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Analog density: kernel-weighted analog count within environmental/geographic limits

Source: R/analog_density.R
analog_density.Rd

Computes, for each focal location, the kernel-weighted sum of all reference locations that satisfy the supplied environmental and geographic constraints.

Usage

analog_density(
  x,
  pool,
  x_cov = NULL,
  weight = NULL,
  coord_type = "auto",
  stat = c("sum_weights"),
  env = NULL,
  geog = NULL,
  normalize = "auto",
  env_res_adj = "auto",
  geog_res_adj = "auto",
  cell_area_weight = "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 environmental variables, or a SpatRaster with environmental variable layers.

pool

The reference dataset to search for analogs. Either:

  • Matrix/data.frame with columns x, y, and environmental variables, or SpatRaster with environmental 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 environmental variables, there are n*(n+1)/2 unique components, ordered as: variances first (diagonals), then covariances (upper triangle by row).

weight

Optional pool site weights for use in aggregation. Numeric vector, single-column matrix/data.frame, or single-layer SpatRaster, with one value per row/cell of pool. For aggregation stats like "weighted_mean", "regression", etc., weights multiply through the weighted aggregation alongside any kernel weighting and cell-area weighting; they do not influence which analogs are selected by knn_* modes (selection remains distance-only). They are reported in pair mode as a user_weight column. Values must be non-negative; NA is allowed and treated as 0 (the point is excluded from aggregation). Default NULL means no user-supplied weights.

If you want to exclude a static subset of pool sites entirely, masking pool (and any associated y / covariates) upfront is more efficient than passing weight = 0 for those sites, since the lattice index will not have to scan or distance-compute against them. Use weight = 0 for cases where the mask varies per query against a shared index, or where some sites have a continuous weight and others should be excluded.

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).

stat

Character vector of one or more density-style summary statistics. Allowed options: "sum_weights" (default), "mean_weights", "count", "ess". See analog_search() for detailed stat descriptions.

env, geog

Per-family distance treatment, each a kernel() object (or NULL). A kernel bundles the hard distance threshold, the weighting kernel shape, and the kernel's scale for one family: environmental (env) or geography (geog). kernel(weight, theta, max, min) where:

  • max: hard upper distance threshold — candidates beyond it (in that family's distance) are excluded. For env, max may be a single Euclidean radius or a per-variable vector of absolute-difference thresholds (length equal to the number of environmental variables); scalar environmental thresholds are in Mahalanobis units when x_cov is supplied. For geog, max is a single radius (kilometers when coord_type = "lonlat", projected units otherwise).

  • min: hard lower distance threshold — candidates closer than it are excluded, so retained candidates form an annulus min <= d <= max. Supported only for geog (a single radius, same units as the geographic max); setting min on env is an error. Mainly used to impose a spatial buffer for cross-validation (see analog_cv()).

  • weight: kernel shape for weighted aggregations — "uniform" (no distance weighting), "gaussian" (exp(-d^2 / (2 theta^2))), or "inverse" (1 / (1 + d / theta)). The overall kernel weight is the product of the two families' weights, so shapes may be mixed (e.g. an inverse environmental kernel with a Gaussian geographic kernel).

  • theta: the kernel's scale (Gaussian bandwidth, or inverse half-weight distance). See kernel_params() for calibrated values.

A NULL kernel (the default for both) applies no threshold and no weighting for that family. See kernel() for details.

normalize

One of TRUE, FALSE, or "auto" (default). Only used if stat includes "sum_weights" or "tabulate" and pool is a raster. When active, results for these stats are divided by a global scalar so that they represent a fraction of a theoretically "perfect" scenario where the full search area within max_geog is occupied wall-to-wall by cells whose environment exactly matches x. See details under analog_search() for more info.

env_res_adj, geog_res_adj

Control the lattice search-index resolution of the environmental and geographic families, each a multiplier on a data-dependent default (targeting ~50 pool points per occupied bin, split between families by effective dimensionality, so it scales with pool size). Each is either:

  • A non-negative number: 1 uses the default for that family, larger values are finer, smaller are coarser, and 0 deactivates it.

  • "auto" (the default for both): tune a single overall resolution scale by optimizing compute time on a subsample of focal points. If focal has relatively few rows, tuning is skipped. Not supported when downsample < 1 (set explicit numeric values instead).

A family that the query does not constrain (no corresponding max_* and not the knn sort key) is automatically deactivated, overriding any explicit value (with a message), since binning an unconstrained family only costs time. Ignored if pool is an analog_index (uses the index's resolution).

cell_area_weight

Controls cell-area weighting when pool is a raster. One of "auto" (default; on for raster pools, off otherwise), TRUE (force on; errors if pool is not a SpatRaster), or FALSE (force off). Cell-area weights correct aggregation statistics for non-uniform cell areas (e.g. lonlat grids near the poles, or projected grids on non-equal-area projections); they are computed via terra::cellSize() and normalized to mean 1. When pool is a pre-built analog_index, this argument must agree with the index's stored configuration: cell_area_weight = FALSE errors if the index was built with cell-area weighting on (rebuild the index instead).

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. When downsample < 1, resolution must be set explicitly via geog_res_adj / env_res_adj (auto-tuning is not supported in this case; see those parameters for details).

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.

...

Additional arguments forwarded to analog_search() (e.g. mean_cell_area for tiled workflows).

Value

A data.frame, or a SpatRaster when x is one. Contains index, x, y, and sum_weights. When normalize = TRUE, the value of D_max is attached as a result attribute. See metadata() for attached metadata attributes.

Details

This function is a wrapper that calls analog_search() using select = "all" and stat = "sum_weights". It also supports "count", "mean_weights", and "ess" as additional stats.

By default (normalize = "auto"), the returned sum_weights column is divided by a global scalar D_max whenever pool meets the prerequisites (raster pool with cell-area weighting active). This gives values on roughly [0, 1], interpretable as the fraction of theoretical maximum analog density achieved at each focal. See analog_search() for more details.

References

Mahony CR, Cannon AJ, Wang T, Aitken SN (2017). "A closer look at novel climates: New methods and insights at continental to landscape scales." Global Change Biology, 23(9), 3934-3955. doi:10.1111/gcb.13645

Abatzoglou JT, Dobrowski SZ, Parks SA (2020). "Multivariate climate departures have outpaced univariate changes across global lands." Scientific Reports, 10(1), 3891. doi:10.1038/s41598-020-60270-5

Williams JW, Jackson ST, Kutzbach JE (2007). "Projected distributions of novel and disappearing climates by 2100 AD." Proceedings of the National Academy of Sciences, 104(14), 5738-5742. doi:10.1073/pnas.0606292104

See also

analog_search() for the underlying flexible analog search function; tiled_analog_search() for memory-safe searches on large raster datasets.

Examples

if (FALSE) { # \dontrun{
# Normalized density (default): returns sum_weights on roughly [0, 1]
dens <- analog_density(
  x = sites,
  pool = climate_data,
  env = kernel("gaussian", theta = 0.2, max = 0.5),
  geog = kernel(max = 100)
)
attr(dens, "D_max")  # the global denominator used

# Raw (unnormalized) kernel-weighted sums
dens_raw <- analog_density(
  x = sites,
  pool = climate_data,
  env = kernel("gaussian", theta = 0.2, max = 0.5),
  geog = kernel(max = 100),
  normalize = FALSE
)

# Joint Gaussian weighting (both climate and geography)
intens_joint <- analog_density(
  x = sites,
  pool = climate_data,
  env = kernel("gaussian", theta = 0.2, max = 0.5),
  geog = kernel("gaussian", theta = 50, max = 100)
)

# With pre-built index (for repeated queries)
index <- build_analog_index(climate_data)
i1 <- analog_density(x = sites1, pool = index,
                     env = kernel("inverse", max = 0.5),
                     geog = kernel(max = 100))
i2 <- analog_density(x = sites2, pool = index,
                     env = kernel("gaussian", theta = 0.3),
                     geog = kernel(max = 100))
} # }