BIOMOD.projection.out: 'BIOMOD_Projection()' output object class
In biomod2: Ensemble Platform for Species Distribution Modeling

BIOMOD.projection.out

R Documentation

`BIOMOD_Projection()` output object class

Description

Class returned by BIOMOD_Projection, and used by BIOMOD_EnsembleForecasting

Usage

## S4 method for signature 'BIOMOD.projection.out,missing'
plot(
  x,
  coord = NULL,
  plot.output,
  do.plot = TRUE,
  std = TRUE,
  scales,
  size,
  maxcell = 5e+05,
  ...
)

## S4 method for signature 'BIOMOD.projection.out'
show(object)

Arguments

`x`	a `BIOMOD.projection.out` object
`coord`	a 2-columns `data.frame` containing the corresponding `X` and `Y`
`plot.output`	(optional, default `facet`) a character determining the type of output: with `plot.output = 'list'` the function will return a list of plots (one plot per model) ; with 'facet' ; with `plot.output = 'facet'` the function will return a single plot with all asked projections as facet.
`do.plot`	(optional, default `TRUE`) a boolean determining whether the plot should be displayed or just returned.
`std`	(optional, default `TRUE`) a boolean controlling the limits of the color scales. With `std = TRUE` color scales are displayed between 0 and 1 (or 1000). With `std = FALSE` color scales are displayed between 0 and the maximum value observed.
`scales`	(optional, default `fixed`) a character determining whether x and y scales are shared among facet. Argument passed to `facet_wrap`. Possible values: 'fixed', 'free_x', 'free_y', 'free'.
`size`	(optional, default `0.75`) a numeric determing the size of points on the plots and passed to `geom_point`.
`maxcell`	maximum number of cells to plot. Argument transmitted to `plot`.
`...`	additional parameters to be passed to `get_predictions` to select the models that will be plotted
`object`	a `BIOMOD.projection.out` object

Slots

modeling.id: a character corresponding to the name (ID) of the simulation set
proj.name: a character corresponding to the projection name
dir.name: a character corresponding to the modeling folder
sp.name: a character corresponding to the species name
expl.var.names: a vector containing names of explanatory variables
coord: a 2-columns matrix or data.frame containing the corresponding X and Y coordinates used to project the species distribution model(s)
scale.models: a logical value defining whether models have been rescaled or not
models.projected: a vector containing names of projected models
models.out: a BIOMOD.stored.data object
type: a character corresponding to the class of the val slot of the proj.out slot
proj.out: a BIOMOD.stored.data object

Author(s)

Damien Georges

Examples


showClass("BIOMOD.projection.out")

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



## ----------------------------------------------------------------------- #
file.out <- paste0(myRespName, "/", myRespName, ".AllModels.models.out")
if (file.exists(file.out)) {
  myBiomodModelOut <- get(load(file.out))
} else {

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

  # Model single models
  myBiomodModelOut <- BIOMOD_Modeling(bm.format = myBiomodData,
                                      modeling.id = 'AllModels',
                                      models = c('RF', 'GLM'),
                                      CV.strategy = 'random',
                                      CV.nb.rep = 2,
                                      CV.perc = 0.8,
                                      OPT.strategy = 'bigboss',
                                      metric.eval = c('TSS','ROC'),
                                      var.import = 3,
                                      seed.val = 42)
}


## ----------------------------------------------------------------------- #
# Project single models
myBiomodProj <- BIOMOD_Projection(bm.mod = myBiomodModelOut,
                                  proj.name = 'Current',
                                  new.env = myExpl,
                                  models.chosen = 'all',
                                  metric.binary = 'all',
                                  metric.filter = 'all',
                                  build.clamping.mask = TRUE)
myBiomodProj
plot(myBiomodProj)

biomod2 documentation built on June 22, 2024, 10:56 a.m.