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

Share:

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.

Author
Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey Mauguen, Agnieszka Krol, Amadou Diakite, Alexandre Laurent and Myriam Lopez
Date of publication
2016-10-19 13:07:20
Maintainer
Virginie Rondeau <Virginie.Rondeau@isped.u-bordeaux2.fr>
License
GPL (>= 2.0)
Version
2.10.3
URLs

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/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/atestWald.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