MK_ProtConn_raster: Protected Connected (ProtConn) using raster nodes

In OscarGOGO/Makurhini: Makurhini: Analyzing landscape connectivity

Protected Connected (ProtConn) using raster nodes

Description

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

Usage

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,
  delta = FALSE,
  plot = FALSE,
  resample_raster = NULL,
  write = NULL,
  parallel = NULL,
  intern = TRUE
)

Arguments

nodes	raster. The file must have a projected coordinate system.
region	object of class raster, rast, sf, sfc, sfg, spatialPolygonsDataFrame. Polygon delimiting the region or study area. It must be in a projected coordinate system.
area_unit	character. (optional, default = "m2") . A character indicating the area units when attribute is NULL. Some options are "m2" (the default), "km2", "cm2", or "ha"; See unit_convert for details.
distance	A matrix or list to establish the distance between each pair of nodes. Distance between nodes may be Euclidean distances (straight-line distance) or effective distances (cost distances) by considering the landscape resistance to the species movements. - If it is a matrix, then the number of columns and rows must be equal to the number of nodes. This distance matrix could be generated by the distancefile function. - If it is a list of parameters, then it must contain the distance parameters necessary to calculate the distance between nodes. For example, two of the most important parameters: “type” and “resistance”. For "type" choose one of the distances: "centroid" (faster), "edge", "least-cost" or "commute-time". If the type is equal to "least-cost" or "commute-time", then you must use the "resistance" argument. For example: distance(type = "least-cost", resistance = raster_resistance). To see more arguments see the distancefile function.
distance_thresholds	A numeric indicating the dispersal distance or distances (meters) of the considered species. If NULL then distance is estimated as the median dispersal distance between nodes. Alternatively, the dispersal_distance function can be used to estimate the dispersal distance using the species home range. Can be the same length as the distance_thresholds parameter.
probability	A numeric value indicating the probability that corresponds to the distance specified in the distance_threshold. For example, if the distance_threshold is a median dispersal distance, use a probability of 0.5 (50%). If the distance_threshold is a maximum dispersal distance, set a probability of 0.05 (5%) or 0.01 (1%). Use in case of selecting the "PC" metric. If probability = NULL, then a probability of 0.5 will be used.
transboundary	numeric. Buffer to select polygons (e.g., PAs) in a second round. The selected polygons will have an attribute value = 0, i.e., their contribution for connectivity would be as stepping stones (Saura et al. 2017). One cross-border value or one for each threshold distance can be set.
transboundary_type	character. Two options: "nodes" (methodology from Saura et al. 2017) or "region". - If it is "nodes", the transboundary is built from the limits of the nodes present in the region (default). - If it is "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.
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.
resample_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.
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.
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. - If delta is TRUE then it returns an sf class object with the importance value (contribution to ProtConn) for each node in the region.

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

## Not run: 
library(Makurhini)
library(raster)
data("Protected_areas_raster", package = "Makurhini")
plot(Protected_areas_raster)
data("Ecoregions", package = "Makurhini")
region <- Ecoregions[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,
                           plot = FALSE, parallel = NULL,
                           write = NULL, intern = FALSE)
test


## End(Not run)

OscarGOGO/Makurhini documentation built on Jan. 9, 2025, 1:20 p.m.