Description Usage Arguments Details Value Author(s) See Also Examples
DF_to_ARRAY and LIST_to_ARRAY are biomod2 internal functions that can be useful to help users to transform a standard biomod2 data.frame
or list
output into the standard array
one.
1 2 | DF_to_ARRAY(df)
LIST_to_ARRAY(ll)
|
df |
a standard biomod2 |
ll |
a standard biomod2 |
This functions can be useful when you want to re-convert biomod2 data.frame
or list
(e.g. projections, evaluations) into their initial array
format (see BIOMOD_Projection
for further details)
A standard biomod2 array
output.
Damien Georges
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 | # 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"))
# Keep only points where we have info
myExpl <- raster::extract(myExpl, myRespXY)
# 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('SRE','RF'),
models.options = myBiomodOption,
NbRunEval=1,
DataSplit=70,
Yweights=NULL,
VarImport=0,
models.eval.meth = c('ROC'),
rescal.all.models = FALSE,
do.full.models = FALSE)
# 4 Projection on current environemental conditions
myBiomodProjection <- BIOMOD_Projection(modeling.output = myBiomodModelOut,
new.env = data.frame(myExpl),
proj.name = 'current',
selected.models = 'all')
# 5. Get projection under data.frame format
myProjDF <- get_predictions(myBiomodProjection, as.data.frame=TRUE)
class(myProjDF)
dim(myProjDF)
dimnames(myProjDF)
# 6. Transform data.frame into array
myProjArray <- DF_to_ARRAY(myProjDF)
class(myProjArray)
dim(myProjArray)
dimnames(myProjArray)
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