fit_density_ratio: Fit density-ratio distribution models in a plug-and-play...

In bmaitner/pbsdm: Small Sample Size Species Distribution Modeling

Fit density-ratio distribution models in a plug-and-play framework.

Description

This function fits density-ratio species distribution models for the specified density-ratio method \insertCiteDrake2018-haS4DM.

Usage

fit_density_ratio(presence = NULL, background = NULL, method = NULL, ...)

Arguments

presence	dataframe of covariates at presence points
background	Dataframe of covariates at background points
method	Character. See "notes" for options.
...	Additional parameters passed to internal functions.

Details

Current methods include: "ulsif", "rulsif", "maxnet"

Value

List of class "dr_model" containing model objects and metadata needed for projecting the fitted models.

References

\insertAllCited

Examples

# load in sample data

 library(S4DM)
 library(terra)

 # occurrence points
   data("sample_points")
   occurrences <- sample_points

 # environmental data
   env <- rast(system.file('ex/sample_env.tif', package="S4DM"))

 # rescale the environmental data

   env <- scale(env)

 # Get presence environmental data

  pres_env <- get_env_pres(coords = occurrences,
                           env = env)

# Get background environmental data

 bg_env <- get_env_bg(coords = occurrences,
                      env = env,width = 100000)


# Note that the functions to get the environmental data return lists,
# and only the "env" element of these is used in the fit function

rulsif_fit <- fit_density_ratio(presence = pres_env$env,
                               background = bg_env$env,
                               method = "rulsif")

bmaitner/pbsdm documentation built on Feb. 8, 2025, 2:27 p.m.