Cmeasures               Concordance measures in shared frailty and Cox
                        proportional hazard models
Diffepoce               Difference of Expected Prognostic Observed
                        Cross-Entropy (EPOCE) estimators and its 95%
                        tracking interval between two joint models.
GenfrailtyPenal         Fit a Shared or a Joint Frailty Generalized
                        Survival Model
SurvIC                  Create a survival object for interval censoring
                        and possibly left truncated data
additivePenal           Fit an Additive Frailty model using a
                        semiparametric penalized likelihood estimation
                        or a parametric estimation
bcos                    Breast Cosmesis Data
cluster                 Identify clusters
colorectal              Follow-up of metastatic colorectal cancer
                        patients: times of new lesions appearance and
                        death
colorectalLongi         Follow-up of metastatic colorectal cancer
                        patients : longitudinal measurements of tumor
                        size
dataAdditive            Simulated data as a gathering of clinical
                        trials databases
dataMultiv              Simulated data for two types of recurrent
                        events and a terminal event
dataNCC                 Simulated data for recurrent events and a
                        terminal event with weigths using nested
                        case-control design
dataNested              Simulated data with two levels of grouping
dataOvarian             Advanced Ovarian Cancer dataset
epoce                   Estimators of the Expected Prognostic Observed
                        Cross-Entropy (EPOCE) for evaluating predictive
                        accuracy of joint models.
event2                  Identify event2 indicator
frailtyDesign           Sample Size calculation and Power Analysis
                        using Gamma-Frailty Models
frailtyPenal            Fit a Shared, Joint or Nested Frailty model
frailtypack-package     General Frailty models: shared, joint and
                        nested frailty models with prediction;
                        Evaluation of Failure-Time Surrogate Endpoints
gastadj                 Advanced Gastric Cancer dataset
hazard                  Hazard function.
jointRecCompet          Competing Joint Frailty Model: A single type of
                        recurrent event and two terminal events.
jointSurrCopSimul       Generate survival times for two endpoints using
                        the joint frailty-copula model for surrogacy
jointSurrSimul          Generate survival times for two endpoints using
                        the joint frailty surrogate model
jointSurroCopPenal      Fit the one-step Joint frailty-copula model for
                        evaluating a canditate surrogate endpoint
jointSurroPenal         Fit the one-step Joint surrogate model for
                        evaluating a canditate surrogate endpoint
jointSurroPenalSimul    Simulation studies based on the one-step Joint
                        surrogate models for the evaluation of a
                        canditate surrogate endpoint
jointSurroTKendall      Kendall's tau estimation using numerical
                        integration methods
longDat                 Longitudinal semicontinuous biomarker dataset
                        (TPJM)
longiPenal              Fit a Joint Model for Longitudinal Data and a
                        Terminal Event
loocv                   The trials leave-one-out crossvalidation for
                        the one-step Joint surrogate model for
                        evaluating a canditate surrogate endpoint.
multivPenal             Fit a multivariate frailty model for two types
                        of recurrent events and a terminal event.
num.id                  Identify individuals in Joint model for
                        clustered data
plot.Diffepoce          Plot difference of EPOCE estimators between two
                        joint frailty models.
plot.additivePenal      Plot Method for an Additive frailty model.
plot.epoce              Plot values of estimators of the Expected
                        Prognostic Observed Cross-Entropy (EPOCE).
plot.frailtyPenal       Plot Method for a Shared frailty model.
plot.jointNestedPenal   Plot method for a joint nested frailty model.
plot.jointPenal         Plot Method for a Joint frailty model.
plot.jointRecCompet     Plot Method for a joint competing risk model
                        with one recurrent event and two terminal
                        events.
plot.jointSurroMed      Plot Method for a joint surrogate mediation
                        analysis model.
plot.jointSurroPenal    Plot Method for the one-step Joint surrogate
                        model for the evaluation of a canditate
                        surrogate endpoint.
plot.jointSurroPenalloocv
                        Plot of trials leave-one-out crossvalidation
                        Outputs from the one-step Joint surrogate model
                        for evaluating a canditate surrogate endpoint.
plot.longiPenal         Plot Method for a joint model for longitudinal
                        data and a terminal event.
plot.multivPenal        Plot Method for a multivariate frailty model.
plot.nestedPenal        Plot Method for a Nested frailty model.
plot.predFrailty        Plot predictions using a Cox or a shared
                        frailty model.
plot.predJoint          Plot predictions using a joint frailty model.
plot.predLongi          Plot predictions using a joint model for
                        longitudinal data and a terminal event or a
                        trivariate joint model for longitudinal data,
                        recurrent events and a terminal event.
plot.trivPenal          Plot Method for a trivariate joint model for
                        longitudinal data, recurrent events and a
                        terminal event.
plot.trivPenalNL        Plot Method for a Non-Linear Trivariate Joint
                        Model for Recurrent Events and a Terminal Event
                        with a Biomarker Described with an ODE.
plotTreatPredJointSurro
                        Plot of the prediction of the treatment effect
                        on the true endpoint and the STE
predict.jointSurroPenal
                        S3method predict for the one-step Joint
                        surrogate models for the evaluation of a
                        canditate surrogate endpoint.
prediction              Prediction probabilities for Cox proportional
                        hazard, Shared, Joint frailty models, Joint
                        models for longitudinal data and a terminal
                        event and Trivariate joint model for
                        longitudinal data, recurrent events and a
                        terminal event (linear and non-linear).
print.Cmeasures         Print a short summary of results of Cmeasure
                        function.
print.additivePenal     Print a Short Summary of parameter estimates of
                        an additive frailty model
print.frailtyDesign     Print a short table of a 'frailtyDesign'
                        result.
print.frailtyPenal      Print a Short Summary of parameter estimates of
                        a shared frailty model
print.jointNestedPenal
                        Print a Short Summary of parameter estimates of
                        a joint nested frailty model
print.jointPenal        Print a Short Summary of parameter estimates of
                        a joint frailty model
print.jointRecCompet    Print a Short Summary of parameter estimates of
                        a joint competing risks midel
print.jointSurroPenal   Summary of the random effects parameters, the
                        fixed treatment effects, and the surrogacy
                        evaluation criteria estimated from a joint
                        surrogate model
print.longiPenal        Print a Summary of parameter estimates of a
                        joint model for longitudinal data and a
                        terminal event
print.multivPenal       Print a Short Summary of parameter estimates of
                        a multivariate frailty model
print.nestedPenal       Print a Short Summary of parameter estimates of
                        a nested frailty model
print.prediction        Print a short summary of results of prediction
                        function.
print.trivPenal         Print a Summary of parameter estimates of a
                        joint model for longitudinal data, recurrent
                        events and a terminal event
print.trivPenalNL       Print a Summary of parameter estimates of a
                        non-linear trivariate joint model for
                        longitudinal data, recurrent events and a
                        terminal event
readmission             Rehospitalization colorectal cancer
reduce                  Delirium in critically ill ICU patients
                        dataset: the REDUCE clinical trial
runShiny                Shiny application for modelisation and
                        prediction of frailty models
simulatejointRecCompet
                        Generating from a joint competing Joint frailty
                        model with a recurrent event and two terminal
                        events.
slope                   Identify variable associated with the random
                        slope
ste                     Surrogate threshold effect for the one-step
                        Joint surrogate model for the evaluation of a
                        canditate surrogate endpoint.
subcluster              Identify subclusters
summary.additivePenal   summary of parameter estimates of an additive
                        frailty model
summary.frailtyDesign   Summarize a 'frailtyDesign' object.
summary.frailtyPenal    summary of parameter estimates of a shared
                        frailty model
summary.jointNestedPenal
                        summary of parameter estimates of a joint
                        nested frailty model
summary.jointPenal      summary of parameter estimates of a joint
                        frailty model
summary.jointRecCompet
                        Summary method for a joint competing risks
                        midel
summary.jointSurroMed   Short summary of the random effects parameters,
                        the fixed treatment effects, and the surrogacy
                        evaluation criteria estimated from a joint
                        surrogate mediation model
summary.jointSurroPenal
                        Short summary of the surrogacy evaluation
                        criteria estimated from a joint surrogate model
summary.jointSurroPenalSimul
                        Short summary of the simulation studies based
                        on a joint surrogate model
summary.longiPenal      Short summary of fixed covariates estimates of
                        a joint model for longitudinal data and a
                        terminal event.
summary.multivPenal     summary of parameter estimates of a
                        multivariate frailty model.
summary.nestedPenal     summary of regression coefficient estimates of
                        a nested frailty model
summary.trivPenal       Short summary of fixed covariates estimates of
                        a joint model for longitudinal data, recurrent
                        events and a terminal event
summary.trivPenalNL     Short summary of fixed covariates estimates of
                        a non-linear trivariate joint model for
                        longitudinal data, recurrent events and a
                        terminal event
survDat                 Survival dataset (TPJM)
survival                Survival function
terminal                Identify terminal indicator
timedep                 Identify time-varying effects
trivPenal               Fit a Trivariate Joint Model for Longitudinal
                        Data, Recurrent Events and a Terminal Event
trivPenalNL             Fit a Non-Linear Trivariate Joint Model for
                        Recurrent Events and a Terminal Event with a
                        Biomarker Described with an ODE Population
                        Model
wts                     Identify weights
