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Candidate analytic changes for the path search

Source: R/path.R
path_changes.Rd

Lists the analytic changes stress_path() may combine. Each change belongs to a family (covariance structure, inference, covariate set, LS-mean weighting, reference-based imputation, analysis data set), and a path changes each family at most once. Participant and site deletions are not analytic changes; they are measured separately by stress_fragility().

Usage

path_changes(
  spec,
  covariance = c("us", "ar1h", "cs"),
  inference = default_inference()[c("Satterthwaite", "Kenward-Roger (linear)",
    "Sandwich, between-within")],
  covariates = TRUE,
  weights = TRUE,
  reference = c("J2R", "CR", "CIR"),
  delta_adjusted = numeric(),
  m = 10,
  data = list()
)

Arguments

spec

A stress_spec().

covariance

Alternative covariance structures.

inference

Named list of list(method = , vcov = ) alternatives.

covariates

TRUE to drop each covariate and (with two or more) all of them; a named list of covariate sets to use instead; FALSE for none.

weights

TRUE to include the other LS-mean weighting.

reference

Reference-based imputation assumptions (any of "MAR", "J2R", "CR", "CIR"); character() for none.

delta_adjusted

Shifts for delta-adjusted imputation under MAR. Each value is one change that adds the shift to every imputed value of the active arm (for example minus half the residual SD, against the active arm). It belongs to the reference-based imputation family, so a path uses at most one missing-data assumption. numeric() for none.

m

Imputations per reference-based analysis.

data

Named list of alternative analysis data sets (for example, other intercurrent-event handlings).

Value

A list of changes, each a list with family, label, type ("spec" or "mi") and value.

Examples

spec <- stress_spec(mmrm::fev_data, "FEV1", "USUBJID", "AVISIT", "ARMCD", "PBO",
                    covariates = ~ RACE + FEV1_BL)
vapply(path_changes(spec, reference = character()), `[[`, "", "label")
#> [1] "ar1h"                     "cs"                      
#> [3] "Satterthwaite"            "Sandwich, between-within"
#> [5] "without RACE"             "without FEV1_BL"         
#> [7] "no covariates"            "observed LS-mean weights"