version 1.0

DESCRIPTION

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+Package: SurrogateTest
+Type: Package
+Title: Early Testing for a Treatment Effect using Surrogate Marker
+        Information
+Version: 1.0
+Date: 2017-10-27
+Author: Layla Parast
+Maintainer: Layla Parast <parast@rand.org>
+Description: Provides functions to test for a treatment effect in terms of the difference in survival between a treatment group and a control group using surrogate marker information obtained at some early time point in a time-to-event outcome setting. Nonparametric kernel estimation is used to estimate the test statistic and perturbation resampling is used for variance estimation. More details will be available in the future in: Parast L, Cai T, Tian L (2017) "Using a Surrogate Marker for Early Testing of a Treatment Effect" (under review).
+License: GPL
+Imports: stats, survival
+NeedsCompilation: no
+Packaged: 2017-10-27 22:12:17 UTC; parast
+Repository: CRAN
+Date/Publication: 2017-10-29 12:49:05 UTC

MD5

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+10d0d0d3b43b55b420faf2d6d249e50c *DESCRIPTION
+45214add8e5de36bef55da759d880fc0 *NAMESPACE
+92a456409d4c1f259471ddc8a3b78bad *R/Functions_SurrogateTest.R
+3195bd13da62111b2183a85569038258 *data/dataA.RData
+9b371c1ce1afa731a856fd90960321c9 *data/dataB.RData
+0e6b97a74d8a9fb00e3429220af41321 *man/Kern.FUN.Rd
+32112c3a9d273321229acd38d8b662c0 *man/VTM.Rd
+77a2efdf23dec3b68cbf935c68e08c17 *man/censor.weight.Rd
+664fddc77f912e2d675a4316e139b68f *man/cumsum2.Rd
+41748c4034dd80eaff977c504e04e9e9 *man/dataA.Rd
+d0695be078b9719316cfc511dc80a29b *man/dataB.Rd
+3f44c10ddc00b5ca7e650d5d07e58d8b *man/delta.ea.single.Rd
+a849ac738665d3e78ec6249eabd6c5b3 *man/delta.eb.single.Rd
+866ebbb68f085b04d7e1c8f65f9efa7d *man/delta.estimate.Rd
+cd05713178adcc175ee3771b87406a11 *man/design.study.Rd
+5434756e7f2139515faf8d9a69d7b0e4 *man/early.delta.test.Rd
+9edc751959b9589fafd8ba0f8bddbdfa *man/helper.si.Rd
+e83c8752610300c075e1cf64bbcf8d77 *man/int.hazc.Rd
+934728f7085c4143bee1c1a277546e55 *man/int.hazc.plan.Rd
+83ebfd07a0170d484334e5ee8df83335 *man/pred.smooth.surv.new.Rd
+f12e85571e7db2d5c7de878c3cc71ced *man/recover.B.Rd
+7f3f8539bbae004c0055c33dfab61504 *man/var.delta.eb.Rd

NAMESPACE

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+importFrom(stats, bw.nrd, dnorm, pnorm, quantile, rexp, sd, var, approx, pexp, qnorm)
+importFrom(survival, survfit, Surv)
+
+exportPattern("^[[:alpha:]]+")

man/Kern.FUN.Rd

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+\name{Kern.FUN}
+\alias{Kern.FUN}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+%%  ~~function to do ... ~~ 
+Calculates kernel matrix
+}
+\description{
+%%  ~~ A concise (1-5 lines) description of what the function does. ~~
+Helper function; this calculates the kernel matrix
+}
+\usage{
+Kern.FUN(zz, zi, bw, kern0)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{zz}{
+%%     ~~Describe \code{zz} here~~
+zz
+}
+  \item{zi}{
+%%     ~~Describe \code{zi} here~~
+zi
+}
+  \item{bw}{
+%%     ~~Describe \code{bw} here~~
+bandwidth
+}
+  \item{kern0}{
+%%     ~~Describe \code{bw} here~~
+kernel distribution
+}
+}
+\value{
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+the kernel matrix
+}
+\author{
+%%  ~~who you are~~
+Layla Parast
+}
+\keyword{smooth}
+\keyword{robust}
+\keyword{nonparametric}
+\keyword{internal}
+% __ONLY ONE__ keyword per line

man/VTM.Rd

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+\name{VTM}
+\alias{VTM}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+%%  ~~function to do ... ~~
+Repeats a row.
+}
+\description{
+%%  ~~ A concise (1-5 lines) description of what the function does. ~~
+Helper function; this function creates a matrix that repeats vc, dm times where each row is equal to the vc vector. 
+}
+\usage{
+VTM(vc, dm)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{vc}{
+%%     ~~Describe \code{vc} here~~
+the vector to repeat.
+}
+  \item{dm}{
+%%     ~~Describe \code{dm} here~~
+number of rows.
+}
+}
+\value{
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+a matrix that repeats vc, dm times where each row is equal to the vc vector
+}
+\keyword{array}
+\keyword{internal}

man/censor.weight.Rd

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+\name{censor.weight}
+\alias{censor.weight}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+%%  ~~function to do ... ~~
+Calculates censoring probability for weighting
+}
+\description{
+%%  ~~ A concise (1-5 lines) description of what the function does. ~~
+Helper function; calculates censoring probability needed for inverse probability of censoring weighting
+}
+\usage{
+censor.weight(data.x, data.delta, t, weight = NULL)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{data.x}{
+%%     ~~Describe \code{data.x} here~~
+numeric vector, the observed event time: X = min(T, C) where T is the time of the primary outcome, C is the censoring time
+}
+  \item{data.delta}{
+%%     ~~Describe \code{data.delta} here~~
+numeric vector of 0/1, the censoring indicator: D = I(T<C) where T is the time of the primary outcome, C is the censoring time
+}
+  \item{t}{
+%%     ~~Describe \code{t} here~~
+number, the time of interest
+}
+  \item{weight}{
+%%     ~~Describe \code{weight} here~~
+a numeric vector or matrix of weights used for perturbation-resampling, default is null.
+
+}
+}
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+Computes the Kaplan Meier estimate of survival for the censoring random variable at the specified time
+}
+\value{
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+Kaplan Meier estimate of survival for censoring at time t
+
+}
+\author{
+%%  ~~who you are~~
+Layla Parast
+}
+\examples{
+data(dataA)
+censor.weight(data.x = dataA$x1, data.delta = dataA$delta1, t=0.5)
+
+}
+
+\keyword{nonparametric}
+\keyword{survival}
+\keyword{internal}

man/cumsum2.Rd

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+\name{cumsum2}
+\alias{cumsum2}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+%%  ~~function to do ... ~~
+Helper function
+
+}
+\description{
+%%  ~~ A concise (1-5 lines) description of what the function does. ~~
+Helper function; should not be called directly by user.
+}
+\usage{
+cumsum2(mydat)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{mydat}{ mydat
+%%     ~~Describe \code{mydat} here~~
+}
+}
+\value{
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+\item{out}{matrix}
+
+}
+\author{
+%%  ~~who you are~~
+Layla Parast
+}
+\keyword{arith}
+\keyword{internal}
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+

man/dataA.Rd

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+\name{dataA}
+\alias{dataA}
+\docType{data}
+\title{
+Hypothetical Study A data
+}
+\description{
+Hypothetical Study A data to be used in examples; t=1 and the landmark time = 0.50.
+
+}
+\usage{data(dataA)}
+\format{
+ A list with 6 elements representing 1000 observations from a control group and 1000 observations from a treatment group:
+  \describe{
+    \item{\code{s1}}{Surrogate marker measurement for treated observations; this marker is measured at time = 0.5. For observations that experience the primary outcome or are censored before 0.5, this value is NA.}
+    \item{\code{x1}}{The observed event or censoring time for treated observations; X  = min(T, C) where T is the time of the primary outcome and C is the censoring time.}
+    \item{\code{delta1}}{The indicator identifying whether the treated observation was observed to have the event or was censored; D =1*(T<C) where T is the time of the primary outcome and C is the censoring time.}
+   \item{\code{s0}}{Surrogate marker measurement for control observations; this marker is measured at time = 0.5. For observations that experience the primary outcome or are censored before 0.5, this value is NA.}
+    \item{\code{x0}}{The observed event or censoring time for control observations; X  = min(T, C) where T is the time of the primary outcome and C is the censoring time.}
+    \item{\code{delta0}}{The indicator identifying whether the control observation was observed to have the event or was censored; D =1*(T<C) where T is the time of the primary outcome and C is the censoring time.}
+}}
+\details{
+Note that if the observation is censored or experienced the primary outcome before the landmark time of 0.50, the surrogate marker measurement is not observed and coded NA. 
+}
+\examples{
+data(dataA)
+names(dataA)
+}
+\keyword{datasets}

man/dataB.Rd

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+\name{dataB}
+\alias{dataB}
+\docType{data}
+\title{
+Hypothetical Study B data
+}
+\description{
+Hypothetical Study B data to be used in examples; landmark time = 0.50.
+}
+\usage{data(dataB)}
+\format{
+ A list with 6 elements representing 1000 observations from a control group and 1000 observations from a treatment group:
+  \describe{
+    \item{\code{s1}}{Surrogate marker measurement for treated observations; this marker is measured at time = 0.5. For observations that experience the primary outcome or are censored before 0.5, this value is NA.}
+    \item{\code{x1}}{The observed event or censoring time for treated observations; X  = min(T, C) where T is the time of the primary outcome and C is the censoring time. This time is administratively censored at 0.55 (see details).}
+    \item{\code{delta1}}{The indicator identifying whether the treated observation was observed to have the event or was censored; D =1*(T<C) where T is the time of the primary outcome and C is the censoring time.}
+   \item{\code{s0}}{Surrogate marker measurement for control observations; this marker is measured at time = 0.5. For observations that experience the primary outcome or are censored before 0.5, this value is NA.}
+    \item{\code{x0}}{The observed event or censoring time for control observations; X  = min(T, C) where T is the time of the primary outcome and C is the censoring time. This time is administratively censored at 0.55 (see details).}
+    \item{\code{delta0}}{The indicator identifying whether the control observation was observed to have the event or was censored; D =1*(T<C) where T is the time of the primary outcome and C is the censoring time.}
+}}
+\details{
+Note that if the observation is censored or experienced the primary outcome before the landmark time of 0.50, the surrogate marker measurement is not observed and coded NA. In addition, Study B data is only observed up to the landmark time plus some epsilon, here epsilon=0.05 such that all observations are essentially adminstratively censored at time=0.55. 
+}
+\examples{
+data(dataB)
+names(dataB)
+}
+\keyword{datasets}