Construct a Baseline Model

Builds a baseline model to account for noise and non-event-related variance. This model may include a drift term, a block intercept term, and nuisance regressors.

Usage

baseline_model(
  basis = c("constant", "poly", "bs", "ns"),
  degree = 1,
  sframe,
  intercept = c("runwise", "global", "none"),
  nuisance_list = NULL,
  nuisance_check = c("warn", "error", "drop", "none"),
  na_action = c("drop", "zero", "median")
)

Arguments

basis

Character; type of basis function ("constant", "poly", "bs", or "ns").

degree

Integer; degree of the spline/polynomial function.

sframe

A sampling_frame object.

intercept

Character; whether to include an intercept ("runwise", "global", or "none"). Ignored when basis == "constant" because the drift term already provides the constant baseline.

nuisance_list

Optional list of nuisance matrices or data frames (one per fMRI block).

nuisance_check

Character; how to handle nuisance diagnostics. "warn" warns on construction-time problems, "error" stops, "drop" removes non-finite, zero-variance, and rank-aliased columns with a warning, and "none" skips these checks.

na_action

Character; how to handle NA values in nuisance_list columns before the diagnostics run. "drop" (default) leaves NAs in place so any column containing one is treated as non-finite and removed by nuisance_check. "zero" replaces NA with 0 (matching the fMRIPrep leading-row convention) and "median" replaces NA with the column median; both repair an isolated leading NA (e.g. in DVARS or framewise displacement) so the regressor is retained. NaN and Inf are never repaired and remain subject to the non-finite drop. Repair is applied even when nuisance_check = "none", preventing NAs from leaking into the design matrix.

Value

An object of class "baseline_model".

Examples

sframe <- fmrihrf::sampling_frame(blocklens = c(100, 100), TR = 2)
bmod <- baseline_model(basis = "bs", degree = 3, sframe = sframe)
bmod_global <- baseline_model(basis = "bs", degree = 3, sframe = sframe, intercept = "global")
bmod_nointercept <- baseline_model(basis = "bs", degree = 3, sframe = sframe, intercept = "none")
stopifnot(ncol(design_matrix(bmod)) == 8)