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pencal (version 2.3.0)

Penalized Regression Calibration (PRC) for the Dynamic Prediction of Survival

Description

Computes penalized regression calibration (PRC), a statistical method for the dynamic prediction of survival when many longitudinal predictors are available. See Signorelli (2024) and Signorelli et al. (2021) for details.

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Install

install.packages('pencal')

Monthly Downloads

243

Version

2.3.0

License

GPL (>= 3)

Maintainer

Mirko Signorelli

Last Published

June 5th, 2025

Functions in pencal (2.3.0)

summarize_mlpmms

Step 2 of PRC-MLPMM (computation of the predicted random effects)
print.prcmlpmm

Print method for PRC-MLPMM model fits
simulate_prcmlpmm_data

Simulate data that can be used to fit the PRC-LMM model
performance_prc

Predictive performance of the PRC-LMM and PRC-MLPMM models
prepare_longdata

Prepare longitudinal data for PRC
simulate_prclmm_data

Simulate data that can be used to fit the PRC-LMM model
simulate_t_weibull

Generate survival data from a Weibull model
print.prclmm

Print method for PRC-LMM model fits
summary.lmmfit

Extract model fits from step 1 of PRC-LMM
summarize_lmms

Step 2 of PRC-LMM (computation of the predicted random effects)
summary.ranefs

Summary for step 2 of PRC
summary.mlpmmfit

Extract model fits from step 1 of PRC-LMM
summary.prcmlpmm

Summary method for PRC-MLPMM model fits
survplot_prc

Visualize survival predictions for a fitted PRC model
survpred_prclmm

Compute the predicted survival probabilities obtained from the PRC models
survpred_prcmlpmm

Compute the predicted survival probabilities obtained from the PRC models
summary.prclmm

Summary method for PRC-LMM model fits
fit_prclmm

Step 3 of PRC-LMM (estimation of the penalized Cox model(s))
fit_lmms

Step 1 of PRC-LMM (estimation of the linear mixed models)
performance_pencox

Predictive performance of the penalized Cox model with time-independent covariates
draw_cluster_bootstrap

Draw a cluster bootstrap sample from a data frame in long format
fit_mlpmms

Step 1 of PRC-MLPMM (estimation of the linear mixed models)
pencox

Estimation of a penalized Cox model with time-independent covariates
fit_prcmlpmm

Step 3 of PRC-MLPMM (estimation of the penalized Cox model(s))
pbc2data

pbc2 dataset
fitted_prcmlpmm

A fitted PRC MLPMM
fitted_prclmm

A fitted PRC LMM