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Species distribution modeling,
calibration and evaluation,
ensemble modeling
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- Stable version
from cran :
install.packages("biomod2", dependencies = TRUE)- Development version
from biomodhub :
library(devtools)
devtools::install_github("biomodhub/biomod2", dependencies = TRUE)
/!\ All changes between versions are detailed in News.
/!\ Please feel free to indicate if you notice some strange new behaviors !
- 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 theget_options()function. - To reduce the tuning calculation time, we update the tuning ranges for ANN, FDA and MARS models.
biomod2has a new model: RFd. It's a Random Forest model with a down-sampling method.- You can now define seed.val for
bm_PseudoAbsences()andBIOMOD_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().
- 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_ModelingOptionsandBIOMOD_Tuningfunctions become secondary functions (bm_ModelingOptionsandbm_Tuning), and modeling options can be directly built throughBIOMOD_Modelingfunction
ModelsTableandOptionsBigbossdatasets (note that improvement of bigboss modeling options is planned in near future)- 3 new vignettes have been created :
- data preparation (questions you should ask yourself before modeling)
- cross-validation (to prepare your own calibration / validation datasets)
- modeling options (to help you navigate through the new way of parametrizing single models)
biomod2now relies on the newterrapackage that aims at replacingrasterandsp.biomod2is still compatible with old format such asRasterStackandSpatialPointsDataFrame.biomod2function will sometimes returnSpatRasterfrom packageterrathat you can always convert intoRasterStackusing functionstackinraster.
/!\ 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 !
- 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
- plot functions have been re-written with
ggplot2 biomod2website has been created, with properroxygen2documentation and help vignettes
- “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)