Calculate habitat connectivity using terra

This performs the entire connectivity workflow, returning a dataframe output. The steps are:

• create_barrier_mask(): Creating barrier mask.

• drop_habitat_under_barrier(): Removes Habitat underneath barrier.

• habitat_buffer(): Buffers the habitat layer by the interpatch distance (m).

• fragment_habitat(): Fragments habitat layer along barrier intersection.

• assign_patches_to_fragments(): Assign patch ID to fragments.

• aggregate_connected_patches(): Summarise area in each patch.

Usage

habitat_connectivity(
  habitat,
  barrier,
  species,
  interpatch_distance = NULL,
  buffer_radius = NULL,
  verbose = TRUE
)

Arguments

habitat

Terra SpatRaster. Habitat raster.

barrier

Terra SpatRaster. Barrier raster.

species

Species name. E.g., "Blue-tongued Lizard".

interpatch_distance

Numeric. The distance (in meters) where habitat patches are considered connected. E.g., if set to 500, patches 498m apart are connected, those 501m apart are not connected. This is passed internally to a spatial operation known as "buffering", where this distance is used as a radius from the edge of the habitat zone. This means the specified interpatch_distance is halved exactly. So an interpatch distance of 500 will be converted to 250. For the buffer to be representable on the raster, keep resolution <= interpatch_distance / 2; below that the buffer is a no-op and a warning is raised. See vignette("interpatch-distance-and-resolution").

buffer_radius

Numeric. The radius in metres around the habitat. Since patches of habitat will be connected when their edge-to-edge gap is <= 2 * buffer radius, we recommend you specify buffer_radius to be half the "interpatch distance". This is the distance past which habitat patches are no longer considered connected. For example, if your interpatch distance is 500m, set buffer_radius = 250. The buffer can only be represented if it is at least one raster cell, i.e. keep resolution <= interpatch_distance / 2. Below that the buffer is a no-op: habitat_buffer() warns and returns the habitat unchanged. See vignette("interpatch-distance-and-resolution").

verbose

Logical. Display progress messages (default: TRUE).

Value

Data frame with connectivity metrics per patch.

See also

vignette("interpatch-distance-and-resolution") for the relationship between interpatch distance, buffer radius, and resolution.

Examples

lizard_habitat <- example_habitat()
lizard_barrier <- example_barrier()
connectivity <- habitat_connectivity(
    habitat = lizard_habitat,
    barrier = lizard_barrier,
    species = "Blue-tongued Lizard",
    interpatch_distance = 12
  )
#> ℹ Creating barrier mask
#> ✔ Creating barrier mask [33ms]
#> 
#> ℹ Removing habitat underneath barrier
#> ✔ Removing habitat underneath barrier [24ms]
#> 
#> ℹ Adding 6m buffer (interpatch distance 12m)
#> ✔ Adding 6m buffer (interpatch distance 12m) [227ms]
#> 
#> ℹ Fragmenting habitat layer along barrier intersection
#> ✔ Fragmenting habitat layer along barrier intersection [23ms]
#> 
#> ℹ Assigning patches ID to fragments
#> ✔ Assigning patches ID to fragments [2.2s]
#> 
#> ℹ Summarising area in each patch
#> ✔ Summarising area in each patch [48ms]
#> 
connectivity
#> # patch_connectivity:  data.frame
#> # Species:             Blue-tongued Lizard
#> # Patches:             399
#> # Resolution:          2x2
#> # Interpatch Distance: 12 m
#>   patch_id   area
#>      <dbl>  <dbl>
#> 1        1 95326.
#> 2        3   364.
#> 3        6  2344.
#> 4       13  1220.
#> 5       48  1112.
#> # ℹ 394 more rows