Protected Connected (ProtConn) using raster nodes

Source: R/MK_ProtConn_raster.R

Estimate Protected Connected (ProtConn) indicator and fractions for one region.

MK_ProtConn_raster(
  nodes,
  region,
  area_unit = "m2",
  distance = list(type = "centroid", resistance = NULL),
  distance_thresholds,
  probability,
  transboundary = NULL,
  transboundary_type = "nodes",
  protconn_bound = FALSE,
  LA = NULL,
  delta = FALSE,
  plot = FALSE,
  write = NULL,
  parallel = NULL,
  aggregate_raster = NULL,
  intern = TRUE
)

Arguments

nodes

raster. The file must have a projected coordinate system.
region

object of class raster, sf, sfc, sfg or SpatialPolygons. The file must have a projected coordinate system.
area_unit

character. Attribute area units. You can set an area unit, "Makurhini::unit_covert()" compatible unit ("m2", "Dam2, "km2", "ha", "inch2", "foot2", "yard2", "mile2"). Default equal to hectares "m2".
distance

list. See distancefile. Example, list(type= "centroid", resistance = NULL).
distance_thresholds

numeric. Distance or distances thresholds to establish connections (meters). For example, one distance: distance_threshold = 30000; two or more specific distances: distance_thresholds = c(30000, 50000); sequence distances: distance_thresholds = seq(10000,100000, 10000).
probability

numeric. Probability of direct dispersal between nodes, Default, 0.5, that is 50 percentage of probability connection. If probability = NULL, then it will be the inverse of the mean dispersal distance for the species (1/α; Hanski and Ovaskainen 2000).
transboundary

numeric. Buffer to select polygons in a second round, their attribute value = 0, see Saura et al. 2017. You can set one transboundary value or one per each threshold distance.
transboundary_type

character. Two options: "nodes" or "region". If it is "nodes" the transboundary is built from the limits of the nodes present in the region (default), if "region" is selected the transboundary is built from the limits of the region.
protconn_bound

logical. If TRUE then the fractions ProtUnConn[design] and ProtConn[bound] will be estimated.
LA

numeric. Maximum Landscape Attribute.
delta

logical. Estimate the contribution of each node to the ProtConn value in the region.
plot

logical. Plot the main ProtConn indicators and fractions, default = FALSE.
write

character. Output folder including the output file name without extension, e.g., "C:/ProtConn/Protfiles".
parallel

numeric. Specify the number of cores to use for parallel processing, default = NULL. Parallelize the function using furrr package and multiprocess plan when there are more than ONE transboundary.
aggregate_raster

numeric.Use this parameter if you work with small high-resolution raster (e.g., less than 150 m) or with very large extents. The value of this parameter is used to resample the raster region, perform buffering and speed up the process of transboundary node selection.
intern

logical. Show the progress of the process, default = TRUE. Sometimes the advance process does not reach 100 percent when operations are carried out very quickly.

Value

Table with the following ProtConn values: ECA, Prot, ProtConn, ProtUnconn, RelConn, ProtUnConn[design], ProtConn[bound], ProtConn[Prot], ProtConn[Within], ProtConn[Contig], ProtConn[Trans], ProtConn[Unprot], ProtConn[Within][land], ProtConn[Contig][land], ProtConn[Unprot][land], ProtConn[Trans][land]

*If plot is not NULL a list is returned with the ProtConn table and a plots.

References

Saura, S., Bastin, L., Battistella, L., Mandrici, A., & Dubois, G. (2017). Protected areas in the world’s ecoregions: How well connected are they? Ecological Indicators, 76, 144–158. Saura, S., Bertzky, B., Bastin, L., Battistella, L., Mandrici, A., & Dubois, G. (2018). Protected area connectivity: Shortfalls in global targets and country-level priorities. Biological Conservation, 219(October 2017), 53–67.

Examples

if (FALSE) {
library(Makurhini)
library(raster)
data("Protected_areas_raster", package = "Makurhini")
data("regions", package = "Makurhini")
region <- regions[2,]
test <- MK_ProtConn_raster(nodes = Protected_areas_raster, region = region,
                           area_unit = "ha",
                           distance = list(type= "centroid"),
                           distance_thresholds = c(50000, 10000),
                           probability = 0.5, transboundary = 50000,
                           LA = NULL, plot = FALSE, parallel = NULL,
                           protconn_bound=TRUE,
                           write = NULL, intern = FALSE)
test

}