Man pages for Surrogate
Evaluation of Surrogate Endpoints in Clinical Trials
| 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... |
| association_gof_copula | Produce Associational GoF plot |
| BifixedContCont | Fits a bivariate fixed-effects model to assess surrogacy in... |
| BimixedCbCContCont | Fits a bivariate mixed-effects model using the... |
| BimixedContCont | Fits a bivariate mixed-effects model to assess surrogacy in... |
| binary_continuous_loglik | Loglikelihood function for binary-continuous copula model |
| Bootstrap.MEP.BinBin | Bootstrap 95% CI around the maximum-entropy ICA and SPF... |
| CausalDiagramBinBin | Draws a causal diagram depicting the median informational... |
| CausalDiagramContCont | Draws a causal diagram depicting the median correlations... |
| cdf_fun | Function factory for distribution functions |
| clayton_loglik_copula_scale | Loglikelihood on the Copula Scale for the Clayton Copula |
| colorectal | The Colorectal dataset with a binary surrogate. |
| colorectal4 | The Colorectal dataset with an ordinal surrogate. |
| comb27.BinBin | Assesses the surrogate predictive value of each of the 27... |
| compute_ICA | Compute Individual Causal Association for a given D-vine... |
| compute_ICA_BinCont | Compute Individual Causal Association for a given D-vine... |
| compute_ICA_ContCont | Compute Individual Causal Association for a given D-vine... |
| compute_ICA_OrdCont | Compute Individual Causal Association for a given D-vine... |
| compute_ICA_OrdOrd | Compute Individual Causal Association for a given D-vine... |
| compute_ICA_SurvSurv | Compute Individual Causal Association for a given D-vine... |
| constructor_ICA_estimator | Function constructor to estimate the ICA given a set of... |
| continuous_continuous_loglik | Loglikelihood function for continuous-continuous copula model |
| delta_method_log_mutinfo | Variance of log-mutual information based on the delta method |
| Dvine_ICA_confint | Confidence interval for the ICA given the unidentifiable... |
| ECT | Apply the Entropy Concentration Theorem |
| estimate_ICA_BinCont | Estimate ICA in Binary-Continuous Setting |
| estimate_ICA_ContCont | Estimate ICA in Ordinal-Ordinal Setting |
| estimate_ICA_OrdCont | Estimate ICA in Ordinal-Continuous Setting |
| estimate_ICA_OrdOrd | Estimate ICA in Ordinal-Ordinal Setting |
| estimate_marginal | Estimate marginal distribution using ML |
| estimate_mutual_information_SurvSurv | Estimate the Mutual Information in the Survival-Survival... |
| Fano.BinBin | Evaluate the possibility of finding a good surrogate in the... |
| FederatedApproachStage1 | Fits the first stage model in the two-stage federated data... |
| FederatedApproachStage2 | Fits the second stage model in the two-stage federated data... |
| fit_copula_ContCont | Fit continuous-continuous vine copula model |
| fit_copula_model_BinCont | Fit copula model for binary true endpoint and continuous... |
| fit_copula_OrdCont | Fit ordinal-continuous vine copula model |
| fit_copula_OrdOrd | Fit ordinal-ordinal vine copula model |
| fit_copula_submodel_BinCont | Fit binary-continuous copula submodel |
| fit_copula_submodel_ContCont | Fit ordinal-continuous copula submodel |
| fit_copula_submodel_OrdCont | Fit ordinal-continuous copula submodel |
| fit_copula_submodel_OrdOrd | Fit ordinal-continuous copula submodel |
| fit_model_SurvSurv | Fit Survival-Survival model |
| 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... |
| frank_loglik_copula_scale | Loglikelihood on the Copula Scale for the Frank Copula |
| gaussian_loglik_copula_scale | Loglikelihood on the Copula Scale for the Gaussian Copula |
| gumbel_loglik_copula_scale | Loglikelihood on the Copula Scale for the Gumbel Copula |
| ICA_alpha_ContCont | Assess surrogacy using a Rényi divergence based family of... |
| 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... |
| ICA.BinCont.BS | 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.ContCont.MultS.MPC | Assess surrogacy in the causal-inference single-trial setting... |
| ICA.ContCont.MultS.PC | Assess surrogacy in the causal-inference single-trial setting... |
| ICA_given_model_constructor | Constructor for the function that returns that ICA as a... |
| ICA_given_model_constructor_SurvSurv | Constructor for the function that returns that ICA as a... |
| ICA.Sample.ContCont | Assess surrogacy in the causal-inference single-trial setting... |
| ICA.Sample.ControlTreat | Assess surrogacy in the causal-inference single-trial setting... |
| ICA_t | The function 'ICA_t()' is to evaluate surrogacy in the... |
| ISTE.ContCont | Individual-level surrogate threshold effect for continuous... |
| loglik_copula_scale | Loglikelihood on the Copula Scale |
| log_likelihood_copula_model | Computes loglikelihood for a given copula model |
| LongToWide | Reshapes a dataset from the 'long' format (i.e., multiple... |
| marginal_distribution | Fit marginal distribution |
| marginal_gof_copula | Produce marginal GoF plot |
| marginal_gof_plots_scr | Marginal survival function goodness of fit |
| marginal_gof_scr_S_plot | Goodness-of-fit plot for the marginal survival functions |
| 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... |
| mean_S_before_T_plot_scr | Goodness of fit plot for the fitted copula |
| MetaAnalyticSurvBin | Compute surrogacy measures for a binary surrogate and a... |
| MetaAnalyticSurvCat | Compute surrogacy measures for a categorical (ordinal)... |
| MetaAnalyticSurvCont | Compute surrogacy measures for a continuous... |
| MetaAnalyticSurvSurv | Compute surrogacy measures for a time-to-event surrogate and... |
| 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... |
| model_fit_measures | Goodness of fit information for survival-survival model |
| MufixedContCont.MultS | Fits a multivariate fixed-effects model to assess surrogacy... |
| MumixedContCont.MultS | Fits a multivariate mixed-effects model to assess surrogacy... |
| new_vine_copula_fit | Constructor for vine copula model |
| new_vine_copula_ss_fit | Constructor for vine copula model |
| ordinal_continuous_loglik | Loglikelihood function for ordinal-continuous copula model |
| ordinal_ordinal_loglik | Loglikelihood function for ordinal-ordinal copula model |
| ordinal_to_cutpoints | Convert Ordinal Observations to Latent Cutpoints |
| Ovarian | The Ovarian dataset |
| PANSS | PANSS subscales and total score based on the data of five... |
| pdf_fun | Function factory for density functions |
| plot.CausalInference | Plots the (Meta-Analytic) Individual Causal Association when... |
| plot.comb27.BinBin | Plots the distribution of prediction error functions in... |
| 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.ICA.BinCont | Plot the individual causal association (ICA) in the... |
| 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.ISTE.ContCont | Plots the individual-level surrogate threshold effect (STE)... |
| 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.MetaAnalyticSurvBin | Generates a plot of the estimated treatment effects for the... |
| plot.MetaAnalyticSurvCat | Generates a plot of the estimated treatment effects for the... |
| plot.MetaAnalyticSurvCont | Generates a plot of the estimated treatment effects for the... |
| plot.MetaAnalyticSurvSurv | Generates a plot of the estimated treatment effects for the... |
| plot.MinSurrContCont | Graphically illustrates the theoretical plausibility of... |
| plot.PPE.BinBin | Plots the distribution of either PPE, RPE or R^2_{H} either... |
| Plot.PredTrialTContCont | Plots the expected treatment effect on the true endpoint in a... |
| plot.SPF.BinCont | Plot the surrogate predictive function (SPF) in the... |
| plot.SPPBinBin | Plots the surrogate predictive function (SPF) in the... |
| 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... |
| plot.vine_copula_fit | Goodness-of-fit plots for the fitted copula models |
| Pos.Def.Matrices | Generate 4 by 4 correlation matrices and flag the positive... |
| PPE.BinBin | Evaluate a surrogate predictive value based on the minimum... |
| Pred.TrialT.ContCont | Compute the expected treatment effect on the true endpoint in... |
| Prentice | Evaluates surrogacy based on the Prentice criteria for... |
| print.MetaAnalyticSurvBin | Prints all the elements of an object fitted with the... |
| print.MetaAnalyticSurvCat | Prints all the elements of an object fitted with the... |
| print.MetaAnalyticSurvCont | Prints all the elements of an object fitted with the... |
| print.MetaAnalyticSurvSurv | Prints all the elements of an object fitted with the... |
| print.vine_copula_fit | Print summary of fitted copula model |
| PROC.BinBin | Evaluate the individual causal association (ICA) and... |
| prostate | The prostate dataset with a continuous surrogate. |
| RandVec | Generate random vectors with a fixed sum |
| Restrictions.BinBin | Examine restrictions in pi_{f} under different montonicity... |
| sample_copula_parameters | Sample Unidentifiable Copula Parameters |
| sample_deltas_BinCont | Sample individual casual treatment effects from given D-vine... |
| sample_dvine | Sample copula data from a given four-dimensional D-vine... |
| Schizo | Data of five clinical trials in schizophrenia |
| Schizo_Bin | Data of a clinical trial in Schizophrenia (with binary... |
| Schizo_BinCont | Data of a clinical trial in schizophrenia, with binary and... |
| Schizo_PANSS | Longitudinal PANSS data of five clinical trials in... |
| sensitivity_analysis_BinCont_copula | Perform Sensitivity Analysis for the Individual Causal... |
| sensitivity_analysis_copula | Perform Sensitivity Analysis for the Individual Causal... |
| sensitivity_analysis_SurvSurv_copula | Sensitivity analysis for individual causal association |
| sensitivity_intervals_Dvine | Compute Sensitivity Intervals |
| 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... |
| SPF.BinCont | Evaluate the surrogate predictive function (SPF) in the... |
| SPP.BinBin | Evaluate the surrogate predictive function (SPF) in the... |
| summary.FederatedApproachStage2 | Provides a summary of the surrogacy measures for an object... |
| summary.gen | Summary |
| summary_level_bootstrap_ICA | Bootstrap based on the multivariate normal sampling... |
| summary.MetaAnalyticSurvBin | Provides a summary of the surrogacy measures for an object... |
| summary.MetaAnalyticSurvCat | Provides a summary of the surrogacy measures for an object... |
| summary.MetaAnalyticSurvCont | Provides a summary of the surrogacy measures for an object... |
| summary.MetaAnalyticSurvSurv | Provides a summary of the surrogacy measures for an object... |
| Surrogate-package | Surrogate: Evaluation of Surrogate Endpoints in Clinical... |
| 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... |
| twostep_BinCont | Fit binary-continuous copula submodel with two-step estimator |
| twostep_SurvSurv | Fit survival-survival copula submodel with two-step estimator |
| UnifixedContCont | Fits univariate fixed-effect models to assess surrogacy in... |
| UnimixedContCont | Fits univariate mixed-effect models to assess surrogacy in... |
