Surrogate: Evaluation of Surrogate Endpoints in Clinical Trials

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 7-th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.

AuthorWim Van der Elst, Paul Meyvisch, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs
Date of publication2016-10-28 00:05:23
MaintainerWim Van der Elst <Wim.vanderelst@gmail.com>
LicenseGPL (>= 2)
Version0.1-79

View on CRAN

Man pages

ARMD: Data of the Age-Related Macular Degeneration Study

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.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.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...

Files in this package

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

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