frailtypack: General Frailty Models: Shared, Joint and Nested Frailty Models with Prediction

The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package: 1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied. 2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope). 3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects. 4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed. 5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms. 6) Joint Nested frailty models in the context of the joint modelling for recurrent events with terminal event, for hierarchically clustered data (with two levels of clustering) by including two iid gamma random effects. 7) Multivariate joint frailty models for two types of recurrent events and a terminal event. 8) Joint models for longitudinal data and a terminal event. 9) Trivariate joint models for longitudinal data, recurrent events and a terminal event. Prediction values are available (for a terminal event or for a new recurrent event). Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.

AuthorVirginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey Mauguen, Agnieszka Krol, Amadou Diakite, Alexandre Laurent and Myriam Lopez
Date of publication2017-01-04 11:37:09
MaintainerVirginie Rondeau <Virginie.Rondeau@isped.u-bordeaux2.fr>
LicenseGPL (>= 2.0)
Version2.10.4
http://virginierondeau.com/BiostatisticalConsulting/Liste_of_examples.html

View on CRAN

Man pages

additivePenal: Fit an Additive Frailty model using a semiparametric...

bcos: Breast Cosmesis Data

cluster: Identify clusters

Cmeasures: Concordance measures in shared frailty and Cox proportional...

colorectal: Follow-up of metastatic colorectal cancer patients: times of...

colorectalLongi: Follow-up of metastatic colorectal cancer patients :...

dataAdditive: Simulated data as a gathering of clinical trials databases

dataMultiv: Simulated data for two types of recurrent events and a...

dataNested: Simulated data with two levels of grouping

Diffepoce: Difference of Expected Prognostic Observed Cross-Entropy...

epoce: Estimators of the Expected Prognostic Observed Cross-Entropy...

event2: Identify event2 indicator

frailtypack-package: General Frailty models: shared, joint and nested frailty...

frailtyPenal: Fit a Shared, Joint or Nested Frailty model

hazard: Hazard function.

longiPenal: Fit a Joint Model for Longitudinal Data and a Terminal Event

multivPenal: Fit a multivariate frailty model for two types of recurrent...

num.id: Identify individuals in Joint model for clustered data

plotAdditive: Plot Method for an Additive frailty model.

plot.Diffepoce: Plot difference of EPOCE estimators between two joint frailty...

plot.epoce: Plot values of estimators of the Expected Prognostic Observed...

plotFrailtyPenal: Plot Method for a Shared frailty model.

plotJointNestedPenal: Plot method for a joint nested frailty model.

plotJointPenal: Plot Method for a Joint frailty model.

plotLongiPenal: Plot Method for a joint model for longitudinal data and a...

plot.multivPenal: Plot Method for a multivariate frailty model.

plotNestedPenal: 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...

plotTrivPenal: Plot Method for a trivariate joint model for longitudinal...

prediction: Prediction probabilities for Cox proportionnal hazard,...

printAdditive: Print a Short Summary of parameter estimates of an additive...

print.Cmeasures: Print a short summary of results of Cmeasure function.

printFrailtyPenal: Print a Short Summary of parameter estimates of a shared...

printJointNestedPenal: Print a Short Summary of parameter estimates of a joint...

printJointPenal: Print a Short Summary of parameter estimates of a joint...

printLongiPenal: Print a Summary of parameter estimates of a joint model for...

print.multivPenal: Print a Short Summary of parameter estimates of a...

printNestedPenal: Print a Short Summary of parameter estimates of a nested...

print.prediction: Print a short summary of results of prediction function.

printTrivPenal: Print a Summary of parameter estimates of a joint model for...

readmission: Rehospitalization colorectal cancer

slope: Identify variable associated with the random slope

subcluster: Identify subclusters

summaryAdditive: summary of parameter estimates of an additive frailty model

summaryFrailtyPenal: summary of parameter estimates of a shared frailty model

summaryJointNestedPenal: summary of parameter estimates of a joint nested frailty...

summaryJointPenal: summary of parameter estimates of a joint frailty model

summaryLongiPenal: Short summary of fixed covariates estimates of a joint model...

summary.multivPenal: summary of parameter estimates of a multivariate frailty...

summaryNestedPenal: summary of regression coefficient estimates of a nested...

summaryTrivPenal: Short summary of fixed covariates estimates of a joint model...

SurvIC: Create a survival object for interval censoring and possibly...

survival: Survival function

terminal: Identify terminal indicator

timedep: Identify time-varying effects

trivPenal: Fit a Trivariate Joint Model for Longitudinal Data, Recurrent...

Files in this package

frailtypack
frailtypack/inst
frailtypack/inst/CITATION
frailtypack/inst/doc
frailtypack/inst/doc/Package_summary.html
frailtypack/inst/doc/Package_summary.Rmd
frailtypack/src
frailtypack/src/funcpajweib.f90
frailtypack/src/funcpaGsplines.f90
frailtypack/src/funcpaMultivSplines.f90
frailtypack/src/funcpaj_tps.f90
frailtypack/src/aresidusMartingale.f90
frailtypack/src/funcpajlongiweib.f90
frailtypack/src/Makevars
frailtypack/src/prediction_Recurr_Sha.f90
frailtypack/src/funcpaGsplines_intcens.f90
frailtypack/src/funcpansplines.f90
frailtypack/src/funcpascpm_intcens.f90
frailtypack/src/funcpaGcpm_intcens.f90
frailtypack/src/funcpaGcpm_log.f90
frailtypack/src/aGhermite.f90
frailtypack/src/funcpassplines_log.f90
frailtypack/src/aaOptim.f90
frailtypack/src/funcpassplines.f90
frailtypack/src/funcpaGcpm.f90
frailtypack/src/funcpaGweib.f90
frailtypack/src/funcpajsplines_intcens.f90
frailtypack/src/nested.f90
frailtypack/src/funcpaMultivWeib.f90
frailtypack/src/Aparameters.f90
frailtypack/src/prediction_biv.f90
frailtypack/src/funcpassplines_intcens.f90
frailtypack/src/funcpajsplines_log.f90
frailtypack/src/funcpasweib_log.f90
frailtypack/src/funcpajsplines_fam.f90
frailtypack/src/frailtypack.f90
frailtypack/src/funcpajsplines.f90
frailtypack/src/distance.f90
frailtypack/src/epoce_log.f90
frailtypack/src/joint.f90
frailtypack/src/prediction.f90
frailtypack/src/funcpaGweib_intcens.f90
frailtypack/src/funcpaasplines.f90
frailtypack/src/funcpancpm.f90
frailtypack/src/Adonnees.f90
frailtypack/src/aaUseFunction.f90
frailtypack/src/joint_longi.f90
frailtypack/src/funcpajweib_intcens.f90
frailtypack/src/funcpaG_tps.f90
frailtypack/src/funcpajweib_fam.f90
frailtypack/src/funcpajlongisplines.f90
frailtypack/src/funcpasweib.f90
frailtypack/src/funcpajcpm.f90
frailtypack/src/aaUseFunctionG.f90
frailtypack/src/epoce_long.f90
frailtypack/src/afuncpasres.f90
frailtypack/src/aamarq98o.f90
frailtypack/src/funcpanweib.f90
frailtypack/src/additive.f90
frailtypack/src/aaOptimres.f90
frailtypack/src/survival.f90
frailtypack/src/funcpaacpm.f90
frailtypack/src/funcpas_tps.f90
frailtypack/src/funcpaaweib.f90
frailtypack/src/funcpaGweib_log.f90
frailtypack/src/funcpajweib_log.f90
frailtypack/src/funcpajgeneral.f90
frailtypack/src/prediction_sha_logn.f90
frailtypack/src/prediction_tri.f90
frailtypack/src/risque.f90
frailtypack/src/ahrmsym.f90
frailtypack/src/epoce.f90
frailtypack/src/AparamMultive.f90
frailtypack/src/funcpaMultivCpm.f90
frailtypack/src/funcpasweib_intcens.f90
frailtypack/src/funcpajcpm_log.f90
frailtypack/src/funcpascpm.f90
frailtypack/src/multiveJoint.f90
frailtypack/src/funcpaGsplines_log.f90
frailtypack/src/funcpascpm_log.f90
frailtypack/NAMESPACE
frailtypack/demo
frailtypack/demo/frailtypack_additivePenal.R
frailtypack/demo/00Index
frailtypack/demo/frailtypack_nestedPenal.R
frailtypack/demo/frailtypack_multivPenal.R
frailtypack/demo/frailtypack_jointPenal.R
frailtypack/demo/frailtypack_frailtyPenal.R
frailtypack/NEWS
frailtypack/data
frailtypack/data/readmission.rda
frailtypack/data/dataNested.rda
frailtypack/data/dataMultiv.rda
frailtypack/data/colorectal.rda
frailtypack/data/colorectalLongi.rda
frailtypack/data/bcos.rda
frailtypack/data/dataAdditive.rda
frailtypack/R
frailtypack/R/print.Cmeasures.R frailtypack/R/summary.nestedPenal.R frailtypack/R/summary.trivPenal.R frailtypack/R/print.jointNestedPenal.R frailtypack/R/summary.multivPenal.R frailtypack/R/longiPenal.R frailtypack/R/print.predFrailty.R frailtypack/R/num.id.R frailtypack/R/cindexes.W.R frailtypack/R/terminal.R frailtypack/R/plot.predLongi.R frailtypack/R/plot.multivPenal.R frailtypack/R/SurvIC.R frailtypack/R/event2.R frailtypack/R/print.predLongi.R frailtypack/R/cindexes.frailty.R frailtypack/R/hazard.R frailtypack/R/plot.epoce.R frailtypack/R/frailtyPenal.R frailtypack/R/print.Diffepoce.R frailtypack/R/print.trivPenal.R frailtypack/R/print.nestedPenal.R frailtypack/R/timedep.R frailtypack/R/summary.additivePenal.R frailtypack/R/summary.longiPenal.R frailtypack/R/subcluster.R frailtypack/R/transfo.table.R frailtypack/R/plot.Diffepoce.R frailtypack/R/print.epoce.R frailtypack/R/print.additivePenal.R frailtypack/R/trivPenal.R frailtypack/R/slope.R frailtypack/R/statFP.R frailtypack/R/summary.frailtyPenal.R frailtypack/R/plot.longiPenal.R frailtypack/R/lines.frailtyPenal.R frailtypack/R/plot.jointNestedPenal.R frailtypack/R/cindexes.B.R frailtypack/R/print.multivPenal.R frailtypack/R/cluster.R frailtypack/R/plot.predJoint.R frailtypack/R/summary.jointNestedPenal.R frailtypack/R/factor.names.R frailtypack/R/timedep.names.R frailtypack/R/plot.predFrailty.R frailtypack/R/survival.R frailtypack/R/prediction.R frailtypack/R/additivePenal.R frailtypack/R/epoce.R frailtypack/R/cindexes.R frailtypack/R/plot.jointPenal.R frailtypack/R/waldtest.R frailtypack/R/plot.nestedPenal.additivePenal.R frailtypack/R/summary.jointPenal.R frailtypack/R/plot.trivPenal.R frailtypack/R/print.longiPenal.R frailtypack/R/print.jointPenal.R frailtypack/R/print.predJoint.R frailtypack/R/print.frailtyPenal.R frailtypack/R/Cmeasures.R frailtypack/R/firstlib.R frailtypack/R/Diffepoce.R frailtypack/R/plot.frailtyPenal.R frailtypack/R/multivPenal.R
frailtypack/vignettes
frailtypack/vignettes/orange_x.png
frailtypack/vignettes/blue_x.png
frailtypack/vignettes/Package_summary.Rmd
frailtypack/MD5
frailtypack/README
frailtypack/build
frailtypack/build/vignette.rds
frailtypack/DESCRIPTION
frailtypack/THANKS
frailtypack/man
frailtypack/man/readmission.Rd frailtypack/man/plot.Diffepoce.Rd frailtypack/man/frailtypack-package.Rd frailtypack/man/Diffepoce.Rd frailtypack/man/prediction.Rd frailtypack/man/bcos.Rd frailtypack/man/summaryNestedPenal.Rd frailtypack/man/subcluster.Rd frailtypack/man/printAdditive.Rd frailtypack/man/trivPenal.Rd frailtypack/man/plotFrailtyPenal.Rd frailtypack/man/summary.multivPenal.Rd frailtypack/man/cluster.Rd frailtypack/man/print.Cmeasures.Rd frailtypack/man/plotAdditive.Rd frailtypack/man/summaryJointPenal.Rd frailtypack/man/terminal.Rd frailtypack/man/plot.multivPenal.Rd frailtypack/man/epoce.Rd frailtypack/man/colorectal.Rd frailtypack/man/summaryTrivPenal.Rd frailtypack/man/SurvIC.Rd frailtypack/man/event2.Rd frailtypack/man/colorectalLongi.Rd frailtypack/man/multivPenal.Rd frailtypack/man/survival.Rd frailtypack/man/frailtyPenal.Rd frailtypack/man/printLongiPenal.Rd frailtypack/man/Cmeasures.Rd frailtypack/man/hazard.Rd frailtypack/man/printJointPenal.Rd frailtypack/man/summaryAdditive.Rd frailtypack/man/plotJointPenal.Rd frailtypack/man/plotNestedPenal.Rd frailtypack/man/print.multivPenal.Rd frailtypack/man/plot.predLongi.Rd frailtypack/man/timedep.Rd frailtypack/man/summaryFrailtyPenal.Rd frailtypack/man/additivePenal.Rd frailtypack/man/printNestedPenal.Rd frailtypack/man/print.prediction.Rd frailtypack/man/dataNested.Rd frailtypack/man/summaryJointNestedPenal.Rd frailtypack/man/printFrailtyPenal.Rd frailtypack/man/num.id.Rd frailtypack/man/printJointNestedPenal.Rd frailtypack/man/slope.Rd frailtypack/man/summaryLongiPenal.Rd frailtypack/man/dataMultiv.Rd frailtypack/man/printTrivPenal.Rd frailtypack/man/longiPenal.Rd frailtypack/man/dataAdditive.Rd frailtypack/man/plotJointNestedPenal.Rd frailtypack/man/plot.epoce.Rd frailtypack/man/plotTrivPenal.Rd frailtypack/man/plot.predJoint.Rd frailtypack/man/plotLongiPenal.Rd frailtypack/man/plot.predFrailty.Rd

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