# 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.

- 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

## 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 |