delta.calculate.extension: Calculates the rank-based test statistic for Y and S and the...

In SurrogateRank: Rank-Based Test to Evaluate a Surrogate Marker

Calculates the rank-based test statistic for Y and S and the difference, delta, accomodating paired data and allowing for a two-sided test

Description

This function calculates the difference in treatment effects on a univariate marker and on a continuous primary response. This extends the delta.calculate() function to the case where samples may be paired instead of independent, and where a two sided test is desired.

Usage

delta.calculate.extension(yone, yzero, sone, szero, paired = FALSE)

Arguments

yone	numeric vector of primary response values in the treated group.
yzero	numeric vector of primary response values in the untreated group.
sone	matrix or dataframe of surrogate candidates in the treated group with dimension n1 x p where n1 is the number of treated samples and p the number of candidates. Sample ordering must match exactly yone.
szero	matrix or dataframe of surrogate candidates in the untreated group with dimension n0 x p where n0 is the number of untreated samples and p the number of candidates. Sample ordering must match exactly yzero.
paired	logical flag giving if the data is independent or paired. If FALSE (default), samples are assumed independent. If TRUE, samples are assumed to be from a paired design. The pairs are specified by matching the rows of yone and sone to the rows of yzero and szero.

Details

This function estimates the difference (delta) between two rank-based statistics (e.g., Wilcoxon statistics or paired ranks) for a primary outcome and a surrogate, under either an independent or paired design.

Value

A list with the following elements:

• u.y: Rank-based test statistic for the primary outcome

• u.s: Rank-based test statistic for the surrogate

• delta.estimate: Estimated difference between outcome and surrogate statistics

• sd.u.y: Standard deviation of the outcome statistic

• sd.u.s: Standard deviation of the surrogate statistic

• sd.delta: Standard error of the delta estimate

Author(s)

Arthur Hughes, Layla Parast

Examples

# Load data
data("example.data")
yone <- example.data$y1
yzero <- example.data$y0
sone <- example.data$s1
szero <- example.data$s0
delta.calculate.extension.result <- delta.calculate.extension(
  yone, yzero, sone, szero,
  paired = TRUE
)

SurrogateRank documentation built on June 8, 2025, 10:27 a.m.