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 Seventh 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 publication2017-03-05 17:30:58
MaintainerWim Van der Elst <Wim.vanderelst@gmail.com>
LicenseGPL (>= 2)
Version0.1-801

View on CRAN

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

Files

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/data/ARMD.MultS.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/ICA.Cont.Cont.MultS_alt.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/AA.MultS.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/ICA.Cont.Cont.MultS.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/ICA.ContCont.MultS.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/ICA.ContCont.Mult_alt.Rd Surrogate/man/plot.MaxEntICABinBin.Rd Surrogate/man/Plot.PredTrialTContCont.Rd Surrogate/man/plot.ICA.ContCont.Mult.Rd Surrogate/man/BifixedContCont.Rd Surrogate/man/FixedBinContIT.Rd Surrogate/man/MaxEntSPFBinBin.Rd Surrogate/man/ICA.Sample.ContCont.Rd Surrogate/man/AA.MultS.Rd Surrogate/man/ARMD.MultS.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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