BIOMOD_FormatingData() output object class — BIOMOD.formated.data • biomod2

Class returned by BIOMOD_FormatingData, and used by bm_Tuning, bm_CrossValidation and BIOMOD_Modeling

# S4 method for class 'numeric,data.frame'
BIOMOD.formated.data(
  sp,
  env,
  xy = NULL,
  dir.name = ".",
  sp.name = NULL,
  eval.sp = NULL,
  eval.env = NULL,
  eval.xy = NULL,
  na.rm = TRUE,
  data.mask = NULL,
  shared.eval.env = FALSE,
  filter.raster = FALSE
)

# S4 method for class 'data.frame,ANY'
BIOMOD.formated.data(
  sp,
  env,
  xy = NULL,
  dir.name = ".",
  sp.name = NULL,
  eval.sp = NULL,
  eval.env = NULL,
  eval.xy = NULL,
  na.rm = TRUE,
  filter.raster = FALSE
)

# S4 method for class 'numeric,matrix'
BIOMOD.formated.data(
  sp,
  env,
  xy = NULL,
  dir.name = ".",
  sp.name = NULL,
  eval.sp = NULL,
  eval.env = NULL,
  eval.xy = NULL,
  na.rm = TRUE,
  filter.raster = FALSE
)

# S4 method for class 'numeric,SpatRaster'
BIOMOD.formated.data(
  sp,
  env,
  xy = NULL,
  dir.name = ".",
  sp.name = NULL,
  eval.sp = NULL,
  eval.env = NULL,
  eval.xy = NULL,
  na.rm = TRUE,
  shared.eval.env = FALSE,
  filter.raster = FALSE
)

# S4 method for class 'BIOMOD.formated.data'
show(object)

Arguments

sp: A vector, a SpatVector without associated data (if presence-only), or a SpatVector object containing binary data (0 : absence, 1 : presence, NA : indeterminate) for a single species that will be used to build the species distribution model(s)
Note that old format from sp are still supported such as SpatialPoints (if presence-only) or SpatialPointsDataFrame object containing binary data.
env: a matrix, data.frame, SpatVector or SpatRaster object containing the explanatory variables (in columns or layers) that will be used to build the species distribution model(s).
Note that old format from raster and sp are still supported such as RasterStack and SpatialPointsDataFrame objects.
xy: (optional, default NULL)
If resp.var is a vector, a 2-columns matrix or data.frame containing the corresponding X and Y coordinates that will be used to build the species distribution model(s)
dir.name: a character corresponding to the modeling folder
sp.name: a character corresponding to the species name
eval.sp: (optional, default NULL)
A vector, a SpatVector without associated data (if presence-only), or a SpatVector object containing binary data (0 : absence, 1 : presence, NA : indeterminate) for a single species that will be used to evaluate the species distribution model(s) with independent data
Note that old format from sp are still supported such as SpatialPoints (if presence-only) or SpatialPointsDataFrame object containing binary data.
eval.env: (optional, default NULL)
A matrix, data.frame, SpatVector or SpatRaster object containing the explanatory variables (in columns or layers) that will be used to evaluate the species distribution model(s) with independent data
Note that old format from raster and sp are still supported such as RasterStack and SpatialPointsDataFrame objects.
eval.xy: (optional, default NULL)
If resp.var is a vector, a 2-columns matrix or data.frame containing the corresponding X and Y coordinates that will be used to evaluate the species distribution model(s) with independent data
na.rm: (optional, default TRUE)
A logical value defining whether points having one or several missing values for explanatory variables should be removed from the analysis or not
data.mask: (optional, default NULL)
A SpatRaster object containing the mask of the studied area
shared.eval.env: (optional, default FALSE)
A logical value defining whether the explanatory variables used for the evaluation dataset are the same than the ones for calibration (if eval.env not provided for example) or not
filter.raster: (optional, default FALSE)
If env is of raster type, a logical value defining whether sp is to be filtered when several points occur in the same raster cell
object: a BIOMOD.formated.data object

Slots

dir.name: a character corresponding to the modeling folder
sp.name: a character corresponding to the species name
coord: a 2-columns data.frame containing the corresponding X and Y coordinates
data.species: a vector containing the species observations (0, 1 or NA)
data.env.var: a data.frame containing explanatory variables
data.mask: a SpatRaster object containing the mask of the studied area
has.data.eval: a logical value defining whether evaluation data is given
eval.coord: (optional, default NULL)
A 2-columns data.frame containing the corresponding X and Y coordinates for evaluation data
eval.data.species: (optional, default NULL)
A vector containing the species observations (0, 1 or NA) for evaluation data
eval.data.env.var: (optional, default NULL)
A data.frame containing explanatory variables for evaluation data

Author

Damien Georges

Examples


showClass("BIOMOD.formated.data")

## ----------------------------------------------------------------------- #
library(terra)

# Load species occurrences (6 species available)
data(DataSpecies)
head(DataSpecies)

# Select the name of the studied species
myRespName <- 'GuloGulo'

# Get corresponding presence/absence data
myResp <- as.numeric(DataSpecies[, myRespName])

# Get corresponding XY coordinates
myRespXY <- DataSpecies[, c('X_WGS84', 'Y_WGS84')]

# Load environmental variables extracted from BIOCLIM (bio_3, bio_4, bio_7, bio_11 & bio_12)
data(bioclim_current)
myExpl <- terra::rast(bioclim_current)

DONTSHOW({
myExtent <- terra::ext(0,30,45,70)
myExpl <- terra::crop(myExpl, myExtent)
})

## ----------------------------------------------------------------------- #
# Format Data with true absences
myBiomodData <- BIOMOD_FormatingData(resp.var = myResp,
                                     expl.var = myExpl,
                                     resp.xy = myRespXY,
                                     resp.name = myRespName)
myBiomodData
plot(myBiomodData)
summary(myBiomodData)

`BIOMOD_FormatingData()` output object class

Arguments

Slots

See also

Author

Examples