test.surrogate.extension: Tests whether the surrogate is valid, extended to the paired, two sided test setting

Description

Calculates the rank-based test statistic for Y and the rank-based test statistic for S and the difference, delta, along with corresponding standard error estimates, then tests whether the surrogate is valid. This extends the test.surrogate() function to the case where samples may be paired instead of independent, and where a two sided test is desired.

Usage

test.surrogate.extension(
  yone,
  yzero,
  sone,
  szero,
  alpha = 0.05,
  power.want.s = NULL,
  epsilon = NULL,
  u.y.hyp = NULL,
  alternative = "less",
  paired = FALSE
)

Value

A list containing:

u.y: Estimated rank-based treatment effect on the outcome.
u.s: Estimated rank-based treatment effect on the surrogate.
delta.estimate: Estimated difference in treatment effects: u.y - u.s.
sd.u.y: Standard deviation of u.y.
sd.u.s: Standard deviation of u.s.
sd.delta: Standard deviation of delta.estimate.
ci.delta: One-sided confidence interval upper bound for delta.estimate.
p.delta: p-value for validity of trial-level surrogacy.
epsilon.used: Non-inferiority threshold used in the test.
is.surrogate: TRUE if the surrogate passes the test, else 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.
alpha: significance level for determining surrogate candidates. Default is 0.05.
power.want.s: numeric in (0,1) - power desired for a test of treatment effect based on the surrogate candidate. Either this or epsilon argument must be specified.
epsilon: numeric in (0,1) - non-inferiority margin for determining surrogate validity. Either this or power.want.s argument must be specified.
u.y.hyp: hypothesised value of the treatment effect on the primary response on the probability scale. If not given, it will be estimated based on the observations.
alternative: character giving the alternative hypothesis type. One of c("less","two.sided"), where "less" corresponds to a non-inferiority test and "two.sided" corresponds to a two one-sided test procedure. Default is "less".
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.

Author

Arthur Hughes, Layla Parast

Examples

Run this code

# Load data
data("example.data")
yone <- example.data$y1
yzero <- example.data$y0
sone <- example.data$s1
szero <- example.data$s0
test.surrogate.extension.result <- test.surrogate.extension(
  yone, yzero, sone, szero,
  power.want.s = 0.8, paired = TRUE, alternative = "two.sided"
)

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