train_mark_model: Train a flexible model for the mark distribution

In ldmppr: Estimate and Simulate from Location Dependent Marked Point Processes

Train a flexible model for the mark distribution

Description

Trains a predictive model for the mark distribution of a spatio-temporal process. data may be either (1) a data.frame containing columns x, y, size and time, (2) a data.frame containing x, y, size (time will be derived via delta), or (3) a ldmppr_fit object returned by estimate_process_parameters. Allows the user to incorporate location specific information and competition indices as covariates in the mark model.

Usage

train_mark_model(
  data,
  raster_list = NULL,
  scaled_rasters = FALSE,
  model_type = "xgboost",
  xy_bounds = NULL,
  delta = NULL,
  save_model = FALSE,
  save_path = NULL,
  parallel = FALSE,
  num_cores = NULL,
  include_comp_inds = FALSE,
  competition_radius = 15,
  edge_correction = "none",
  selection_metric = "rmse",
  cv_folds = 5,
  tuning_grid_size = 200,
  seed = 0,
  verbose = TRUE
)

Arguments

data	a data.frame or a ldmppr_fit object. See Description.
raster_list	list of raster objects used for mark-model training.
scaled_rasters	TRUE or FALSE indicating whether rasters are already scaled.
model_type	the machine learning model type ("xgboost" or "random_forest").
xy_bounds	a vector of domain bounds (2 for x, 2 for y). If data is an ldmppr_fit and xy_bounds is NULL, defaults to c(0, b_x, 0, b_y) derived from fit.
delta	(optional) numeric scalar used only when data contains (x,y,size) but not time. If data is an ldmppr_fit and time is missing, the function will infer the delta value from the fit.
save_model	TRUE or FALSE indicating whether to save the generated model.
save_path	path for saving the generated model.
parallel	TRUE or FALSE. If TRUE, tuning is parallelized over resamples. For small datasets, parallel overhead may outweigh speed gains.
num_cores	number of workers to use when parallel=TRUE. Ignored when parallel=FALSE.
include_comp_inds	TRUE or FALSE indicating whether to generate and use competition indices as covariates.
competition_radius	positive numeric distance used when include_comp_inds = TRUE.
edge_correction	type of edge correction to apply ("none", "toroidal", or "truncation").
selection_metric	metric to use for identifying the optimal model ("rmse", "mae", or "rsq").
cv_folds	number of cross-validation folds to use in model training. If cv_folds <= 1, tuning is skipped and the model is fit once with default hyperparameters.
tuning_grid_size	size of the tuning grid for hyperparameter tuning.
seed	integer seed for reproducible resampling/tuning/model fitting.
verbose	TRUE or FALSE indicating whether to show progress of model training.

Value

an object of class "ldmppr_mark_model" containing the trained mark model.

Examples

# Load the small example data
data(small_example_data)

# Load example raster data
raster_paths <- list.files(system.file("extdata", package = "ldmppr"),
  pattern = "\\.tif$", full.names = TRUE
)
raster_paths <- raster_paths[!grepl("_med\\.tif$", raster_paths)]
rasters <- lapply(raster_paths, terra::rast)

# Scale the rasters
scaled_raster_list <- scale_rasters(rasters)


# Train the model
mark_model <- train_mark_model(
  data = small_example_data,
  raster_list = scaled_raster_list,
  scaled_rasters = TRUE,
  model_type = "xgboost",
  xy_bounds = c(0, 25, 0, 25),
  delta = 1,
  parallel = FALSE,
  include_comp_inds = FALSE,
  competition_radius = 10,
  edge_correction = "none",
  selection_metric = "rmse",
  cv_folds = 3,
  tuning_grid_size = 2,
  verbose = TRUE
)

print(mark_model)

ldmppr documentation built on March 3, 2026, 9:06 a.m.