prepare_projection: Preparation of data for model projections

In kuenm2: Detailed Development of Ecological Niche Models

Preparation of data for model projections

Description

This function prepared data for model projections to multiple scenarios, storing the paths to the rasters representing each scenario.

Usage

prepare_projection(models = NULL, variable_names = NULL, present_dir = NULL,
                   past_dir = NULL, past_period = NULL, past_gcm = NULL,
                   future_dir = NULL, future_period = NULL,
                   future_pscen = NULL, future_gcm = NULL,
                   write_file = FALSE, filename = NULL,
                   raster_pattern = ".tif*")

Arguments

models	an object of class fitted_models returned by the fit_selected() function. Default is NULL.
variable_names	(character) names of the variables used to fit the model or do the PCA in the prepare_data() function. Only applicable if models argument is not provided. Default is NULL.
present_dir	(character) path to the folder containing variables that represent the current scenario for projection. Default is NULL.
past_dir	(character) path to the folder containing subfolders with variables representing past scenarios for projection. Default is NULL.
past_period	(character) names of the subfolders within past_dir, representing specific time periods (e.g., 'LGM' or 'MID').
past_gcm	(character) names of the subfolders within past_period folders, representing specific General Circulation Models (GCMs).
future_dir	(character) path to the folder containing subfolders with variables representing future scenarios for projection. Default is NULL.
future_period	(character) names of the subfolders within future_dir, representing specific time periods (e.g., '2041-2060' or '2081-2100'). Default is NULL.
future_pscen	(character) names of the subfolders within future_period, representing specific emission scenarios (e.g., 'ssp126' or 'ssp585'). Default is NULL.
future_gcm	(character) names of the subfolders within future_pscen folders, representing specific General Circulation Models (GCMs). Default is NULL.
write_file	(logical) whether to write the object containing the paths to the structured folders. This object is required for projecting models across multiple scenarios using the project_selected() function. Default is FALSE.
filename	(character) the path or name of the folder where the object will be saved. This is only applicable if write_file = TRUE. Default is NULL.
raster_pattern	(character) pattern used to identify the format of raster files within the folders. Default is ".tif*".

Value

An object of class prepared_projection containing the following elements:

• Present, Past, and Future: paths to the variables structured in subfolders.

• Raster_pattern: the pattern used to identify the format of raster files within the folders.

• PCA: if a principal component analysis (PCA) was performed on the set of variables with prepare_data(), a list with class "prcomp" will be returned. See ?stats::prcomp() for details.

• variables: names of the raw predictor variables used to project.

See Also

organize_future_worldclim()

Examples

# Import example of fitted_models (output of fit_selected())
data("fitted_model_maxnet", package = "kuenm2")

# Organize and structure future climate variables from WorldClim
# Import the current variables used to fit the model.
# In this case, SoilType will be treated as a static variable (constant
# across future scenarios).
var <- terra::rast(system.file("extdata", "Current_variables.tif",
                               package = "kuenm2"))

# Create a "Current_raw" folder in a temporary directory and copy the raw
# variables there.
out_dir_current <- file.path(tempdir(), "Current_raw")
dir.create(out_dir_current, recursive = TRUE)

# Save current variables in temporary directory
terra::writeRaster(var, file.path(out_dir_current, "Variables.tif"))

# Set the input directory containing the raw future climate variables.
# For this example, the data is located in the "inst/extdata" folder.
in_dir <- system.file("extdata", package = "kuenm2")

# Create a "Future_raw" folder in a temporary directory and copy the raw
# variables there.
out_dir_future <- file.path(tempdir(), "Future_raw")

# Organize and rename the future climate data, structuring it by year and GCM.
# The 'SoilType' variable will be appended as a static variable in each scenario.
# The files will be renamed following the "bio_" format
organize_future_worldclim(input_dir = in_dir,
                          output_dir = out_dir_future,
                          name_format = "bio_", variables = NULL,
                          static_variables = var$SoilType, mask = NULL,
                          overwrite = TRUE)

# Prepare projections using fitted models to check variables
pr <- prepare_projection(models = fitted_model_maxnet,
                         present_dir = out_dir_current,
                         past_dir = NULL,
                         past_period = NULL,
                         past_gcm = NULL,
                         future_dir = out_dir_future,
                         future_period = c("2041-2060", "2081-2100"),
                         future_pscen = c("ssp126", "ssp585"),
                         future_gcm = c("ACCESS-CM2", "MIROC6"),
                         write_file = FALSE,
                         filename = NULL,
                         raster_pattern = ".tif*")
pr

# Prepare projections using variables names
pr_b <- prepare_projection(models = NULL,
                           variable_names = c("bio_1", "bio_7", "bio_12"),
                           present_dir = out_dir_current,
                           past_dir = NULL,
                           past_period = NULL,
                           past_gcm = NULL,
                           future_dir = out_dir_future,
                           future_period = c("2041-2060", "2081-2100"),
                           future_pscen = c("ssp126", "ssp585"),
                           future_gcm = c("ACCESS-CM2", "MIROC6"),
                           write_file = FALSE,
                           filename = NULL,
                           raster_pattern = ".tif*")
pr_b

kuenm2 documentation built on April 21, 2026, 1:07 a.m.