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.

Author | Wim Van der Elst, Paul Meyvisch, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs |

Date of publication | 2016-10-28 00:05:23 |

Maintainer | Wim Van der Elst <Wim.vanderelst@gmail.com> |

License | GPL (>= 2) |

Version | 0.1-79 |

**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...

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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