BIOMOD.formated.data: `BIOMOD_FormatingData()` output object class

Description

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

Usage

# S4 method for 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
)
# S4 method for 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
)
# S4 method for 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
)
# S4 method for numeric,RasterStack
BIOMOD.formated.data(
  sp,
  env,
  xy = NULL,
  dir.name = ".",
  sp.name = NULL,
  eval.sp = NULL,
  eval.env = NULL,
  eval.xy = NULL,
  na.rm = TRUE
)
# S4 method for BIOMOD.formated.data,missing
plot(x, coord = NULL, col = NULL)
# S4 method for BIOMOD.formated.data
show(object)

Arguments

sp: a vector, SpatialPoints (if presence-only) or SpatialPointsDataFrame 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)
env: a matrix, data.frame, SpatialPointsDataFrame or RasterStack object containing the explanatory variables (in columns or layers) that will be used to build the species distribution model(s)
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, SpatialPoints (if presence-only) or SpatialPointsDataFrame 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
eval.env: (optional, default NULL)
A matrix, data.frame, SpatialPointsDataFrame or RasterStack object containing the explanatory variables (in columns or layers) that will be used to evaluate the species distribution model(s) with independent data
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: a RasterStack object containing the mask of the studied area
x: a BIOMOD.formated.data.PA object
coord: a 2-columns data.frame containing X and Y coordinates for plot
col: a vector containing colors for plot (default : c('green', 'red', 'orange', 'grey'))
object: a BIOMOD.formated.data.PA 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 RasterStack 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

Run this code


showClass("BIOMOD.formated.data")

## ----------------------------------------------------------------------- #

# Load species occurrences (6 species available)
myFile <- system.file('external/species/mammals_table.csv', package = 'biomod2')
DataSpecies <- read.csv(myFile, row.names = 1)
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)
myFiles <- paste0('external/bioclim/current/bio', c(3, 4, 7, 11, 12), '.grd')
myExpl <- raster::stack(system.file(myFiles, package = 'biomod2'))

# \dontshow{
myExtent <- raster::extent(0,30,45,70)
myExpl <- raster::stack(raster::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)