mirkosignorelli / pencal_devel

R package pencal (development version). pencal is the R package that implements Penalized Regression Calibration (Signorelli et al., 2021), a method for the dynamic prediction of survival that can deal with a large number of longitudinal covariates

R package pencal (development version)

pencal: what's that?

pencal is the R package that implements Penalized Regression Calibration (PRC), a statistical method that we proposed in Signorelli et al. (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. A detailed description of how to use PRC to do dynamic prediction of survival can be found in Signorelli (2024). pencal: an R Package for the Dynamic Prediction of Survival with Many Longitudinal Predictors. To appear in: The R Journal.

About this repository

This repository contains the development version of the R package. The latest CRAN version can be found here.

Installing pencal

CRAN version (recommended)

To install the latest CRAN version of the package you may use:

install.packages('pencal')

If you encounter problems with packages on which pencal depends, you may alternatively install the package using BiocManager:

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install('pencal')

Development version

You can install the development version of pencal from GitHub with:

# install.packages("devtools")
devtools::install_github("mirkosignorelli/pencal_devel")

Further information

More information on PRC can be found at the following pages:

• CRAN package page;
• my personal website;
• vignette that illustrates with examples how to use pencal.

pencal_devel's Issues

Add a LICENSE file

This package is licensed with GPLv3, as you can see in the DESCRIPTION file. However, a license file is missing in the root. This file is useful for multiple things; clarity first of all, but also, GitHub looks for this file to provide license information on the page and in searches.

Running usethis::use_gpl3_license() in the project should add the license file to the root.

Installation issue: survcomp is not available

ERROR: dependency ‘survcomp’ is not available for package ‘pencal’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/pencal’
Warning messages:
1: package ‘survcomp’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages 
2: In i.p(...) :
  installation of package ‘/var/folders/35/k2hft7b906g7502vy51zrbz40000gn/T//RtmpQMoEP3/file123a82c22baf2/pencal_1.3.2.tar.gz’ had non-zero exit status

My R is version 4.3.1 (2023-06-16).