SurvBal enables the selection of microbiome balances in relation to censored survival or time-to-event outcomes, which are of considerable interest in many biomedical studies. The most commonly used survival models – the Cox proportional hazards and parametric survival (including accelerated failure time) models are included in the package, which are used in combination with step-wise selection procedures to identify the optimal associated balance of microbiome, i.e., the ratio of the geometric means of two groups of taxa’s relative abundances.
Please make sure you install the R package zCompositions with version number <= 1.4.0.1 before installing SurvBal:
require(remotes)
install_version("zCompositions", version = "1.4.0.1", repos = "http://cran.us.r-project.org")
Then you can install SurvBal from GitHub by:
# install.packages("devtools")
devtools::install_github("yinglia/SurvBal")
Please skip the recommended update about zCompositions.
All functions in SurvBal are described in the manual:
https://github.com/yinglia/SurvBal/blob/main/SurvBal_1.2.0.pdf
The vignette of SurvBal includes the instructions to run the method on the example dataset, with the input and output clearly described, which can be found at:
https://yinglia.github.io/SurvBal-Vignette/
A Shiny app of SurvBal: