select_sites: Select sites for sampling

In dhope/BASSr: Benefit Applied Strategic Sampling

Select sites for sampling

Description

Selection methods for processing site selection using GRTS, random sampling, clustering, or shortest path methods.

Usage

select_sites(
  sites,
  type,
  n_samples,
  min_dist,
  cluster_size = NULL,
  min_dist_cluster = NULL,
  os = NULL,
  hex_id = hex_id,
  site_id = site_id,
  ARUonly = FALSE,
  useGRTS = TRUE,
  progress = TRUE,
  seed = NULL
)

Arguments

sites	Spatial Data frame. Site points created in create_sites(). Requires columns identifying the Hex ID as well as the Site ID (see hex_id and site_id respectively).
type	String. Method to select sites. Must be one of "cluster" - Clustered sampling. Sample a single point, then cluster_size samples around that point. "path" - Shortest Path sampling. Sample a single point, then cluster_size samples in a path from that point. "Random" - Random sampling. Sample a random set of points.
n_samples	Numeric. Number of samples to draw for each hex.
min_dist	Numeric. Minimum distance between points, or if Clusters, between cluster centres.
cluster_size	Integer. For Clusters, number of points per cluster. For Shortest Paths, number of points per path. Only applies to Clusters and Paths.
min_dist_cluster	Numeric. Minimum distance between ARU samples within clusters. Only applies to Clusters.
os	Numeric. Over sample size (proportional). Only applies to Clusters and Random.
hex_id	Column. Identifies hexagon IDs (e.g., default hex_id).
site_id	Column. Identifies site IDs (default site_id).
ARUonly	Logical. Return only ARU locations. If FALSE Clusters return point count locations as well. Only applies to Clusters and Random sampling.
useGRTS	Logical. Should the program be run using GRTS? Only applies to Clusters or Random samples.
progress	Logical. Show progress bars if applicable.
seed	Numeric. Random seed to use for random sampling. Seed only applies to specific sampling events (does not change seed in the environment). NULL does not set a seed.

Value

• If Clustered, returns a data frame of clustered points selected from sites.

• If Random, returns a data frame of sampled points selected from sites.

• If Shortest Path, returns a list of the points on the path and the original points selected to create the path.

Examples

library(dplyr)
library(ggplot2)

sites <- psu_hexagons |>
    slice_sample(n = 7) |>
    create_sites(spacing = 5) |>
    mutate(scaled_benefit = 1, benefit = 0.95)

# Basic clusters
s <- select_sites(sites = sites, hex_id = hex_id, site_id = site_id,
                  type = "cluster", os = 0.75, n_samples = 7, cluster_size = 5,
                  ARUonly = FALSE, seed = 1234, useGRTS = TRUE,
                  min_dist = 25, min_dist_cluster = 9)
ggplot() +
  geom_sf(data = psu_hexagons) +                   # Hex grid
  geom_sf(data = sites, alpha = 0.4) +      # Sites on selected Hex grids
  geom_sf(data = s, aes(colour = aru)) + # Selected sites
  scale_colour_viridis_d()

# Random samples

s <- select_sites(sites = sites, hex_id = hex_id, site_id = site_id,
                  type = "random", os = 1.0, n_samples = 2,
                  ARUonly = FALSE, seed = 1234, min_dist = 10)

ggplot() +
  geom_sf(data = psu_hexagons) +                   # Hex grid
  geom_sf(data = sites, alpha = 0.4) +      # Sites on selected Hex grids
  geom_sf(data = s, aes(colour = siteuse)) + # Selected sites
  scale_colour_viridis_d()

# Shortest Path

s <- select_sites(sites = sites, hex_id = hex_id, site_id = site_id,
                  type = "path", n_samples = 8, cluster_size = 4,
                  ARUonly = FALSE, seed = 1234, useGRTS = TRUE,
                  min_dist = 10, progress = FALSE)

ggplot() +
  geom_sf(data = sites, alpha = 0.4) + # Sites on selected Hex grid
  geom_sf(data = s$routes, aes(colour = factor(route))) + # Selected sites
  scale_colour_viridis_d()

dhope/BASSr documentation built on April 12, 2024, 9:54 p.m.