Surrogate3.4.1 package

Compute the multiple-surrogate adjusted association

Produce Associational GoF plot

Fits a bivariate fixed-effects model to assess surrogacy in the meta-a...

Fits a bivariate mixed-effects model using the cluster-by-cluster (CbC...

Fits a bivariate mixed-effects model to assess surrogacy in the meta-a...

Loglikelihood function for binary-continuous copula model

Bootstrap 95% CI around the maximum-entropy ICA and SPF (surrogate pre...

Draws a causal diagram depicting the median informational coefficients...

Draws a causal diagram depicting the median correlations between the c...

Function factory for distribution functions

Loglikelihood on the Copula Scale for the Clayton Copula

The Colorectal dataset with a binary surrogate.

The Colorectal dataset with an ordinal surrogate.

Assesses the surrogate predictive value of each of the 27 prediction f...

Compute Individual Causal Association for a given D-vine copula model ...

Compute Individual Causal Association for a given D-vine copula model ...

Compute Individual Causal Association for a given D-vine copula model ...

Compute Individual Causal Association for a given D-vine copula model ...

Compute Individual Causal Association for a given D-vine copula model ...

Compute Individual Causal Association for a given D-vine copula model ...

Function constructor to estimate the ICA given a set of sampled patien...

Loglikelihood function for continuous-continuous copula model

Variance of log-mutual information based on the delta method

Confidence interval for the ICA given the unidentifiable parameters

Apply the Entropy Concentration Theorem

Estimate ICA in Binary-Continuous Setting

Estimate ICA in Ordinal-Ordinal Setting

Estimate ICA in Ordinal-Continuous Setting

Estimate ICA in Ordinal-Ordinal Setting

Estimate marginal distribution using ML

Estimate the Mutual Information in the Survival-Survival Setting

Evaluate the possibility of finding a good surrogate in the setting wh...

Fits the first stage model in the two-stage federated data analysis ap...

Fits the second stage model in the two-stage federated data analysis a...

Fit continuous-continuous vine copula model

Fit copula model for binary true endpoint and continuous surrogate end...

Fit ordinal-continuous vine copula model

Fit ordinal-ordinal vine copula model

Fit binary-continuous copula submodel

Fit ordinal-continuous copula submodel

Fit ordinal-continuous copula submodel

Fit ordinal-continuous copula submodel

Fit Survival-Survival model

Fits (univariate) fixed-effect models to assess surrogacy in the binar...

Fits (univariate) fixed-effect models to assess surrogacy in the case ...

Fits (univariate) fixed-effect models to assess surrogacy in the case ...

Fits (univariate) fixed-effect models to assess surrogacy in the conti...

Investigates surrogacy for binary or ordinal outcomes using the Inform...

Loglikelihood on the Copula Scale for the Frank Copula

Loglikelihood on the Copula Scale for the Gaussian Copula

Loglikelihood on the Copula Scale for the Gumbel Copula

Assess surrogacy using a Rényi divergence based family of metrics in t...

Constructor for the function that returns that ICA as a function of th...

Constructor for the function that returns that ICA as a function of th...

The function ICA_t() is to evaluate surrogacy in the single-trial ca...

Assess surrogacy in the causal-inference single-trial setting in the b...

Assess surrogacy in the causal-inference single-trial setting in the b...

Assess surrogacy in the causal-inference single-trial setting in the b...

Assess surrogacy in the causal-inference single-trial setting in the b...

Assess surrogacy in the causal-inference single-trial setting (Individ...

Assess surrogacy in the causal-inference single-trial setting (Individ...

Assess surrogacy in the causal-inference single-trial setting (Individ...

Assess surrogacy in the causal-inference single-trial setting (Individ...

Assess surrogacy in the causal-inference single-trial setting (Individ...

Assess surrogacy in the causal-inference single-trial setting (Individ...

Assess surrogacy in the causal-inference single-trial setting in the b...

ICA (binary-binary setting) that is obtaied when the counterfactual co...

Assess surrogacy in the causal-inference single-trial setting in the b...

Assess surrogacy in the causal-inference single-trial setting (Individ...

Individual-level surrogate threshold effect for continuous normally di...

Computes loglikelihood for a given copula model

Loglikelihood on the Copula Scale

Reshapes a dataset from the 'long' format (i.e., multiple lines per pa...

Fit marginal distribution

Produce marginal GoF plot

Marginal survival function goodness of fit

Goodness-of-fit plot for the marginal survival functions

Computes marginal probabilities for a dataset where the surrogate and ...

Use the maximum-entropy approach to compute ICA in the binary-binary s...

Use the maximum-entropy approach to compute ICA in the continuous-cont...

Use the maximum-entropy approach to compute SPF (surrogate predictive ...

Goodness of fit plot for the fitted copula

Compute surrogacy measures for a binary surrogate and a time-to-event ...

Compute surrogacy measures for a categorical (ordinal) surrogate and a...

Compute surrogacy measures for a continuous (normally-distributed) sur...

Compute surrogacy measures for a time-to-event surrogate and a time-to...

Assess surrogacy in the causal-inference multiple-trial setting (Meta-...

Assess surrogacy in the causal-inference multiple-trial setting (Meta-...

Examine the plausibility of finding a good surrogate endpoint in the C...

Fits (univariate) mixed-effect models to assess surrogacy in the conti...

Goodness of fit information for survival-survival model

Fits a multivariate fixed-effects model to assess surrogacy in the met...

Fits a multivariate mixed-effects model to assess surrogacy in the met...

Constructor for vine copula model

Constructor for vine copula model

Loglikelihood function for ordinal-continuous copula model

Loglikelihood function for ordinal-ordinal copula model

Convert Ordinal Observations to Latent Cutpoints

Function factory for density functions

Plots the (Meta-Analytic) Individual Causal Association when S and T a...

Plots the distribution of prediction error functions in decreasing ord...

Plots the distribution of $R^2_{HL}$ either as a density or as functio...

Provides plots of trial-level surrogacy in the Information-Theoretic f...

Plot the individual causal association (ICA) in the causal-inference s...

Plots the Individual Causal Association in the setting where there are...

Plots the (Meta-Analytic) Individual Causal Association and related me...

Provides plots of trial- and individual-level surrogacy in the Informa...

Provides plots of trial- and individual-level surrogacy in the Informa...

Provides plots of trial- and individual-level surrogacy in the Informa...

Plots the individual-level surrogate threshold effect (STE) values and...

Plots the sensitivity-based and maximum entropy based Individual Causa...

Plots the sensitivity-based and maximum entropy based Individual Causa...

Plots the sensitivity-based and maximum entropy based surrogate predic...

Provides plots of trial- and individual-level surrogacy in the meta-an...

Generates a plot of the estimated treatment effects for the surrogate ...

Generates a plot of the estimated treatment effects for the surrogate ...

Generates a plot of the estimated treatment effects for the surrogate ...

Generates a plot of the estimated treatment effects for the surrogate ...

Graphically illustrates the theoretical plausibility of finding a good...

Plots the distribution of either $PPE$, $RPE$ or $R^2_{H}$ either as a...

Plots the expected treatment effect on the true endpoint in a new tria...

Plot the surrogate predictive function (SPF) in the causal-inference s...

Plots the surrogate predictive function (SPF) in the binary-binary set...

Provides a plots of trial-level surrogacy in the information-theoretic...

Provides a plots of trial-level surrogacy in the meta-analytic framewo...

Plots trial-level surrogacy in the meta-analytic framework when two su...

Goodness-of-fit plots for the fitted copula models

Generate 4 by 4 correlation matrices and flag the positive definite on...

Evaluate a surrogate predictive value based on the minimum probability...

Compute the expected treatment effect on the true endpoint in a new tr...

Evaluates surrogacy based on the Prentice criteria for continuous endp...

Prints all the elements of an object fitted with the 'MetaAnalyticSurv...

Prints all the elements of an object fitted with the 'MetaAnalyticSurv...

Prints all the elements of an object fitted with the 'MetaAnalyticSurv...

Prints all the elements of an object fitted with the 'MetaAnalyticSurv...

Print summary of fitted copula model

Evaluate the individual causal association (ICA) and reduction in prob...

Generate random vectors with a fixed sum

Examine restrictions in $\bold{\pi}_{f}$ under different montonicity a...

Sample Unidentifiable Copula Parameters

Sample individual casual treatment effects from given D-vine copula mo...

Sample copula data from a given four-dimensional D-vine copula

Perform Sensitivity Analysis for the Individual Causal Association wit...

Perform Sensitivity Analysis for the Individual Causal Association bas...

Sensitivity analysis for individual causal association

Compute Sensitivity Intervals

Simulate a dataset that contains counterfactuals

Simulate a dataset that contains counterfactuals for binary endpoints

Simulates a dataset that can be used to assess surrogacy in the multip...

Simulates a dataset that can be used to assess surrogacy in the single...

Simulates a dataset that can be used to assess surrogacy in the single...

Conducts a surrogacy analysis based on the single-trial meta-analytic ...

Evaluate the surrogate predictive function (SPF) in the causal-inferen...

Evaluate the surrogate predictive function (SPF) in the binary-binary ...

Bootstrap based on the multivariate normal sampling distribution

Provides a summary of the surrogacy measures for an object fitted with...

Summary

Provides a summary of the surrogacy measures for an object fitted with...

Provides a summary of the surrogacy measures for an object fitted with...

Provides a summary of the surrogacy measures for an object fitted with...

Provides a summary of the surrogacy measures for an object fitted with...

Surrogate: Evaluation of Surrogate Endpoints in Clinical Trials

Assess surrogacy for two survival endpoints based on information theor...

Test whether the data are compatible with monotonicity for S and/or T ...

Estimates trial-level surrogacy in the information-theoretic framework

Estimates trial-level surrogacy in the meta-analytic framework

Assess trial-level surrogacy for two survival endpoints using a two-st...

Fit binary-continuous copula submodel with two-step estimator

Fit survival-survival copula submodel with two-step estimator

Fits univariate fixed-effect models to assess surrogacy in the meta-an...

Fits univariate mixed-effect models to assess surrogacy in the meta-an...