BIOMOD.formated.data {biomod2}

BIOMOD_FormatingData() output object class

Description

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

Usage

## S4 method for signature '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 signature '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 signature '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 signature '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 signature '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(s)

Damien Georges

See Also

BIOMOD_FormatingData, BIOMOD_Tuning, bm_CrossValidation, BIOMOD_Modeling, bm_RunModelsLoop

Other Toolbox objects: BIOMOD.ensemble.models.out, BIOMOD.formated.data.PA, BIOMOD.models.options, BIOMOD.models.out, BIOMOD.projection.out, BIOMOD.stored.data, biomod2_ensemble_model, biomod2_model

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)



## ----------------------------------------------------------------------- #
# 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)