Shared, Joint (Generalized) Frailty Models; Surrogate Endpoints

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Documentation for package ‘frailtypack’ version 3.6.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Code demos. Use demo() to run them.
• Package NEWS.

Help Pages

A B C D E F G H J L M N P R S T W misc

frailtypack-package

General Frailty models: shared, joint and nested frailty models with prediction; Evaluation of Failure-Time Surrogate Endpoints

-- A --

additivePenal

Fit an Additive Frailty model using a semiparametric penalized likelihood estimation or a parametric estimation

-- B --

bcos	Breast Cosmesis Data

-- C --

CbootstrapFP	Concordance measures in shared frailty and Cox proportional hazard models
cindexes	Concordance measures in shared frailty and Cox proportional hazard models
cindexes.B	Concordance measures in shared frailty and Cox proportional hazard models
cindexes.frailty	Concordance measures in shared frailty and Cox proportional hazard models
cindexes.W	Concordance measures in shared frailty and Cox proportional hazard models
cluster	Identify clusters
Cmeasures	Concordance measures in shared frailty and Cox proportional hazard models
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

-- D --

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
Diffepoce	Difference of Expected Prognostic Observed Cross-Entropy (EPOCE) estimators and its 95% tracking interval between two joint models.

-- E --

epoce	Estimators of the Expected Prognostic Observed Cross-Entropy (EPOCE) for evaluating predictive accuracy of joint models.
event2	Identify event2 indicator

-- F --

factor.names	Fit a Shared, Joint or Nested Frailty model
for	Fit a multivariate frailty model for two types of recurrent events and a terminal event.
frailty	Fit a multivariate frailty model for two types of recurrent events and a terminal event.
frailtypack	General Frailty models: shared, joint and nested frailty models with prediction; Evaluation of Failure-Time Surrogate Endpoints
frailtyPenal	Fit a Shared, Joint or Nested Frailty model

-- G --

gastadj	Advanced Gastric Cancer dataset
GenfrailtyPenal	Fit a Shared or a Joint Frailty Generalized Survival Model

-- H --

hazard

Hazard function.

-- J --

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
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
jointSurrSimul	Generate survival times for two endpoints using the joint frailty surrogate model

-- L --

lines.additivePenal	Plot Method for an Additive frailty model.
lines.frailtyPenal	Plot Method for a Shared frailty model.
lines.jointNestedPenal	Plot method for a joint nested frailty model.
lines.jointPenal	Plot Method for a Joint frailty model.
lines.jointSurroPenal	Plot Method for the one-step Joint surrogate model for the evaluation of a canditate surrogate endpoint.
lines.longiPenal	Plot Method for a joint model for longitudinal data and a terminal event.
lines.nestedPenal	Plot Method for a Nested frailty model.
lines.trivPenal	Plot Method for a trivariate joint model for longitudinal data, recurrent events and a terminal event.
lines.trivPenalNL	Plot Method for a Non-Linear Trivariate Joint Model for Recurrent Events and a Terminal Event with a Biomarker Described with an ODE.
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.

-- M --

model	Fit a multivariate frailty model for two types of recurrent events and a terminal event.
multivariate	Fit a multivariate frailty model for two types of recurrent events and a terminal event.
multivPenal	Fit a multivariate frailty model for two types of recurrent events and a terminal event.

-- N --

num.id

Identify individuals in Joint model for clustered data

-- P --

plot.additivePenal	Plot Method for an Additive frailty model.
plot.Diffepoce	Plot difference of EPOCE estimators between two joint frailty models.
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.additivePenal	Print a Short Summary of parameter estimates of an additive frailty model
print.Cmeasures	Print a short summary of results of Cmeasure function.
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.predFrailty	Print a short summary of results of prediction function.
print.prediction	Print a short summary of results of prediction function.
print.predJoint	Print a short summary of results of prediction function.
print.predLongi	Print a short summary of results of prediction function.
print.summary.additivePenal	summary of parameter estimates of an additive frailty model
print.summary.frailtyPenal	summary of parameter estimates of a shared frailty model
print.summary.jointNestedPenal	summary of parameter estimates of a joint nested frailty model
print.summary.jointPenal	summary of parameter estimates of a joint frailty model
print.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
print.summary.jointSurroPenalSimul	Short summary of the simulation studies based on a joint surrogate model
print.summary.longiPenal	Short summary of fixed covariates estimates of a joint model for longitudinal data and a terminal event.
print.summary.nestedPenal	summary of regression coefficient estimates of a nested frailty model
print.summary.trivPenal	Short summary of fixed covariates estimates of a joint model for longitudinal data, recurrent events and a terminal event
print.summary.trivPenalNL	Short summary of fixed covariates estimates of a non-linear trivariate joint model for longitudinal data, recurrent events and a terminal event
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

-- R --

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

-- S --

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
statFP	Concordance measures in shared frailty and Cox proportional hazard models
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.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)
SurvIC	Create a survival object for interval censoring and possibly left truncated data
survival	Survival function

-- T --

terminal	Identify terminal indicator
timedep	Identify time-varying effects
timedep.names	Fit a Shared, Joint or Nested Frailty model
transfo.table	Fit a multivariate frailty model for two types of recurrent events and a terminal event.
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

-- W --

waldtest	Fit a Shared, Joint or Nested Frailty model
wts	Identify weights

-- misc --

_PACKAGE

General Frailty models: shared, joint and nested frailty models with prediction; Evaluation of Failure-Time Surrogate Endpoints