Surrogate: Evaluation of Surrogate Endpoints in Clinical Trials
Version 0.1-801

In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a (bio)marker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's Seventh Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.

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AuthorWim Van der Elst, Paul Meyvisch, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs
Date of publication2017-03-05 17:30:58
MaintainerWim Van der Elst <Wim.vanderelst@gmail.com>
LicenseGPL (>= 2)
Version0.1-801
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("Surrogate")

Man pages

AA.MultS: Compute the multiple-surrogate adjusted association
ARMD: Data of the Age-Related Macular Degeneration Study
ARMD.MultS: Data of the Age-Related Macular Degeneration Study with...
BifixedContCont: Fits a bivariate fixed-effects model to assess surrogacy in...
BimixedContCont: Fits a bivariate mixed-effects model to assess surrogacy in...
CausalDiagramBinBin: Draws a causal diagram depicting the median informational...
CausalDiagramContCont: Draws a causal diagram depicting the median correlations...
CIGTS: Data of the Collaborative Initial Glaucoma Treatment Study
Fano.BinBin: Evaluate the possibility of finding a good surrogate in the...
FixedBinBinIT: Fits (univariate) fixed-effect models to assess surrogacy in...
FixedBinContIT: Fits (univariate) fixed-effect models to assess surrogacy in...
FixedContBinIT: Fits (univariate) fixed-effect models to assess surrogacy in...
FixedContContIT: Fits (univariate) fixed-effect models to assess surrogacy in...
FixedDiscrDiscrIT: Investigates surrogacy for binary or ordinal outcomes using...
ICABinBin: Assess surrogacy in the causal-inference single-trial setting...
ICABinBinCounterAssum: ICA (binary-binary setting) that is obtaied when the...
ICA.BinBin.Grid.Full: Assess surrogacy in the causal-inference single-trial setting...
ICA.BinBin.Grid.Sample: Assess surrogacy in the causal-inference single-trial setting...
ICA.BinBin.Grid.Sample.Uncert: Assess surrogacy in the causal-inference single-trial setting...
ICABinCont: Assess surrogacy in the causal-inference single-trial setting...
ICAContCont: Assess surrogacy in the causal-inference single-trial setting...
ICA.ContCont.Mult_alt: Assess surrogacy in the causal-inference single-trial setting...
ICA.ContCont.MultS: Assess surrogacy in the causal-inference single-trial setting...
ICA.Sample.ContCont: Assess surrogacy in the causal-inference single-trial setting...
LongToWide: Reshapes a dataset from the 'long' format (i.e., multiple...
MarginalProbs: Computes marginal probabilities for a dataset where the...
MaxEntICABinBin: Use the maximum-entropy approach to compute ICA in the...
MaxEntICAContCont: Use the maximum-entropy approach to compute ICA in the...
MaxEntSPFBinBin: Use the maximum-entropy approach to compute SPF (surrogate...
MICAContCont: Assess surrogacy in the causal-inference multiple-trial...
MICA.Sample.ContCont: Assess surrogacy in the causal-inference multiple-trial...
MinSurrContCont: Examine the plausibility of finding a good surrogate endpoint...
MixedContContIT: Fits (univariate) mixed-effect models to assess surrogacy in...
Ovarian: The Ovarian dataset
plot.CausalInference: Plots the (Meta-Analytic) Individual Causal Association when...
plot.Fano.BinBin: Plots the distribution of R^2_{HL} either as a density or as...
Plot.FixedDiscrDiscrIT: Provides plots of trial-level surrogacy in the...
plot.ICABinBin: Plots the (Meta-Analytic) Individual Causal Association and...
plot.ICABinCont: Plots the (Meta-Analytic) Individual Causal Association and...
plot.ICA.ContCont.Mult: Plots the Individual Causal Association in the setting where...
plot.InformationTheoretic: Provides plots of trial- and individual-level surrogacy in...
plot.InformationTheoreticBinCombn: Provides plots of trial- and individual-level surrogacy in...
plot.InformationTheoreticSurvSurv: Provides plots of trial- and individual-level surrogacy in...
plot.MaxEntContCont: Plots the sensitivity-based and maximum entropy based...
plot.MaxEntICABinBin: Plots the sensitivity-based and maximum entropy based...
plot.MaxEntSPFBinBin: Plots the sensitivity-based and maximum entropy based...
plot.MetaAnalytic: Provides plots of trial- and individual-level surrogacy in...
plot.MinSurrContCont: Graphically illustrates the theoretical plausibility of...
Plot.PredTrialTContCont: Plots the expected treatment effect on the true endpoint in a...
plot.SPPBinBin: Plots the surrogate predictive function (SPF).
plot.TrialLevelIT: Provides a plots of trial-level surrogacy in the...
plot.TrialLevelMA: Provides a plots of trial-level surrogacy in the...
plot.TwoStageSurvSurv: Plots trial-level surrogacy in the meta-analytic framework...
Pos.Def.Matrices: Generate 4 by 4 correlation matrices and flag the positive...
Pred.TrialT.ContCont: Compute the expected treatment effect on the true endpoint in...
Prentice: Evaluates surrogacy based on the Prentice criteria for...
RandVec: Generate random vectors with a fixed sum
Restrictions.BinBin: Examine restrictions in pi_{f} under different montonicity...
Schizo: Data of five clinical trials in schizophrenia
Schizo_Bin: Data of a clinical trial in Schizophrenia (with binary...
Schizo_PANSS: Longitudinal PANSS data of five clinical trials in...
Sim.Data.Counterfactuals: Simulate a dataset that contains counterfactuals
Sim.Data.CounterfactualsBinBin: Simulate a dataset that contains counterfactuals for binary...
Sim.Data.MTS: Simulates a dataset that can be used to assess surrogacy in...
Sim.Data.STS: Simulates a dataset that can be used to assess surrogacy in...
Sim.Data.STSBinBin: Simulates a dataset that can be used to assess surrogacy in...
Single.Trial.RE.AA: Conducts a surrogacy analysis based on the single-trial...
SPP.BinBin: Evaluate the surrogate predictive function (SPF) in the...
summary.gen: Summary
SurvSurv: Assess surrogacy for two survival endpoints based on...
Test.Mono: Test whether the data are compatible with monotonicity for S...
TrialLevelIT: Estimates trial-level surrogacy in the information-theoretic...
TrialLevelMA: Estimates trial-level surrogacy in the meta-analytic...
TwoStageSurvSurv: Assess trial-level surrogacy for two survival endpoints using...
UnifixedContCont: Fits univariate fixed-effect models to assess surrogacy in...
UnimixedContCont: Fits univariate mixed-effect models to assess surrogacy in...

Functions

AA.MultS Man page Source code
ARMD Man page
ARMD.MultS Man page
BifixedContCont Man page Source code
BimixedContCont Man page Source code
CIGTS Man page
CausalDiagramBinBin Man page Source code
CausalDiagramContCont Man page Source code
Data.Processing Source code
Fano.BinBin Man page Source code
FixedBinBinIT Man page Source code
FixedBinContIT Man page Source code
FixedContBinIT Man page Source code
FixedContContIT Man page Source code
FixedDiscrDiscrIT Man page Source code
ICA.BinBin Man page Source code
ICA.BinBin.CounterAssum Man page Source code
ICA.BinBin.Grid.Full Man page Source code
ICA.BinBin.Grid.Sample Man page Source code
ICA.BinBin.Grid.Sample.Uncert Man page Source code
ICA.BinCont Man page Source code
ICA.ContCont Man page Source code
ICA.ContCont.MultS Man page Source code
ICA.ContCont.MultS_alt Man page Source code
ICA.Sample.ContCont Man page Source code
LongToWide Man page Source code
MICA.ContCont Man page Source code
MICA.Sample.ContCont Man page Source code
MarginalProbs Man page Source code
MaxEntContCont Man page Source code
MaxEntICABinBin Man page Source code
MaxEntSPFBinBin Man page Source code
MinSurrContCont Man page Source code
MixedContContIT Man page Source code
Ovarian Man page
Pos.Def.Matrices Man page Source code
Pred.TrialT.ContCont Man page Source code
Prentice Man page Source code
RandVec Man page Source code
Restrictions.BinBin Man page Source code
SPF.BinBin Man page Source code
Schizo Man page
Schizo_Bin Man page
Schizo_PANSS Man page
Sim.Data.Counterfactuals Man page Source code
Sim.Data.CounterfactualsBinBin Man page Source code
Sim.Data.MTS Man page Source code
Sim.Data.STS Man page Source code
Sim.Data.STSBinBin Man page Source code
Single.Trial.RE.AA Man page Source code
SurvSurv Man page Source code
Test.Mono Man page Source code
TrialLevelIT Man page Source code
TrialLevelMA Man page Source code
TwoStageSurvSurv Man page Source code
UnifixedContCont Man page Source code
UnimixedContCont Man page Source code
plot Causal-Inference BinBin Man page
plot Causal-Inference BinCont Man page
plot Causal-Inference ContCont Man page
plot FixedDiscrDiscrIT Man page
plot Information-Theoretic Man page
plot Information-Theoretic BinCombn Man page
plot MaxEnt ContCont Man page
plot MaxEntICA BinBin Man page
plot MaxEntSPF BinBin Man page
plot Meta-Analytic Man page
plot MinSurrContCont Man page
plot PredTrialTContCont Man page
plot SPF BinBin Man page
plot.BifixedContCont Man page
plot.BimixedContCont Man page Source code
plot.Fano.BinBin Man page Source code
plot.FixedBinBinIT Man page
plot.FixedBinContIT Man page
plot.FixedContBinIT Man page Source code
plot.FixedContContIT Man page
plot.FixedDiscrDiscrIT Man page Source code
plot.ICA.BinBin Man page Source code
plot.ICA.BinCont Man page Source code
plot.ICA.ContCont Man page Source code Source code
plot.ICA.ContCont.MultS Man page Source code
plot.ICA.ContCont.MultS_alt Man page
plot.MICA.ContCont Man page Source code Source code
plot.MaxEntContCont Man page Source code
plot.MaxEntICA.BinBin Man page Source code
plot.MaxEntSPF.BinBin Man page Source code
plot.MinSurrContCont Man page Source code
plot.MixedContContIT Man page
plot.PredTrialTContCont Man page Source code
plot.SPF.BinBin Man page Source code
plot.Single.Trial.RE.AA Man page Source code
plot.SurvSurv Man page Source code
plot.TrialLevelIT Man page Source code
plot.TrialLevelMA Man page Source code
plot.TwoStageSurvSurv Man page Source code
plot.UnifixedContCont Man page
plot.UnimixedContCont Man page Source code
summary Man page
summary.AA.MultS Man page Source code
summary.BifixedContCont Man page Source code
summary.BimixedContCont Man page Source code
summary.Fano.BinBin Man page Source code
summary.FixedBinBinIT Man page
summary.FixedBinContIT Man page
summary.FixedContBinIT Man page Source code
summary.FixedContContIT Man page Source code
summary.FixedDiscrDiscrIT Man page Source code
summary.ICA.BinBin Man page Source code
summary.ICA.BinCont Man page Source code
summary.ICA.ContCont Man page Source code Source code
summary.ICA.ContCont.MultS Man page Source code
summary.MICA.ContCont Man page Source code Source code
summary.MaxEntContCont Man page Source code
summary.MaxEntICA.BinBin Man page Source code
summary.MaxEntSPF.BinBin Man page Source code
summary.MinSurrContCont Man page Source code
summary.MixedContContIT Man page Source code
summary.PredTrialTContCont Man page Source code
summary.Prentice Man page Source code
summary.SPF.BinBin Man page Source code
summary.Single.Trial.RE.AA Man page Source code
summary.SurvSurv Man page Source code
summary.TrialLevelIT Man page Source code
summary.TrialLevelMA Man page Source code
summary.TwoStageSurvSurv Man page Source code
summary.UnifixedContCont Man page
summary.UnimixedContCont Man page

Files

NAMESPACE
NEWS
data
data/CIGTS.rda
data/Ovarian.rda
data/Schizo_Bin.rda
data/Schizo_PANSS.rda
data/ARMD.rda
data/Schizo.rda
data/ARMD.MultS.rda
R
R/plot.SurvSurv.R
R/summary.Fano.BinBin.R
R/LongToWide.R
R/summary.FixedDIscrDiscrIT.R
R/FixedContBinIT.r
R/CausalDiagramContCont.R
R/FixedDiscrDiscrIT.R
R/plot.MaxEntSPF.BinBin.R
R/SimDataSTSBinBin.R
R/ICA.BinBin.Grid.Full.R
R/plot.MaxEntContCont.R
R/summary.SurvSurv.R
R/Prentice.R
R/Sim.Data.MTS.R
R/UnifixedContCont.R
R/RandVec.R
R/BimixedContCont.R
R/SimDataCounterfactualsBinBin.R
R/Single.Trial.RE.AA.R
R/ICA.BinBin.Grid.Sample.R
R/Fano.BinBin.R
R/FixedBinBinIT.r
R/Data.Processing.R
R/summary.TrialLevelIT.R
R/Sim.Data.Counterfactuals.R
R/BifixedContCont.R
R/SummaryMaxEntSPFBinBin.R
R/plot.MetaAnalyticMTS.R
R/plot.MetaAnalyticSTS.R
R/Sim.Data.STS.R
R/SummarySPPBinBin.R
R/ICA.Sample.ContCont.R
R/TrialLevelMA.R
R/TrialLevelIT.R
R/plot_SPPBinBin.R
R/SummaryITContCont.R
R/MICA.Sample.ContCont.R
R/MinSurrContCont.R
R/ICA.Cont.Cont.MultS_alt.R
R/MICAContCont.R
R/UnimixedContCont.R
R/plot_ICABinBin.R
R/MaxEntContCont.R
R/plot_ICABinCont.R
R/ICA.BinBin.Grid.Sample.Uncert.R
R/plot.TwoStageSurvSurv.R
R/FixedContContIT.r
R/Pos.Def.Matrices.R
R/ICABinBinCounterAssum.R
R/Restrictions.BinBin.R
R/SummaryMetaAnalyticSTSContCont.R
R/TwoStageSurvSurv.R
R/MaxEntSPFBinBin.R
R/SummaryMetaAnalyticMTSContCont.R
R/summaryBinContCombnIT.R
R/Plot.FixedDiscrDiscrIT.R
R/CausalDiagramBinBin.R
R/Pred.TrialT.ContCont.R
R/MaxEntICABinBin.R
R/plot.BinContCombnIT.R
R/summary_MaxEntICABinBin.R
R/ICABinBin.R
R/AA.MultS.R
R/FixedBinContIT.r
R/ICA.BinCont.R
R/summary_MaxEntContCont.R
R/plot.TrialLevelIT.R
R/MarginalProbs.R
R/MixedContContIT.R
R/plot.Fano.BinBin.R
R/plot_MaxEntICABinBin.R
R/SummaryTrialLevelMA.R
R/summary_ICABinBin.R
R/plot.TrialLevelMA.R
R/Test.Mono.R
R/SurvSurv.R
R/ICA.Cont.Cont.MultS.R
R/summary.TwoStageSurvSurv.R
R/SPP.BinBin.R
R/plot.InfoTheoretic.R
R/summary_ICABinCont.R
R/ICAContCont.R
MD5
DESCRIPTION
man
man/Schizo.Rd
man/BimixedContCont.Rd
man/FixedDiscrDiscrIT.Rd
man/Restrictions.BinBin.Rd
man/CausalDiagramContCont.Rd
man/Sim.Data.MTS.Rd
man/plot.SPPBinBin.Rd
man/ICA.ContCont.MultS.Rd
man/Pred.TrialT.ContCont.Rd
man/FixedContContIT.Rd
man/TrialLevelMA.Rd
man/Test.Mono.Rd
man/MixedContContIT.Rd
man/Plot.FixedDiscrDiscrIT.Rd
man/plot.MaxEntContCont.Rd
man/ICABinCont.Rd
man/RandVec.Rd
man/plot.InformationTheoreticBinCombn.Rd
man/plot.ICABinCont.Rd
man/plot.MetaAnalytic.Rd
man/Sim.Data.Counterfactuals.Rd
man/ARMD.Rd
man/Schizo_PANSS.Rd
man/Sim.Data.CounterfactualsBinBin.Rd
man/plot.MaxEntSPFBinBin.Rd
man/plot.InformationTheoretic.Rd
man/MaxEntICAContCont.Rd
man/Prentice.Rd
man/TwoStageSurvSurv.Rd
man/MaxEntICABinBin.Rd
man/plot.InformationTheoreticSurvSurv.Rd
man/Sim.Data.STS.Rd
man/UnifixedContCont.Rd
man/ICA.ContCont.Mult_alt.Rd
man/plot.MaxEntICABinBin.Rd
man/Plot.PredTrialTContCont.Rd
man/plot.ICA.ContCont.Mult.Rd
man/BifixedContCont.Rd
man/FixedBinContIT.Rd
man/MaxEntSPFBinBin.Rd
man/ICA.Sample.ContCont.Rd
man/AA.MultS.Rd
man/ARMD.MultS.Rd
man/CIGTS.Rd
man/SPP.BinBin.Rd
man/Ovarian.Rd
man/summary.gen.Rd
man/MICA.Sample.ContCont.Rd
man/ICA.BinBin.Grid.Sample.Rd
man/UnimixedContCont.Rd
man/ICA.BinBin.Grid.Sample.Uncert.Rd
man/ICA.BinBin.Grid.Full.Rd
man/plot.Fano.BinBin.Rd
man/FixedBinBinIT.Rd
man/ICAContCont.Rd
man/plot.MinSurrContCont.Rd
man/MICAContCont.Rd
man/Pos.Def.Matrices.Rd
man/Fano.BinBin.Rd
man/Single.Trial.RE.AA.Rd
man/plot.CausalInference.Rd
man/ICABinBinCounterAssum.Rd
man/FixedContBinIT.Rd
man/LongToWide.Rd
man/MarginalProbs.Rd
man/Schizo_Bin.Rd
man/plot.ICABinBin.Rd
man/plot.TwoStageSurvSurv.Rd
man/SurvSurv.Rd
man/ICABinBin.Rd
man/Sim.Data.STSBinBin.Rd
man/MinSurrContCont.Rd
man/TrialLevelIT.Rd
man/CausalDiagramBinBin.Rd
man/plot.TrialLevelIT.Rd
man/plot.TrialLevelMA.Rd
Surrogate documentation built on May 19, 2017, 8:40 p.m.