Package 'SurrogateRank'

Calculates the rank-based test statistic for Y and S and the difference, delta

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

Usage

delta.calculate(full.data = NULL, yone = NULL, yzero = NULL, sone = NULL, szero = NULL)

Arguments

full.data	either full.data or yone, yzero, sone, szero must be supplied; if full data is supplied it must be in the following format: one observation per row, Y is in the first column, S is in the second column, treatment group (0 or 1) is in the third column.
yone	primary outcome, Y, in group 1
yzero	primary outcome, Y, in group 0
sone	surrogate marker, S, in group 1
szero	surrogate marker, S, in group 0

Value

u.y	rank-based test statistic for Y
u.s	rank-based test statistic for S
delta	difference, u.y-u.s
sd.u.y	standard error estimate of u.y
sd.u.s	standard error estimate of u.s
sd.delta	standard error estimate of delta

Author(s)

Layla Parast

Examples

data(example.data)
delta.calculate(yone = example.data$y1, yzero = example.data$y0, sone = example.data$s1, 
szero = example.data$s0)

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Estimated power to detect a valid surrogate

Description

Calculates the estimated power to detect a valid surrogate given a total sample size and specified alternative

Usage

est.power(n.total, rho = 0.8, u.y.alt, delta.alt, power.want.s = 0.7)

Arguments

n.total	total sample size in study
rho	rank correlation between Y and S in group 0, default is 0.8
u.y.alt	specified alternative for u.y
delta.alt	specified alternative for u.s
power.want.s	desired power for u.s, default is 0.7

Value

estimated power

Author(s)

Layla Parast

Examples

est.power(n.total = 50, rho = 0.8, u.y.alt=0.9, delta.alt = 0.1)

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Example data

Description

Example data use to illustrate the functions

Usage

data("example.data")

Format

A list with 4 elements representing 25 observations from a treatment group (group 1) and 25 observations from a control group (group 0):

y1

the primary outcome,Y, in group 1

y0

the primary outcome, Y, in group 0

s1

the surrogate marker, S, in group 1

s0

the surrogate marker, S, in group 0

Examples

data(example.data)

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Tests whether the surrogate is valid

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

Usage

test.surrogate(full.data = NULL, yone = NULL, yzero = NULL, sone = NULL, 
szero = NULL, epsilon = NULL, power.want.s = 0.7, u.y.hyp = NULL)

Arguments

full.data	either full.data or yone, yzero, sone, szero must be supplied; if full data is supplied it must be in the following format: one observation per row, Y is in the first column, S is in the second column, treatment group (0 or 1) is in the third column.
yone	primary outcome, Y, in group 1
yzero	primary outcome, Y, in group 0
sone	surrogate marker, S, in group 1
szero	surrogate marker, S, in group 0
epsilon	threshold to use for delta, default calculates epsilon as a function of desired power for S
power.want.s	desired power for S, default is 0.7
u.y.hyp	hypothesized value of u.y used in the calculation of epsilon, default uses estimated valued of u.y

Value

u.y	rank-based test statistic for Y
u.s	rank-based test statistic for S
delta	difference, u.y-u.s
sd.u.y	standard error estimate of u.y
sd.u.s	standard error estimate of u.s
sd.delta	standard error estimate of delta
ci.delta	1-sided confidence interval for delta
epsilon.used	the epsilon value used for the test
is.surrogate	logical, TRUE if test indicates S is a good surrogate, FALSE otherwise

Author(s)

Layla Parast

Examples

data(example.data)
test.surrogate(yone = example.data$y1, yzero = example.data$y0, sone = example.data$s1, 
szero = example.data$s0)

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