Load models built within BIOMOD_Modeling function
This function was implemented to help biomod2 users to load individual models built during the BIOMOD_Modeling step.
BIOMOD_LoadModels(bm.out, ... )
bm.out |
a |
... |
additional arguments (see details) |
This function is particularly useful when you plane to make some response plot analyses. It will induce models, built at BIOMOD_Modeling step, loading in your working space.
If you run this function referencing only bm.out argument, all models built will be loaded. However, you can make a models subselection using the additional arguments (see below).
Additional arguments (...) : All the following arguments are optional.
models: a character vector defining the names of models (e.g c(‘GLM’, ‘GAM’, ‘RF’) ) you want to load (models subselection)
run.eval: a character vector defining the names of evaluation run (e.g c(‘RUN1’, ‘Full’) ) you want to load (repetition subselection)
data.set: a character vector defining the names of data.set (e.g c(‘PA1’, ‘PA2’)) you want to load (pseudo absences subselection)
path: the path to file where the species folder is. To be filled if species folder is different from your working directory)
A character vector filled with the loaded models names.
SRE models are not supported yet. They will be automatically excluded even if they are selected.
Damien Georges
# species occurrences
DataSpecies <- read.csv(system.file("external/species/mammals_table.csv",
package="biomod2"), row.names = 1)
head(DataSpecies)
# the name of studied species
myRespName <- 'GuloGulo'
# the presence/absences data for our species
myResp <- as.numeric(DataSpecies[,myRespName])
# the XY coordinates of species data
myRespXY <- DataSpecies[,c("X_WGS84","Y_WGS84")]
# Environmental variables extracted from BIOCLIM (bio_3, bio_4, bio_7, bio_11 & bio_12)
myExpl = raster::stack( system.file( "external/bioclim/current/bio3.grd",
package="biomod2"),
system.file( "external/bioclim/current/bio4.grd",
package="biomod2"),
system.file( "external/bioclim/current/bio7.grd",
package="biomod2"),
system.file( "external/bioclim/current/bio11.grd",
package="biomod2"),
system.file( "external/bioclim/current/bio12.grd",
package="biomod2"))
# 1. Formatting Data
myBiomodData <- BIOMOD_FormatingData(resp.var = myResp,
expl.var = myExpl,
resp.xy = myRespXY,
resp.name = myRespName)
# 2. Defining Models Options using default options.
myBiomodOption <- BIOMOD_ModelingOptions()
# 3. Doing Modelisation
myBiomodModelOut <- BIOMOD_Modeling( myBiomodData,
models = c('RF'),
models.options = myBiomodOption,
NbRunEval=2,
DataSplit=70,
models.eval.meth = c('TSS'),
SaveObj = TRUE,
do.full.models = FALSE)
# 4. Loading some models built
myLoadedModels <- BIOMOD_LoadModels(myBiomodModelOut, models='RF')
myLoadedModelsPlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.