fit_density_ratio {S4DM} | R Documentation |
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 (Drake and Richards 2018).
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
Drake JM, Richards RL (2018). “Estimating environmental suitability.” Ecosphere, 9(9), e02373. https://onlinelibrary.wiley.com/doi/10.1002/ecs2.2373.
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")
[Package S4DM version 0.0.1 Index]