enmtools.rf: Takes an emtools.species object with presence and background...

In ENMTools: Analysis of Niche Evolution using Niche and Distribution Models

Takes an emtools.species object with presence and background points, and builds a random forest model

Description

Takes an emtools.species object with presence and background points, and builds a random forest model

Usage

enmtools.rf(
  species,
  env,
  f = NULL,
  test.prop = 0,
  eval = TRUE,
  nback = 1000,
  env.nback = 10000,
  report = NULL,
  overwrite = FALSE,
  rts.reps = 0,
  bg.source = "default",
  verbose = FALSE,
  clamp = TRUE,
  corner = NA,
  bias = NA,
  ...
)

Arguments

species	An enmtools.species object
env	A SpatRaster of environmental data.
f	A formula for fitting the model
test.prop	Proportion of data to withhold randomly for model evaluation, or "block" for spatially structured evaluation.
eval	Determines whether model evaluation should be done. Turned on by default, but moses turns it off to speed things up.
nback	Number of background points to draw from range or env, if background points aren't provided
env.nback	Number of points to draw from environment space for environment space discrimination metrics.
report	Optional name of an html file for generating reports
overwrite	TRUE/FALSE whether to overwrite a report file if it already exists
rts.reps	The number of replicates to do for a Raes and ter Steege-style test of significance
bg.source	Source for drawing background points. If "points", it just uses the background points that are already in the species object. If "range", it uses the range raster. If "env", it draws points at randome from the entire study area outlined by the first environmental layer.
verbose	Controls printing of various messages progress reports. Defaults to FALSE.
clamp	When set to TRUE, clamps the environmental layers so that predictions made outside the min/max of the training data for each predictor are set to the value for the min/max for that predictor. Prevents the model from extrapolating beyond the min/max bounds of the predictor space the model was trained in, although there could still be projections outside the multivariate training space if predictors are strongly correlated.
corner	An integer from 1 to 4. Selects which corner to use for "block" test data. By default the corner is selected randomly.
bias	An optional raster estimating relative sampling effort per grid cell. Will be used for drawing background data.
...	Arguments to be passed to rf()

Value

An enmtools model object containing species name, model formula (if any), model object, suitability raster, marginal response plots, and any evaluation objects that were created.

Examples

enmtools.rf(iberolacerta.clade$species$monticola, env = euro.worldclim, nback = 500)

ENMTools documentation built on April 11, 2023, 6:09 p.m.