Surrogate: Evaluation of Surrogate Endpoints in Clinical Trials

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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

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