Man pages for Surrogate
Evaluation of Surrogate Endpoints in Clinical Trials

AA.MultSCompute the multiple-surrogate adjusted association
ARMDData of the Age-Related Macular Degeneration Study
ARMD.MultSData of the Age-Related Macular Degeneration Study with...
BifixedContContFits a bivariate fixed-effects model to assess surrogacy in...
BimixedCbCContContFits a bivariate mixed-effects model using the...
BimixedContContFits a bivariate mixed-effects model to assess surrogacy in...
binary_continuous_loglikLoglikelihood function for binary-continuous copula model
Bootstrap.MEP.BinBinBootstrap 95% CI around the maximum-entropy ICA and SPF...
CausalDiagramBinBinDraws a causal diagram depicting the median informational...
CausalDiagramContContDraws a causal diagram depicting the median correlations...
cdf_funFunction factory for distribution functions
clayton_loglik_copula_scaleLoglikelihood on the Copula Scale for the Clayton Copula
colorectalThe Colorectal dataset with a binary surrogate.
colorectal4The Colorectal dataset with an ordinal surrogate.
comb27.BinBinAssesses the surrogate predictive value of each of the 27...
compute_ICA_BinContCompute Individual Causal Association for a given D-vine...
compute_ICA_SurvSurvCompute Individual Causal Association for a given D-vine...
delta_method_log_mutinfoVariance of log-mutual information based on the delta method
Dvine_ICA_confintConfidence interval for the ICA given the unidentifiable...
ECTApply the Entropy Concentration Theorem
estimate_ICA_BinContEstimate ICA in Binary-Continuous Setting
estimate_mutual_information_SurvSurvEstimate the Mutual Information in the Survival-Survival...
Fano.BinBinEvaluate the possibility of finding a good surrogate in the...
FederatedApproachStage1Fits the first stage model in the two-stage federated data...
FederatedApproachStage2Fits the second stage model in the two-stage federated data...
fit_copula_model_BinContFit copula model for binary true endpoint and continuous...
fit_copula_submodel_BinContFit binary-continuous copula submodel
fit_model_SurvSurvFit Survival-Survival model
FixedBinBinITFits (univariate) fixed-effect models to assess surrogacy in...
FixedBinContITFits (univariate) fixed-effect models to assess surrogacy in...
FixedContBinITFits (univariate) fixed-effect models to assess surrogacy in...
FixedContContITFits (univariate) fixed-effect models to assess surrogacy in...
FixedDiscrDiscrITInvestigates surrogacy for binary or ordinal outcomes using...
frank_loglik_copula_scaleLoglikelihood on the Copula Scale for the Frank Copula
gaussian_loglik_copula_scaleLoglikelihood on the Copula Scale for the Gaussian Copula
gumbel_loglik_copula_scaleLoglikelihood on the Copula Scale for the Gumbel Copula
ICABinBinAssess surrogacy in the causal-inference single-trial setting...
ICABinBinCounterAssumICA (binary-binary setting) that is obtaied when the...
ICA.BinBin.Grid.FullAssess surrogacy in the causal-inference single-trial setting...
ICA.BinBin.Grid.SampleAssess surrogacy in the causal-inference single-trial setting...
ICA.BinBin.Grid.Sample.UncertAssess surrogacy in the causal-inference single-trial setting...
ICABinContAssess surrogacy in the causal-inference single-trial setting...
ICA.BinCont.BSAssess surrogacy in the causal-inference single-trial setting...
ICAContContAssess surrogacy in the causal-inference single-trial setting...
ICA.ContCont.Mult_altAssess surrogacy in the causal-inference single-trial setting...
ICA.ContCont.MultSAssess surrogacy in the causal-inference single-trial setting...
ICA.ContCont.MultS.MPCAssess surrogacy in the causal-inference single-trial setting...
ICA.ContCont.MultS.PCAssess surrogacy in the causal-inference single-trial setting...
ICA_given_model_constructorConstructor for the function that returns that ICA as a...
ICA.Sample.ContContAssess surrogacy in the causal-inference single-trial setting...
ISTE.ContContIndividual-level surrogate threshold effect for continuous...
loglik_copula_scaleLoglikelihood on the Copula Scale
log_likelihood_copula_modelComputes loglikelihood for a given copula model
LongToWideReshapes a dataset from the 'long' format (i.e., multiple...
marginal_distributionFit marginal distribution
marginal_gof_plots_scrMarginal survival function goodness of fit
marginal_gof_scr_S_plotGoodness-of-fit plot for the marginal survival functions
MarginalProbsComputes marginal probabilities for a dataset where the...
MaxEntICABinBinUse the maximum-entropy approach to compute ICA in the...
MaxEntICAContContUse the maximum-entropy approach to compute ICA in the...
MaxEntSPFBinBinUse the maximum-entropy approach to compute SPF (surrogate...
mean_S_before_T_plot_scrGoodness of fit plot for the fitted copula
MetaAnalyticSurvBinCompute surrogacy measures for a binary surrogate and a...
MetaAnalyticSurvCatCompute surrogacy measures for a categorical (ordinal)...
MetaAnalyticSurvContCompute surrogacy measures for a continuous...
MetaAnalyticSurvSurvCompute surrogacy measures for a time-to-event surrogate and...
MICAContContAssess surrogacy in the causal-inference multiple-trial...
MICA.Sample.ContContAssess surrogacy in the causal-inference multiple-trial...
MinSurrContContExamine the plausibility of finding a good surrogate endpoint...
MixedContContITFits (univariate) mixed-effect models to assess surrogacy in...
model_fit_measuresGoodness of fit information for survival-survival model
MufixedContCont.MultSFits a multivariate fixed-effects model to assess surrogacy...
MumixedContCont.MultSFits a multivariate mixed-effects model to assess surrogacy...
new_vine_copula_ss_fitConstructor for vine copula model
OvarianThe Ovarian dataset
PANSSPANSS subscales and total score based on the data of five...
pdf_funFunction factory for density functions
plot.CausalInferencePlots the (Meta-Analytic) Individual Causal Association when...
plot.comb27.BinBinPlots the distribution of prediction error functions in...
plot.Fano.BinBinPlots the distribution of R^2_{HL} either as a density or as...
Plot.FixedDiscrDiscrITProvides plots of trial-level surrogacy in the...
plot.ICABinBinPlots the (Meta-Analytic) Individual Causal Association and...
plot.ICA.BinContPlot the individual causal association (ICA) in the...
plot.ICA.ContCont.MultPlots the Individual Causal Association in the setting where...
plot.InformationTheoreticProvides plots of trial- and individual-level surrogacy in...
plot.InformationTheoreticBinCombnProvides plots of trial- and individual-level surrogacy in...
plot.InformationTheoreticSurvSurvProvides plots of trial- and individual-level surrogacy in...
plot.ISTE.ContContPlots the individual-level surrogate threshold effect (STE)...
plot.MaxEntContContPlots the sensitivity-based and maximum entropy based...
plot.MaxEntICABinBinPlots the sensitivity-based and maximum entropy based...
plot.MaxEntSPFBinBinPlots the sensitivity-based and maximum entropy based...
plot.MetaAnalyticProvides plots of trial- and individual-level surrogacy in...
plot.MetaAnalyticSurvBinGenerates a plot of the estimated treatment effects for the...
plot.MetaAnalyticSurvCatGenerates a plot of the estimated treatment effects for the...
plot.MetaAnalyticSurvContGenerates a plot of the estimated treatment effects for the...
plot.MetaAnalyticSurvSurvGenerates a plot of the estimated treatment effects for the...
plot.MinSurrContContGraphically illustrates the theoretical plausibility of...
plot.PPE.BinBinPlots the distribution of either PPE, RPE or R^2_{H} either...
Plot.PredTrialTContContPlots the expected treatment effect on the true endpoint in a...
plot.SPF.BinContPlot the surrogate predictive function (SPF) in the...
plot.SPPBinBinPlots the surrogate predictive function (SPF) in the...
plot.TrialLevelITProvides a plots of trial-level surrogacy in the...
plot.TrialLevelMAProvides a plots of trial-level surrogacy in the...
plot.TwoStageSurvSurvPlots trial-level surrogacy in the meta-analytic framework...
Pos.Def.MatricesGenerate 4 by 4 correlation matrices and flag the positive...
PPE.BinBinEvaluate a surrogate predictive value based on the minimum...
Pred.TrialT.ContContCompute the expected treatment effect on the true endpoint in...
PrenticeEvaluates surrogacy based on the Prentice criteria for...
print.MetaAnalyticSurvBinPrints all the elements of an object fitted with the...
print.MetaAnalyticSurvCatPrints all the elements of an object fitted with the...
print.MetaAnalyticSurvContPrints all the elements of an object fitted with the...
print.MetaAnalyticSurvSurvPrints all the elements of an object fitted with the...
PROC.BinBinEvaluate the individual causal association (ICA) and...
prostateThe prostate dataset with a continuous surrogate.
RandVecGenerate random vectors with a fixed sum
Restrictions.BinBinExamine restrictions in pi_{f} under different montonicity...
sample_copula_parametersSample Unidentifiable Copula Parameters
sample_deltas_BinContSample individual casual treatment effects from given D-vine...
sample_dvineSample copula data from a given four-dimensional D-vine...
SchizoData of five clinical trials in schizophrenia
Schizo_BinData of a clinical trial in Schizophrenia (with binary...
Schizo_BinContData of a clinical trial in schizophrenia, with binary and...
Schizo_PANSSLongitudinal PANSS data of five clinical trials in...
sensitivity_analysis_BinCont_copulaPerform Sensitivity Analysis for the Individual Causal...
sensitivity_analysis_SurvSurv_copulaSensitivity analysis for individual causal association
sensitivity_intervals_DvineCompute Sensitivity Intervals
Sim.Data.CounterfactualsSimulate a dataset that contains counterfactuals
Sim.Data.CounterfactualsBinBinSimulate a dataset that contains counterfactuals for binary...
Sim.Data.MTSSimulates a dataset that can be used to assess surrogacy in...
Sim.Data.STSSimulates a dataset that can be used to assess surrogacy in...
Sim.Data.STSBinBinSimulates a dataset that can be used to assess surrogacy in...
Single.Trial.RE.AAConducts a surrogacy analysis based on the single-trial...
SPF.BinContEvaluate the surrogate predictive function (SPF) in the...
SPP.BinBinEvaluate the surrogate predictive function (SPF) in the...
summary.FederatedApproachStage2Provides a summary of the surrogacy measures for an object...
summary.genSummary
summary_level_bootstrap_ICABootstrap based on the multivariate normal sampling...
summary.MetaAnalyticSurvBinProvides a summary of the surrogacy measures for an object...
summary.MetaAnalyticSurvCatProvides a summary of the surrogacy measures for an object...
summary.MetaAnalyticSurvContProvides a summary of the surrogacy measures for an object...
summary.MetaAnalyticSurvSurvProvides a summary of the surrogacy measures for an object...
SurvSurvAssess surrogacy for two survival endpoints based on...
Test.MonoTest whether the data are compatible with monotonicity for S...
TrialLevelITEstimates trial-level surrogacy in the information-theoretic...
TrialLevelMAEstimates trial-level surrogacy in the meta-analytic...
TwoStageSurvSurvAssess trial-level surrogacy for two survival endpoints using...
twostep_BinContFit binary-continuous copula submodel with two-step estimator
twostep_SurvSurvFit survival-survival copula submodel with two-step estimator
UnifixedContContFits univariate fixed-effect models to assess surrogacy in...
UnimixedContContFits univariate mixed-effect models to assess surrogacy in...
Surrogate documentation built on June 22, 2024, 9:16 a.m.