Latent-space transforms for template-based similarity

These helpers convert densities to low-dimensional vectors before similarity is computed. They are intended to be passed via the `similarity_transform` argument of `template_similarity`.

Usage

latent_pca_transform(
  ref_tab,
  source_tab,
  match_on,
  refvar = "density",
  sourcevar = "density",
  comps = 30,
  center = TRUE,
  scale. = FALSE,
  ...
)

contract_transform(
  ref_tab,
  source_tab,
  match_on,
  refvar = "density",
  sourcevar = "density",
  shrink = 1e-06,
  fit_by = NULL,
  unique_match_only = FALSE,
  ...
)

affine_transform(
  ref_tab,
  source_tab,
  match_on,
  refvar = "density",
  sourcevar = "density",
  shrink = 1e-06,
  fit_by = NULL,
  unique_match_only = FALSE,
  ...
)

coral_transform(
  ref_tab,
  source_tab,
  match_on,
  refvar = "density",
  sourcevar = "density",
  comps = 30,
  center = TRUE,
  scale. = FALSE,
  shrink = 0.001,
  fit_by = NULL,
  ...
)

cca_transform(
  ref_tab,
  source_tab,
  match_on,
  refvar = "density",
  sourcevar = "density",
  comps = 10,
  center = TRUE,
  scale. = FALSE,
  shrink = 0.001,
  fit_by = NULL,
  unique_match_only = FALSE,
  ...
)

Arguments

ref_tab, source_tab

Data frames passed from `template_similarity`.

match_on

Column used for matching rows between tables.

refvar, sourcevar

Density column names to transform.

comps

Number of latent components to retain (post-PCA).

center, scale.

Logical flags passed to `stats::prcomp`.

...

Additional arguments (currently unused; reserved for extension).

shrink

Ridge term for covariance regularization.

fit_by

Optional character vector of column names used to fit CORAL, CCA, or geometric transforms separately within strata shared by `ref_tab` and `source_tab`.

unique_match_only

Logical; if `TRUE`, supervised fitting uses at most one matched pair per `match_on` key within each fitting stratum.

Value

A list with `ref_tab`, `source_tab`, `refvar`, `sourcevar`, and `info`.