environmental variable

##### Internal Changes

* New internal function `.categorical2numeric` to transform categorical variables into numeric within a `data.frame`.
* New internal function `.get_categorical_names` to retrieve categorical variable names from a `data.frame`.
* Split `load_stored_object` method into a method for `BIOMOD.stored.SpatRaster` and a method for all other `BIOMOD.stored.data`.
* `BIOMOD.stored.SpatRaster` stores `PackedSpatraster` and not `SpatRaster`.
* New internal function `.CompteurSp` based on old function CompteurSp that was defined within a function.
* Removed obsolete function `check_data_range()`.

#### 4.1-3

##### Bugfix

* Ensemble models that fails (e.g. EMcv with only one models) will not crash the full ensemble run. Instead a warning is generally displayed at the beginning and the resulting object will list failed models.
* Fixed CTA raster prediction for categorical variables.
* Fixed binary transformation in `BIOMOD_EnsembleForecasting`.

#### Internal Changes

* New internal function .get_kept_models to generate list of models kept by ensemble modeling depending on `metric.select`.
* Improved checks for `BIOMOD_EnsembleModeling` to generate warnings when ensemble models are expected to be run with <= 1 models.
* Repaired support for cross-validation table given as `data.frame` instead of `matrix`.

#### 4.1-2 (2022-09-29)

##### Major changes

* `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 (*use* `get_[...]`*,* `load_stored_object` *and* `BIOMOD_LoadModels`*, instead of* `get(load(...))`) and the workflow within `get_[...]` functions (*use* `load_stored_object` *and similar arguments such as* `as.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_predictions` 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.


##### Miscellaneous

  * Using models with a single predictor requires updating `gbm` package to its development version at rpatin/gbm can be used. (see issue *<https://github.com/biomodhub/biomod2/issues/102>*)

#### 4.1-1 (2022-08-30)

  * 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


### <i class="fas fa-charging-station"></i> 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
  

### <i class="fas fa-battery-full"></i> 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.**)


### <i class="fas fa-battery-three-quarters"></i> 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` 


### <i class="fas fa-battery-half"></i> 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


### <i class="fas fa-battery-quarter"></i> 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.**) 


### <i class="fas fa-battery-empty"></i> 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 raster in disk pseudo-absence 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-absence 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`)


### <i class="fas fa-bahai"></i> Year 0

#### 1.x.x

  * development phase
