Basis expansions for smooths — basis • gratia

Basis expansions from a definition of a smoother using the syntax of mgcv's smooths via mgcv::s()., mgcv::te(), mgcv::ti(), and mgcv::t2(), or directly from a fitted GAM(M).

Usage

basis(object, ...)

# S3 method for class 'gam'
basis(
  object,
  select = NULL,
  term = deprecated(),
  data = NULL,
  n = 100,
  n_2d = 50,
  n_3d = 16,
  n_4d = 4,
  partial_match = FALSE,
  envir = NULL,
  ...
)

# S3 method for class 'scam'
basis(
  object,
  select = NULL,
  term = deprecated(),
  data = NULL,
  n = 100,
  n_2d = 50,
  n_3d = 16,
  n_4d = 4,
  partial_match = FALSE,
  ...
)

# S3 method for class 'gamm'
basis(
  object,
  select = NULL,
  term = deprecated(),
  data = NULL,
  n = 100,
  n_2d = 50,
  n_3d = 16,
  n_4d = 4,
  partial_match = FALSE,
  ...
)

# S3 method for class 'gamm4'
basis(
  object,
  select = NULL,
  term = deprecated(),
  data = NULL,
  n = 100,
  n_2d = 50,
  n_3d = 16,
  n_4d = 4,
  partial_match = FALSE,
  ...
)

# Default S3 method
basis(
  object,
  data,
  knots = NULL,
  constraints = FALSE,
  at = NULL,
  diagonalize = FALSE,
  coefficients = NULL,
  envir = NULL,
  ...
)

Arguments

object: a smooth specification, the result of a call to one of mgcv::s()., mgcv::te(), mgcv::ti(), or mgcv::t2(), or a fitted GAM(M) model.
...: other arguments passed to mgcv::smoothCon().
select: character; select smooths in a fitted model
term: This argument has been renamed select
data: a data frame containing the variables used in smooth.
n: numeric; the number of points over the range of the covariate at which to evaluate a univariate smooth.
n_2d: numeric; the number of points along each of the first two axes of a smooth surface, including surface panels of higher-dimensional smooths. The default is 50 in plotting and plot-preparation functions. If NULL, use n instead. Ignored when evaluation data are supplied. Factor levels are retained, and curves with only one continuous covariate use n.
n_3d: numeric; the number of new observations to generate for the third dimension of a 3D smooth.
n_4d: numeric; the number of new observations to generate for the dimensions higher than 2 (!) of a kD smooth (k >= 4). For example, if the smooth is a 4D smooth, each of dimensions 3 and 4 will get n_4d new observations.
partial_match: logical; in the case of character select, should select match partially against smooths? If partial_match = TRUE, select must only be a single string, a character vector of length 1.
envir: an optional environment supplying functions and constants used in model expressions. The available model formula environment is used when NULL. Covariate observations should be supplied in data.
knots: a list or data frame with named components containing knots locations. Names must match the covariates for which the basis is required. See mgcv::smoothCon().
constraints: logical; should identifiability constraints be applied to the smooth basis. See argument absorb.cons in mgcv::smoothCon().
at: a data frame containing values of the smooth covariate(s) at which the basis should be evaluated.
diagonalize: logical; if TRUE, reparameterises the smooth such that the associated penalty is an identity matrix. This has the effect of turning the last diagonal elements of the penalty to zero, which highlights the penalty null space.
coefficients: numeric; vector of values for the coefficients of the basis functions.

Value

A tibble.

Details

When evaluating a fitted smooth at explicit data, missing covariates required by that smooth produce NA basis values. Missing values in other model variables do not discard otherwise evaluable rows.

Author

Gavin L. Simpson

Examples

load_mgcv()
df <- data_sim("eg4", n = 400, seed = 42)

bf <- basis(s(x0), data = df)
bf <- basis(s(x2, by = fac, bs = "bs"), data = df, constraints = TRUE)