summarize_lmms {pencal}

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

Description

This function performs the second step for the estimation of the PRC-LMM model proposed in Signorelli et al. (2021)

Usage

summarize_lmms(object, n.cores = 1, verbose = TRUE)

Arguments

object

a list of objects as produced by fit_lmms

n.cores

number of cores to use to parallelize part of the computations. If ncores = 1 (default), no parallelization is done. Pro tip: you can use parallel::detectCores() to check how many cores are available on your computer

verbose

if TRUE (default and recommended value), information on the ongoing computations is printed in the console

Value

A list containing the following objects:

• call: the function call

• ranef.orig: a matrix with the predicted random effects computed for the original data;

• n.boots: number of bootstrap samples;

• boot.ids: a list with the ids of bootstrapped subjects (when n.boots > 0);

• ranef.boot.train: a list where each element is a matrix that contains the predicted random effects for each bootstrap sample (when n.boots > 0);

• ranef.boot.valid: a list where each element is a matrix that contains the predicted random effects on the original data, based on the lmms fitted on the cluster bootstrap samples (when n.boots > 0);

Author(s)

Mirko Signorelli

References

Signorelli, M. (2023). pencal: an R Package for the Dynamic Prediction of Survival with Many Longitudinal Predictors. arXiv preprint: arXiv:2309.15600

Signorelli, M., Spitali, P., Al-Khalili Szigyarto, C, The MARK-MD Consortium, Tsonaka, R. (2021). Penalized regression calibration: a method for the prediction of survival outcomes using complex longitudinal and high-dimensional data. Statistics in Medicine, 40 (27), 6178-6196. DOI: 10.1002/sim.9178

See Also

fit_lmms (step 1), fit_prclmm (step 3), performance_prc

Examples

# generate example data
set.seed(1234)
p = 4 # number of longitudinal predictors
simdata = simulate_prclmm_data(n = 100, p = p, p.relev = 2, 
             seed = 123, t.values = c(0, 0.2, 0.5, 1, 1.5, 2))
             
# specify options for cluster bootstrap optimism correction
# procedure and for parallel computing 
do.bootstrap = FALSE
# IMPORTANT: set do.bootstrap = TRUE to compute the optimism correction!
n.boots = ifelse(do.bootstrap, 100, 0)
more.cores = FALSE
# IMPORTANT: set more.cores = TRUE to parallelize and speed computations up!
if (!more.cores) n.cores = 1
if (more.cores) {
   # identify number of available cores on your machine
   n.cores = parallel::detectCores()
   if (is.na(n.cores)) n.cores = 8
}

# step 1 of PRC-LMM: estimate the LMMs
y.names = paste('marker', 1:p, sep = '')
step1 = fit_lmms(y.names = y.names, 
                 fixefs = ~ age, ranefs = ~ age | id, 
                 long.data = simdata$long.data, 
                 surv.data = simdata$surv.data,
                 t.from.base = t.from.base,
                 n.boots = n.boots, n.cores = n.cores)
                 
# step 2 of PRC-LMM: compute the summaries 
# of the longitudinal outcomes
step2 = summarize_lmms(object = step1, n.cores = n.cores)
summary(step2)