Multiple-direction quadratic score test — ciftest

Combines several Fleming–Harrington score directions in the quadratic form proposed by Ditzhaus and Friedrich. Each component is fitted with the same outcome-specific ciftest() branch. Classical log-rank components use the joint, finite-population-corrected hypergeometric covariance, with cross-direction blocks weighted by w_r(t) * w_s(t). Classical Gray components analogously use the joint Gray (1988) covariance, including the target-event, competing-event, and censoring contributions. Score and augmented components use the cross-product of the stacked individual score contributions. The default chi-square reference uses the numerical rank of the joint covariance. This function does not perform the permutation calibration from the original two-sample survival proposal.

Usage

ciftest_mdir(
  formula,
  data,
  directions = c("early", "late", "unweighted"),
  weights = NULL,
  subset.condition = NULL,
  outcome.type = "auto",
  test = "auto",
  code.event1 = 1,
  code.event2 = 2,
  code.censoring = 0,
  iteration = 0L,
  tolerance = NULL,
  strata = NULL,
  strata.censor = NULL,
  strata.competing.risk = NULL,
  tau = NULL,
  prob.bound = 1e-07,
  prob.truncation = NULL,
  na.action = stats::na.omit
)

Arguments

formula: A two-sided formula with an Event() or Surv() response and one grouping variable on the right-hand side.
data: A data frame containing variables in the formula.
directions: Fleming–Harrington directions. A character vector may contain "unweighted", "early", and "late". Alternatively supply a two-column numeric matrix/data frame with rho and gamma, or a named list of numeric length-two vectors. In this multiple-direction interface, the default character presets correspond to (2, 0), (0, 2), and (0, 0). The stronger early/late directions keep the default set linearly independent.
weights: Optional numeric case weights or the name of a weight column. The standard Gray branch currently accepts integer frequency weights.
subset.condition: Optional character string giving a logical condition to subset data (default NULL).
outcome.type: One of "auto", "competing-risk", or "survival". The aliases "C" and "S" are accepted.
test: Underlying component test: "auto", "logrank", "gray", "score", or "augmented". The corresponding aliases documented for ciftest() are accepted. Put early and late choices in directions.
code.event1: Integer code of the event of interest (default 1).
code.event2: Integer code of the competing risk (default 2).
code.censoring: Integer code of censoring (default 0).
iteration: Non-negative integer giving the number of Scheike fixed-point refinements. 0 returns the closed-form augmented score; positive values use the closed-form-anchored AIPWCC difference.
tolerance: Optional positive convergence tolerance. NULL performs exactly the requested number of finite iterations.
strata: Optional character vector of one or more column names defining analysis strata. Multiple columns define their observed interaction. The grouping variable cannot be included. Event risk sets, null event distributions, and Fleming–Harrington weight processes are constructed separately within these strata, and their score vectors are summed. This is distinct from the two nuisance-model strata.
strata.censor: Optional character vector of one or more column names defining censoring Kaplan-Meier strata. The grouping variable may be included explicitly when group-specific censoring distributions are required.
strata.competing.risk: Optional character vector of one or more column names defining the exposure-by-stratum working Aalen-Johansen models used for the competing-risk nuisance distribution. The grouping variable must not be included because it is crossed with these strata automatically.
tau: Optional finite non-negative analysis horizon.
prob.bound: Strictly positive numerical/positivity bound. Required nuisance probabilities at or below this value produce an error rather than being silently replaced.
prob.truncation: Optional probability lower truncation strictly above prob.bound. It is applied only to positive censoring and working-survival denominators used by score and augmented tests.
na.action: A function specifying the action to take on missing values (default na.omit).

Value

An object inheriting from "ciftest_mdir", "ciftest", and "htest". Component fits are available in components; the unmodified individual contributions are in score.iid, and the covariance actually used by the quadratic statistic is in vcov.score.

References

Ditzhaus M, Friedrich S. More powerful logrank permutation tests for two-sample survival data. arXiv preprint (2018).