Analog availability: count of all analogs within climate/geographic limits

Computes, for each focal location, how many reference locations satisfy the supplied climate and geographic constraints. This is useful for mapping analog "availability" or environmental similarity density.

Usage

analog_availability(
  x,
  pool,
  x_cov = NULL,
  coord_type = "auto",
  max_clim = NULL,
  max_geog = NULL,
  index_res = "auto",
  n_threads = NULL,
  downsample = 1,
  seed = NULL,
  progress = FALSE
)

Arguments

x

Focal locations for which analogs will be found. Should be a matrix/data.frame with columns x, y, and climate variables, or a SpatRaster with climate variable layers.

pool

The reference dataset to search for analogs. Either:

Matrix/data.frame with columns x, y, and climate variables, or SpatRaster with climate variable layers, OR
An analog_index object created by build_analog_index() (for repeated queries).

x_cov

Optional focal-specific covariance matrices for Mahalanobis distance calculations. Should be a matrix or data.frame with one row per focal location and one column per unique covariance component, or a SpatRaster with a layer for each component. For n climate variables, there are n*(n+1)/2 unique components, ordered as: variances first (diagonals), then covariances (upper triangle by row).

coord_type

Coordinate system type:

"auto" (default): Automatically detect from coordinate ranges.
"lonlat": Unprojected lon/lat coordinates (uses great-circle distance; assumes max_geog is in km).
"projected": Projected XY coordinates (uses planar distance; assumes max_geog is in projection units).

max_clim

Maximum climate distance constraint (default: NULL = no climate constraint). Can be either:

A scalar: Euclidean radius in climate space (e.g., 0.5)
A vector: Per-variable absolute differences (length must equal number of climate variables)

Only reference locations within this climate distance are considered. When x_cov is provided, scalar thresholds are interpreted in Mahalanobis distance units.

max_geog

Maximum geographic distance constraint (default: NULL = no geographic constraint). When specified, only reference locations within this distance are considered. Radius units should be specified in kilometers if coord_type = "lonlat", or in projected coordinate units if coord_type = "projected".

index_res

Tuning parameter giving the number of bins per dimension of the internally-used lattice search index. Either:

A positive integer.
"auto" (the default): Automatically tune the index resolution by optimizing compute time on a subsample of focal points. If focal has relatively few rows, auto-tuning is skipped and a default resolution of 16 is used.

Ignored if pool is an analog_index (uses index's resolution).

n_threads

Optional integer number of threads to use for the computation. If NULL (default), the global RcppParallel setting is used (see RcppParallel::setThreadOptions).

downsample

Optional downsampling rate (0-1) for the reference pool, indicating the proportion of points to retain. Values < 1 reduce memory and improve speed at some cost to precision. Default is 1.0 (no downsampling). Ignored if pool is a pre-built index.

seed

Optional random seed for reproducible downsampling. If NULL (default), uses current R random state. Ignored if pool is a pre-built index or downsample = 1.

progress

Logical; if TRUE, display a progress bar during computation. Progress tracking works by splitting the focal dataset into chunks and processing them sequentially. Useful for large datasets. Default is FALSE.

Value

Return type depends on input format and query mode.

Returns a data.frame, unless x is a SpatRaster and results have exactly one record per input cell (aggregation mode, or pairwise with k = 1), in which case returns a SpatRaster with one layer per output variable.

Pairwise mode (stat = NULL or "none") returns one row per focal-analog pair, with the following variables:

index, x, y: Focal location (1-based index and coordinates) corresponding to input x
analog_index, analog_x, analog_y: Analog location corresponding to input pool
clim_dist: Climate distance (Euclidean or Mahalanobis)
geog_dist: Geographic distance (km for lonlat, projection units otherwise)
Value columns (if values provided): one per variable

Aggregation mode (one or more stat values) returns one row per focal location, with the following variables:

index, x, y: Focal location
One column per requested statistic. For stat with single values variable: column named by stat (e.g., sum, mean). For stat with multiple values variables: columns named {stat}_{varname} (e.g., sum_biomass, mean_richness)

All results include metadata attributes (select, stat, weight, etc.). Use analog_summary() to view a formatted summary.

Details

This function is a wrapper that calls analog_search() using select = "all" and stat = "count".

References

Stralberg D, Carroll C, Pedlar JH, Wilsey CB, McKenney DW, Nielsen SE (2018). "Macrorefugia for North American trees and songbirds: Climatic limiting factors and multi-scale topographic influences." Global Ecology and Biogeography, 27(6), 690-703. doi:10.1111/geb.12731

Carroll C, Lawler JJ, Roberts DR, Hamann A (2015). "Biotic and climatic velocity identify contrasting areas of vulnerability to climate change." PLOS ONE, 10(10), e0140486. doi:10.1371/journal.pone.0140486

Parks SA, Holsinger LM, Abatzoglou JT, Littlefield CE, Zeller KA (2023). "Protected areas not likely to serve as steppingstones for species undergoing climate-induced range shifts." Global Change Biology, 29(10), 2681-2696. doi:10.1111/gcb.16629

Examples

if (FALSE) { # \dontrun{
# One-shot query
avail <- analog_availability(
  x = sites,
  pool = climate_data,
  max_clim = 0.5,
  max_geog = 100
)

# With pre-built index (for repeated queries)
index <- build_analog_index(climate_data)
a1 <- analog_availability(x = sites1, pool = index, max_clim = 0.5, max_geog = 100)
a2 <- analog_availability(x = sites2, pool = index, max_clim = 0.3, max_geog = 50)
} # }