test.surrogate.extension {SurrogateRank} | R Documentation |
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
)
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 |
szero |
matrix or dataframe of surrogate candidates in the untreated group
with dimension |
alpha |
significance level for determining surrogate candidates. Default is
|
power.want.s |
numeric in (0,1) - power desired for a test of treatment effect based
on the surrogate candidate. Either this or |
epsilon |
numeric in (0,1) - non-inferiority margin for determining surrogate
validity. Either this or |
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
|
paired |
logical flag giving if the data is independent or paired. If
|
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 ofu.y
. -
sd.u.s
Standard deviation ofu.s
. -
sd.delta
Standard deviation ofdelta.estimate
. -
ci.delta
One-sided confidence interval upper bound fordelta.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, elseFALSE
.
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
test.surrogate.extension.result <- test.surrogate.extension(
yone, yzero, sone, szero,
power.want.s = 0.8, paired = TRUE, alternative = "two.sided"
)