preprocess_input {restoptr}

Restopr input preprocessing function.

Description

From a binary, possibly high resolution, habitat raster, this function produces three input rasters for restopt:

Usage

preprocess_input(habitat, habitat_threshold = 1, aggregation_factor = 1)

Arguments

habitat

terra::rast() Raster object containing binary values that indicate if each planning unit contains habitat or not. Cells with the value 1 must correspond to existing habitat. Cells with the value 0 must correspond to degraded (or simply non-habitat) areas. Finally, NA (or NO_DATA) cells are considered to be outside of the landscape.

habitat_threshold

numeric Number between 0 and 1 indicating, when the habitat raster is downsampled, the minimum proportion of habitat cells (from the original raster) are required within the downsampled raster to be considered as habitat.

aggregation_factor

integer positive integer corresponding to the level of downsampling that will be applied to the habitat. This parameter is important to ensure the tractability of a problem.

Details

• The binary habitat raster (existing_habitat), which can be the same as the input (aggregation factor = 1), but most often is a downsampled version of it, to ensure the tractability of the problem.

• The restorable habitat raster (restorable_habitat), which is a raster indicating how much habitat can be restored. If the aggregation factor = 1, the the restorable habitat raster is binary and the inverse of the habitat raster. Else, the surface of habitat is computed according to the spatial resolution, and the number of habitat pixel present in one larger aggregated cell.

• The cell area raster (cell_area), which correspond for each aggregated cell to the number of number of cells in the input raster. This is necessary because the cell area can be less than expected if the aggregated cell lies in the boundary of study area.

This preprocessing function produces the necessary inputs of a restopt problem from a single binary habitat raster (habitat), which can be at high resolution. Restopt solves a hard constrained combinatorial problem (it can be reduced to a constrained 0/1 knapsack problem, which is know to be NP-Complete), thus the input resolution might need to be reduced to ensure a tractable problem. Performing this downsampling in a systematic and reproducible way is the aim of this function, which relies on the terra::aggregate() function to do it. The aggregation_factor parameter indicates how much the resolution must be reduced. An aggregated pixel will contain at most aggregation_factor^2 pixels from the input habitat raster (cell_area raster in this function outputs). If an aggregated pixel is close to the spatial boundaries of the problem (i.e. NA cells), it can contain less than aggregation_factor^2 fine grained pixels. The habitat_threshold parameter indicates the minimum proportion of habitat pixels (relative to cell_area) whose value is 1 to consider an aggregated pixel as habitat (downsampled_habitat output raster). The restorable_area output raster correspond to the number of pixel with value 0 in aggregated pixels.

Value

A list : list( existing_habitat=downsampled_habitat, restorable_habitat=restorable_habitat, cell_area=cell_area )

Examples

# load data
habitat_data <- rast(
  system.file("extdata", "habitat_hi_res.tif", package = "restoptr"))
data <- preprocess_input(
    habitat = habitat_data,
    habitat_threshold = 0.7,
    aggregation_factor = 16
)