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Distribution Modeling","monthly_downloads":6308,"total_dependent_repos":11,"total_dependent_packages":7,"readme":"[![Cran Version](https://www.r-pkg.org/badges/version/biomod2?color=yellow)](https://cran.r-project.org/package=biomod2)\n[![Github Version](https://img.shields.io/badge/devel%20version-4.3--4--6-blue.svg)](https://github.com/biomodhub/biomod2)\n[![Last Commit](https://img.shields.io/github/last-commit/biomodhub/biomod2.svg)](https://github.com/biomodhub/biomod2/commits/master)\n[![R-CMD-check](https://github.com/biomodhub/biomod2/actions/workflows/R-CMD-check.yml/badge.svg)](https://github.com/biomodhub/biomod2/actions/workflows/R-CMD-check.yml)\n\n\u003c!-- [![Download](http://cranlogs.r-pkg.org/badges/grand-total/biomod2?color=yellow)](https://cran.r-project.org/package=segclust2d) --\u003e\n\u003c!-- \nbadge for github version :\nbadger::badge_github_version(\"biomodhub/biomod2\", \"blue\") \n--\u003e\n\n\u003cstyle\u003e\n.zoom p {\nwidth:800px;\nmargin-left: auto;\nmargin-right: auto;\n}\n.zoom p:hover {\nwidth:1500px;\nposition: relative;\nz-index: 10;\n}\n\u003c/style\u003e\n\n\n\u003cdiv align=\"center\"\u003e\n\u003cp\u003e\u003cimg src=\"articles/pictures/LogoBiomod.png\" alt=\"Logo biomod2\" width=150px\u003e\u003c/img\u003e\u003c/p\u003e\n\n\u003cb\u003e------------------------------------------------------------\u003cbr/\u003e\nSpecies distribution modeling, \u003cbr/\u003e\ncalibration and evaluation, \u003cbr/\u003e\nensemble modeling \u003cbr/\u003e\n------------------------------------------------------------\u003cbr/\u003e\n\u003c/b\u003e\n\nhttps://biomodhub.github.io/biomod2/\n\u003c/div\u003e\n\n\n### \u003ci class=\"fas fa-tools\"\u003e\u003c/i\u003e Installation\n\n\u003cbr/\u003e\n\n- **Stable version** [![v](https://www.r-pkg.org/badges/version/biomod2?color=yellow)](https://cran.r-project.org/package=biomod2) from [cran](https://CRAN.R-project.org/package=biomod2) :\n\n```R\ninstall.packages(\"biomod2\", dependencies = TRUE)\n```\n\n\u003cbr/\u003e\n\n- **Development version** [![v](https://img.shields.io/badge/devel%20version-4.3--4--6-blue.svg)](https://github.com/biomodhub/biomod2) from [biomodhub](https://github.com/biomodhub/biomod2) :\n\n```R\nlibrary(devtools)\ndevtools::install_github(\"biomodhub/biomod2\", dependencies = TRUE)\n```\n\n\u003cbr/\u003e\u003cbr/\u003e\n\u003ci class=\"fas fa-exclamation-triangle\"\u003e\u003c/i\u003e All changes between versions are detailed in [News](https://biomodhub.github.io/biomod2/articles/news.html).\n\n\u003ci class=\"fas fa-video\"\u003e\u003c/i\u003e A new video tutorial is available on the [Video page](https://biomodhub.github.io/biomod2/articles/videos_2_biomod2.html).\n\u003cbr/\u003e\u003cbr/\u003e\n\u003cbr/\u003e\u003cbr/\u003e\n\n\n### \u003ci class=\"fas fa-envelope-open-text\"\u003e\u003c/i\u003e `biomod 4.3-4-6` - Abundance modeling\n\n\u003ci class=\"fas fa-exclamation-triangle\"\u003e\u003c/i\u003e Please **feel free to indicate if you notice some strange new behaviors** !\n\n#### \u003ci class=\"fas fa-exchange-alt\"\u003e\u003c/i\u003e What is changed ?\n\n- Nothing for presence/absence (or presence-only) modelling.\n- `bm_RangeSize` computes the difference between binary predictions, \u003cbr/\u003e and is called by `BIOMOD_RangeSize` which can take as input `BIOMOD.projection.out` objects.\n- Vignettes and example tutorials have been updated.\n \n#### \u003ci class=\"fas fa-plus-square\"\u003e\u003c/i\u003e What is new ?\n\n- **Non-binary** data ! Check the [Main functions (abund)](https://biomodhub.github.io/biomod2/articles/examples_1_mainFunctions_AB.html) page for examples.\n- 6 values can be given to `data.type` new parameter in `BIOMOD_FormatingData` : \u003cbr/\u003e *binary*, *count*, *multiclass*, *ordinal*, *relative*, *abundance*.\n- 2 new ensemble models have been added to deal with qualitative data type : `EMmode` and `EMfreq`. \u003cbr/\u003e\u003cbr/\u003e\n- **DNN** (Deep Neural Network) model has been added through `cito` package. It can be used with all data types. \u003cbr/\u003e\nBe sure to have a look at [cito documentation](https://citoverse.github.io/cito/reference/cito.html) before, especially the part about the `torch` installation. \u003cbr/\u003e\u003cbr/\u003e\n- `bm_ModelAnalysis` renders classical graphics to explore the quality of single models\n- `BIOMOD_Report` renders `.html` reports to help summarize modeling steps\n\n\u003cbr/\u003e\u003cbr/\u003e\n\n\u003cdiv class=\"zoom\"\u003e\n\u003cp\u003e\u003cimg src=\"articles/pictures/SCHEMA_BIOMOD2_WORKFLOW_functions.png\" alt=\"Main workflow\"\u003e\u003c/img\u003e\u003c/p\u003e\n\u003c/div\u003e\n\n\u003cbr/\u003e\u003cbr/\u003e\n\u003cbr/\u003e\u003cbr/\u003e\n\u003cbr/\u003e\u003cbr/\u003e\n\u003cbr/\u003e\u003cbr/\u003e\n\n\n### \u003ci class=\"fas fa-envelope\"\u003e\u003c/i\u003e `biomod 4.2-6` - Improved OptionsBigBoss and new model\n\n#### \u003ci class=\"fas fa-exchange-alt\"\u003e\u003c/i\u003e What is changed ?\n\n- To improve the models, we made some change in the options for [**`OptionsBigboss`**](https://biomodhub.github.io/biomod2/reference/OptionsBigboss.html). (This only affects the ANN, CTA and RF models.) You can check all your options with the `get_options()` function.\n- To reduce the tuning calculation time, we update the tuning ranges for ANN, FDA and MARS models.\n\n#### \u003ci class=\"fas fa-plus-square\"\u003e\u003c/i\u003e What is new ?\n\n- `biomod2` has a new model: **RFd**. It's a Random Forest model with a down-sampling method.\n- You can now define _seed.val_ for `bm_PseudoAbsences()` and `BIOMOD_FormatingData()`.\n- New _fact.aggr_ argument, for pseudo-absences selection with the random and disk methods, allows to reduce the resolution of the environment.\n- Possibility to give the same options for all datasets with _\"for_all_datasets\"_ in `bm_ModelingOptions()`.\n\n\u003cbr/\u003e\n\n\n### \u003ci class=\"fas fa-envelope\"\u003e\u003c/i\u003e `biomod 4.2-5` - Modeling options \u0026 Tuning Update\n\n#### \u003ci class=\"fas fa-exchange-alt\"\u003e\u003c/i\u003e What is changed ?\n\n- modeling options are now automatically retrieved from single models functions, normally allowing the use of all arguments taken into account by these functions\n- tuning has been cleaned up, but keep in mind that it is still a quite long running process\n- in consequence, `BIOMOD_ModelingOptions` and `BIOMOD_Tuning` functions become secondary functions (`bm_ModelingOptions` and `bm_Tuning`), and modeling options can be directly built through `BIOMOD_Modeling` function\n\n#### \u003ci class=\"fas fa-plus-square\"\u003e\u003c/i\u003e What is new ?\n\n- `ModelsTable` and `OptionsBigboss` datasets (*note that improvement of bigboss modeling options is planned in near future*)\n- 3 new vignettes have been created :\n    - [data preparation](https://biomodhub.github.io/biomod2/articles/vignette_dataPreparation.html) (*questions you should ask yourself before modeling*)\n    - [cross-validation](https://biomodhub.github.io/biomod2/articles/vignette_crossValidation.html) (*to prepare your own calibration / validation datasets*)\n    - [modeling options](https://biomodhub.github.io/biomod2/articles/vignette_modelingOptions.html) (*to help you navigate through the new way of parametrizing single models*)\n\n\u003cbr/\u003e\n\n\n### \u003ci class=\"fas fa-envelope\"\u003e\u003c/i\u003e `biomod 4.2` - Terra Update\n\n#### \u003ci class=\"fas fa-exchange-alt\"\u003e\u003c/i\u003e What is changed ?\n\n- `biomod2` now relies on the new [`terra`](https://github.com/rspatial/terra) package that aims at replacing `raster`and `sp`.\n- `biomod2` is still compatible with old format such as `RasterStack`and `SpatialPointsDataFrame`.\n- `biomod2` function will sometimes return `SpatRaster` from package `terra` that you can always convert into `RasterStack` using function `stack` in `raster`.\n\n\u003cbr/\u003e\n\n\n### \u003ci class=\"fas fa-envelope\"\u003e\u003c/i\u003e `biomod 4.1` is now available\n\n`/!\\` Package fresh start... meaning some changes in function names and parameters. We apologize for the trouble `\u003e{o.o}\u003c` \u003cbr/\u003e\nSorry for the inconvenience, and please **feel free to indicate if you notice some strange new behaviors** !\n\n#### \u003ci class=\"fas fa-exchange-alt\"\u003e\u003c/i\u003e What is changed ?\n\n- all code functions have been cleaned, and old / unused functions have been removed\n- function names have been standardized (`BIOMOD_` for main functions, `bm_` for secondary functions)\n- parameter names have been standardized (same typo, same names for similar parameters across functions)\n- all documentation and examples have been cleaned up\n\n#### \u003ci class=\"fas fa-plus-square\"\u003e\u003c/i\u003e What is new ?\n\n- plot functions have been re-written with `ggplot2`\n- [`biomod2` website](https://biomodhub.github.io/biomod2/) has been created, with proper `roxygen2` documentation and help vignettes\n\n#### \u003ci class=\"fas fa-question-circle\"\u003e\u003c/i\u003e But... why ?\n\n- “*For every minute spent on organizing, an hour is earned.*” — Benjamin Franklin\n  - better documentation, better formation, better help provided\n  - new improvements to come (update of single models, implementation of abundance models, etc)\n\n\u003cbr/\u003e\u003cbr/\u003e\n\n\n\n\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["species","ecology","species-distribution-modelling","ecological-modelling"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/165876","html_url":"https://ost.ecosyste.ms/projects/165876"}