Logo biomod2

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Species distribution modeling,
calibration and evaluation,
ensemble modeling
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https://biomodhub.github.io/biomod2/

Installation


  • Stable version v from cran :
install.packages("biomod2", dependencies = TRUE)


library(devtools)
devtools::install_github("biomodhub/biomod2", dependencies = TRUE)



All changes between versions are detailed in News.



biomod 4.3-4-1 - Abundance modelling, but better !

Please feel free to indicate if you notice some strange new behaviors !

What is changed ?

  • Nothing for presence/absence (or presence-only) modelling.
  • bm_RangeSize computes the difference between binary predictions, and is called by BIOMOD_RangeSize which can take as input BIOMOD.projection.out objects.

What is new ?

  • You can now use non-binary data ! All the information can be found in the Abundance Vignette.
  • 6 values can be given to data.type new parameter in BIOMOD_FormatingData :
    binary, count, multiclass, ordinal, relative, abundance.
  • 2 new ensemble models have been added, to deal with qualitative data type : EMmode and EMfreq.
  • DNN (Deep Neural Network) model has been added with the cito package. It can be used with all data types.
    Be sure to have a look at cito documentation before, especially the part about the torch installation.
  • bm_ModelAnalysis provides classical graphics to explore the quality of your single models.
  • Discover BIOMOD_Report, a new function to help you summarize all your modeling steps.



Main workflow









biomod 4.2-6 - Improved OptionsBigBoss and new model

What is changed ?

  • To improve the models, we made some change in the options for OptionsBigboss. (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 :


biomod 4.2 - Terra Update

What is changed ?

  • biomod2 now relies on the new terra package that aims at replacing rasterand sp.
  • biomod2 is still compatible with old format such as RasterStackand 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 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)