SOFTWARE
R Packages
Rsurrogate(CRAN), an R package for robust estimation of the proportion of treatment effect on the primary outcome that is explained by the treatment effect on a potential surrogate marker; includes functions to correct for measurement error and functions to evaluate multiple surrogate markers.
hetsurr(CRAN), an R package to examine and test for heterogeneity in the utility of the surrogate marker with respect to a baseline covariate.
survivalsurrogate(GitHub), an R package with influence function-based methods to evaluate a longitudinal surrogate marker in a censored time-to-event outcome setting, with plug-in and targeted minimum loss-based estimation options, written by Denis Agniel, on GitHub.
SurrogateSeq(CRAN), an R package implementing group sequential procedures that allow for early stopping of treatment effect testing using a surrogate. [Tutorial]
freebird(CRAN), an R package to evaluate a high-dimensional surrogate marker using a parametric approach, written by Dr. Rachel Zhou.
PTERP(CRAN), an R package to evaluate the strength of a surrogate marker by via the relative power for the optimally-transformed version of the surrogate, written by Dr. Xuan Wang, on CRAN.
CMFsurrogate(CRAN), an R package to estimate the proportion of the treatment effect explained by multiple surrogate markers using a calibrated model fusion approach, written by Dr. Xuan Wang.
crossurr(CRAN), an R package to evaluate a high-dimensional surrogate marker using a doubly robust method via crossfitting, written by Dr. Denis Agniel and Boris Hejblum.
landest(CRAN), an R package with functions to estimate survival and a treatment effect using a landmark estimation approach.
landmix(CRAN), an R package for nonparametric prediction of survival outcomes for mixture data that incorporates covariates and landmarking, co-written with Dr. Tanya Garcia.
etsi(GitHub), an R package for treatment effect estimation, hypothesis testing, and future study design for settings where a surrogate is used in place of the primary outcome for individuals for whom the surrogate is valid, and the primary outcome is purposefully measured in the remaining patients, written by Rebecca Knowlton, on GitHub. [Tutorial]
SBdecomp(CRAN), an R package with parametric and nonparametric methods to quantify the proportion of the estimated selection bias explained by each confounder.
cohetsurr(CRAN), an R package for assessing complex heterogeneity in the strength of a surrogate marker with respect to multiple baseline covariates, written by Rebecca Knowlton, on GitHub. [Tutorial]
SurrogateParadoxTest(CRAN), an R package to nonparametrically assess assumptions necessary to prevent the surrogate paradox through hypothesis tests of stochastic dominance, monotonicity of regression functions, and non-negative residual treatment effects, written by Emily Hsiao, on CRAN. [Tutorial]
SurrogateTest(CRAN), an R package for early testing for a treatment effect using surrogate marker information.
landpred(CRAN), an R package for landmark prediction of a survival outcome incorporating covariate and short-term event information.
OSsurvival(CRAN), an R package to nonparametrically estimate the proportion of the treatment effect on a censored primary outcome that is explained by an optimally transformed surrogate marker measured at an earlier time, written by Dr. Xuan Wang.
hettest(CRAN), an R package to test for a treatment effect using surrogate marker information accounting for heterogeneity in the utility of the surrogate.
SurrogateRank(CRAN), an R package implementing a rank-based nonparametric approach to evaluate a surrogate marker in a small sample size setting, on CRAN.
SurrogateOutcome(CRAN), an R package to estimate the proportion of treatment effect on a censored primary outcome that is explained by the treatment effect on a censored surrogate outcome/event.
hetsurrSurv(CRAN), an R package to an R package to assess and test for heterogeneity in the utility of a surrogate marker with respect to a baseline covariate using censored data, on CRAN.
SurrogateBMA(CRAN), an R package to estimate the proportion of treatment effect explained by the surrogate marker using Bayesian Model Averaging approach, written by Yunshan Duan, on CRAN.
OptimalSurrogate(CRAN), an R package to identify an optimal transformation of a potential surrogate marker such that the proportion of the treatment effect on a primary outcome can be inferred based on the treatment effect on this identified optimal transformation, written by Dr. Xuan Wang.
longsurr(CRAN), an R package for analyzing the surrogate value of longitudinal markers, and quantifying the proportion of a treatment effect explained by a longitudinal surrogate marker, written by Dr. Denis Agniel.
MonotonicityTest(CRAN), an R package implementing the nonparametric test for detecting monotonicity in regression functions from Hall P and Heckman N (2000) with efficient computation via C++, written by Dylan Huynh, on CRAN. [Shiny App]