------------------------------------------------------------
Species distribution modeling,
calibration and evaluation,
ensemble modeling
------------------------------------------------------------
- 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.
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()
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_ModelingOptions
andBIOMOD_Tuning
functions become secundary functions (bm_ModelingOptions
andbm_Tuning
), and modeling options can be directly built throughBIOMOD_Modeling
function
ModelsTable
andOptionsBigboss
datasets (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 parameterizing single models)
biomod2
now relies on the newterra
package that aims at replacingraster
andsp
.biomod2
is still compatible with old format such asRasterStack
andSpatialPointsDataFrame
.biomod2
function will sometimes returnSpatRaster
from packageterra
that you can always convert intoRasterStack
using functionstack
inraster
.
/!\
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 secundary 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
biomod2
website has been created, with properroxygen2
documentation 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)