SDMtune-class: SDMtune class

In SDMtune: Species Distribution Model Selection

SDMtune class

Description

Class used to save the results of one of the following functions: gridSearch, randomSearch or optimizeModel.

Plot an SDMtune object. Use the interactive argument to create an interactive chart.

Usage

## S4 method for signature 'SDMtune'
show(object)

## S4 method for signature 'SDMtune,missing'
plot(x, title = "", interactive = FALSE)

Arguments

object	SDMtune object
x	SDMtune object.
title	character. The title of the plot.
interactive	logical, if TRUE plot an interactive chart.

Value

If interactive = FALSE the function returns a ggplot object otherwise it returns an SDMtuneChart object that contains the path of the temporary folder where the necessary files to create the chart are saved. In both cases the objects are returned as invisible.

Slots

results

data.frame. Results with the evaluation of the models.

models

list. List of SDMmodel or SDMmodelCV objects.

Author(s)

Sergio Vignali

Examples

# Acquire environmental variables
files <- list.files(path = file.path(system.file(package = "dismo"), "ex"),
                    pattern = "grd", full.names = TRUE)
predictors <- terra::rast(files)

# Prepare presence and background locations
p_coords <- virtualSp$presence
bg_coords <- virtualSp$background

# Create SWD object
data <- prepareSWD(species = "Virtual species", p = p_coords, a = bg_coords,
                   env = predictors, categorical = "biome")

# Split presence locations in training (80%) and testing (20%) datasets
datasets <- trainValTest(data, test = 0.2, only_presence = TRUE)
train <- datasets[[1]]
test <- datasets[[2]]

# Train a model
model <- train(method = "Maxnet", data = train, fc = "l")

# Define the hyperparameters to test
h <- list(reg = 1:5, fc = c("lqp", "lqph"))

# Run the gridSearch function using as metric the AUC
output <- gridSearch(model, hypers = h, metric = "auc", test = test)
output

# Plot the output
plot(output, title = "My experiment")

# Plot the interactive chart
p <- plot(output, title = "My experiment", interactive = TRUE)
# Print the temporary folder that stores the files used to create the chart
str(p)

SDMtune documentation built on July 9, 2023, 6:03 p.m.