response_curve: Variable response curves for GLMs

In enmpa: Ecological Niche Modeling using Presence-Absence Data

Variable response curves for GLMs

Description

A view of variable responses in models. Responses based on single or multiple models can be provided.

Usage

response_curve(fitted, variable, data = NULL, modelID = NULL,  n = 100,
               new_data = NULL,  extrapolate = TRUE, show_lines = TRUE,
               xlab = NULL, ylab = "Probability", col = "red", ...)

Arguments

fitted	an object of class glm, a list of GLMs obtained using the function fit_glms, or an object enmpa_fitted_models from fit_selected .
variable	(character) name of the variables to be plotted.
data	data.frame or matrix of data used in the model calibration step. Default = NULL.
modelID	(character) vector of ModelID(s) to be considered when the fitted models is an enmpa_fitted_object. By default all models are included. Default = NULL.
n	(numeric) an integer guiding the number of breaks. Default = 100
new_data	a SpatRaster, data.frame, or matrix of variables representing the range of variable values in an area of interest. Default = NULL. It must be defined in case the model entered does not explicitly include a data component.
extrapolate	(logical) whether to allow extrapolation to study the behavior of the response outside the calibration limits. Ignored if new_data is defined. Default = TRUE.
show_lines	(logical) whether to show variable responses of distinct models as different lines. Default = TRUE. If
xlab	(character) a label for the x axis. The default, NULL, uses the name defined in variable.
ylab	(character) a label for the y axis. Default = "Probability".
col	(character) color for lines. Default = "red".
...	additional arguments passed to plot.

Details

The function calculates these probabilities by focusing on a single environmental variable while keeping all other variables constant at their mean values.

When responses for multiple models are to be plotted, and show_lines = FALSE, the mean and confidence intervals for the set of responses are calculated using a GAM.

Value

A plot with the response curve for a variable.

Examples

# Load a fitted selected model
data(sel_fit, package = "enmpa")

# Response curve for single models
response_curve(sel_fit, modelID = "ModelID_7", variable = "bio_1")

# Response curve when model(s) are in a list (only one model in this one)
response_curve(sel_fit, variable = "bio_12")

enmpa documentation built on Dec. 15, 2025, 1:07 a.m.