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https://github.com/biomodhub/biomod2
BIOMOD is a computer platform for ensemble forecasting of species distributions, enabling the treatment of a range of methodological uncertainties in models and the examination of species-environment relationships.
https://github.com/biomodhub/biomod2
Last synced: about 2 months ago
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BIOMOD is a computer platform for ensemble forecasting of species distributions, enabling the treatment of a range of methodological uncertainties in models and the examination of species-environment relationships.
- Host: GitHub
- URL: https://github.com/biomodhub/biomod2
- Owner: biomodhub
- Created: 2018-02-26T15:55:28.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2024-10-24T12:21:10.000Z (2 months ago)
- Last Synced: 2024-10-29T20:37:31.466Z (2 months ago)
- Language: R
- Size: 22.4 MB
- Stars: 86
- Watchers: 9
- Forks: 22
- Open Issues: 39
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
- open-sustainable-technology - biomod2 - A computer platform for ensemble forecasting of species distributions, enabling the treatment of a range of methodological uncertainties in models and the examination of species-environment relationships. (Biosphere / Species Distribution Modeling)
README
[](https://cran.r-project.org/package=biomod2)
[](https://github.com/biomodhub/biomod2)
[](https://github.com/biomodhub/biomod2/commits/master)
[](https://github.com/biomodhub/biomod2/actions/workflows/R-CMD-check.yml)
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------------------------------------------------------------
Species distribution modeling,
calibration and evaluation,
ensemble modeling
------------------------------------------------------------
https://biomodhub.github.io/biomod2/
### Installation
- **Stable version** [](https://cran.r-project.org/package=biomod2) from [cran](https://CRAN.R-project.org/package=biomod2) :
```R
install.packages("biomod2", dependencies = TRUE)
```
- **Development version** [](https://github.com/biomodhub/biomod2) from [biomodhub](https://github.com/biomodhub/biomod2) :
```R
library(devtools)
devtools::install_github("biomodhub/biomod2", dependencies = TRUE)
```
`/!\` All changes between versions are detailed in [News](https://biomodhub.github.io/biomod2/articles/news.html).
### `biomod 4.2-6` - Improved OptionsBigBoss and new model
`/!\` Please **feel free to indicate if you notice some strange new behaviors** !
#### What is changed ?
- 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.
- To reduce the tuning calculation time, we update the tuning ranges for ANN, FDA and MARS models.
#### What is new ?
- `biomod2` has a new model: **RFd**. It's a Random Forest model with a down-sampling method.
- You can now define _seed.val_ for `bm_PseudoAbsences()` and `BIOMOD_FormatingData()`.
- New _fact.aggr_ argument, for pseudo-absences selection with the random and disk methods, allows to reduce the resolution of the environment.
- Possibility to give the same options for all datasets with _"for_all_datasets"_ in `bm_ModelingOptions()`.
### `biomod 4.2-5` - Modeling options & Tuning Update
#### What is changed ?
- modeling options are now automatically retrieved from single models functions, normally allowing the use of all arguments taken into account by these functions
- tuning has been cleaned up, but keep in mind that it is still a quite long running process
- 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
#### What is new ?
- `ModelsTable` and `OptionsBigboss` datasets (*note that improvement of bigboss modeling options is planned in near future*)
- 3 new vignettes have been created :
- [data preparation](https://biomodhub.github.io/biomod2/articles/vignette_dataPreparation.html) (*questions you should ask yourself before modeling*)
- [cross-validation](https://biomodhub.github.io/biomod2/articles/vignette_crossValidation.html) (*to prepare your own calibration / validation datasets*)
- [modeling options](https://biomodhub.github.io/biomod2/articles/vignette_dataPreparation.html) (*to help you navigate through the new way of parametrizing single models*)
### `biomod 4.2` - Terra Update
#### What is changed ?
- `biomod2` now relies on the new [`terra`](https://github.com/rspatial/terra) package that aims at replacing `raster`and `sp`.
- `biomod2` is still compatible with old format such as `RasterStack`and `SpatialPointsDataFrame`.
- `biomod2` function will sometimes return `SpatRaster` from package `terra` that you can always convert into `RasterStack` using function `stack` in `raster`.
### `biomod 4.1` is now available
`/!\` Package fresh start... meaning some changes in function names and parameters. We apologize for the trouble `>{o.o}<`
Sorry for the inconvenience, and please **feel free to indicate if you notice some strange new behaviors** !
#### What is changed ?
- all code functions have been cleaned, and old / unused functions have been removed
- function names have been standardized (`BIOMOD_` for main functions, `bm_` for secondary functions)
- parameter names have been standardized (same typo, same names for similar parameters across functions)
- all documentation and examples have been cleaned up
#### What is new ?
- plot functions have been re-written with `ggplot2`
- [`biomod2` website](https://biomodhub.github.io/biomod2/) has been created, with proper `roxygen2` documentation and help vignettes
#### But... why ?
- “*For every minute spent on organizing, an hour is earned.*” — Benjamin Franklin
- better documentation, better formation, better help provided
- new improvements to come (update of single models, implementation of abundance models, etc)