** IMPORTANT NOTE: THIS PACKAGE IS COMPLETE FOR "CR" ENDPOINT, BUT THE REPO IS BEING UPDATED WITH ON-GOING DEVELOPMENT FOR "RE" ENDPOINT, and will continue to update until this note is removed (estimated completion: end of January 2025). **

itrSurv

itrSurv is an R package designed to estimate optimal individualized treatment regimes for various survival endpoints. This package provides tools for survival data involving competing risks or recurrent events. Please use as appropriate for your data. The authors introduce an multi-utility value function that determine the optimal rule via prioritizing survival while also accounting for a secondary endpoint. itrSurv works for multiple treatment options, but is only applicable to the single stage disease setting. Please refer to our papers for technical details.

This is the doctoral dissertation thesis work of Christina W Zhou under the mentorship of Michael R Kosorok at UNC-CH Department of Biostatistics.

Installation

You can install the package directly from GitHub:

# install.packages("devtools")
devtools::install_github("cwzhou/itrSurv")

Currently, itrSurv is only applicable to settings with either 1) competing risks with a priority cause of interest (as of April 2024), or 2) recurrent events with terminal events (on-going, as of June 2024).

Useful Code

• Simulation Studies: R code for simulation studies is located at https://github.com/cwzhou/Analyses/tree/main/Simulations/Paper1_CR.
• University Cohort Application: R code for applying the methodology to the university cohort can be found at https://github.com/cwzhou/Analyses/tree/main/RDA/Paper1_CR.

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Updates

• CURRENTLY: On-going updates for developing RCIF and the itrSurv estimator for RE setting.
• June 2024: Now incorporating a second endpoint, recurrent events in the recurrent with terminal events setting. NOTE: data must be properly inputted before running itrSurv function!! Please read the documentation!!
• 1/17/24:

To install in cluster (linux): First, build source .tar.gz file from .RProj on local machine, then copy to cluster location. Then, unzip the file by doing the following:

1. go to the folder that has the R scripts you want to run
2. open R by typing R (make sure you module load r/4.1.2 the right version)
3. type: install.packages('[location of .tar.gz file]/itrSurv_0.1.0.tar.gz', repos = NULL, type='source')
4. library(itrSurv)
5. exit and run bash CR_S2run.sh

! If package is ONLY binary and not source, then go to DESCRIPTION and delete the line with "BUILT" and "PACKAGED"