eb_check function

EB Assumption Check

Generate the empirical and prior distribution of both the location parameter gamma and the scale parameter delta.

eb_check(
  data,
  bat,
  covar = NULL,
  model = lm,
  formula = NULL,
  robust.LS = FALSE,
  ref.batch = NULL,
  ...
)

Arguments

• data: n x p data frame or matrix of observations where p is the number of features and n is the number of subjects.
• bat: Factor indicating batch (often equivalent to site or scanner).
• covar: Data frame or matrix of covariates supplied to model.
• model: The model function that ComBat Family supports: lm, lmer, gam.
• formula: Formula for model starting with y ~ where y represents each feature.
• robust.LS: If TRUE, uses robust location and scale estimators for error variance and site effect parameters. Currently uses median and biweight midvariance.
• ref.batch: Reference batch, must take value in levels(bat).
• ...: Additional arguments to model.

Returns

eb_check returns a dataframe containing the empirical and prior distribution of both the location parameter (gamma) and the scale parameter (delta).

Examples

eb_check(data = adni[1:500,43:53], bat = as.factor(adni$manufac[1:500]),
covar = adni[1:500, c("AGE", "SEX")], model = lm, formula = y ~ AGE + SEX)