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

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Documentation for package ‘pencal’ version 2.2.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

fitted_prclmm	A fitted PRC LMM
fitted_prcmlpmm	A fitted PRC MLPMM
fit_lmms	Step 1 of PRC-LMM (estimation of the linear mixed models)
fit_mlpmms	Step 1 of PRC-MLPMM (estimation of the linear mixed models)
fit_prclmm	Step 3 of PRC-LMM (estimation of the penalized Cox model(s))
fit_prcmlpmm	Step 3 of PRC-MLPMM (estimation of the penalized Cox model(s))
pbc2data	pbc2 dataset
pencox	Estimation of a penalized Cox model with time-independent covariates
performance_pencox	Predictive performance of the penalized Cox model with time-independent covariates
performance_prc	Predictive performance of the PRC-LMM and PRC-MLPMM models
print.prclmm	Print method for PRC-LMM model fits
print.prcmlpmm	Print method for PRC-MLPMM model fits
simulate_prclmm_data	Simulate data that can be used to fit the PRC-LMM model
simulate_prcmlpmm_data	Simulate data that can be used to fit the PRC-LMM model
simulate_t_weibull	Generate survival data from a Weibull model
summarize_lmms	Step 2 of PRC-LMM (computation of the predicted random effects)
summarize_mlpmms	Step 2 of PRC-MLPMM (computation of the predicted random effects)
summary.lmmfit	Extract model fits from step 1 of PRC-LMM
summary.mlpmmfit	Extract model fits from step 1 of PRC-LMM
summary.prclmm	Summary method for PRC-LMM model fits
summary.prcmlpmm	Summary method for PRC-MLPMM model fits
summary.ranefs	Summary for step 2 of PRC
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