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My analysis aims to apply Cox regression models to microbiome data with different transformations to identify significant associations with survival outcomes.

The analysis is based on a phyloseq object, which is a structured R object used for microbiome data integration and analysis. It contains multiple types of information commonly used in microbiome studies, including:

1. Install Required Packages

For handling microbiome data (OTU tables, taxonomy, sample data):

install.packages("BiocManager")
BiocManager::install("phyloseq")

For compositional data analysis and penalized Cox regression models:

install.packages("coda4microbiome")

For survival analysis functions

install.packages("survival")

2-Source Custom Function:
The script includes a custom function abund_coxnet2, which implements a penalized Cox regression model on different data transformations (e.g., ILR, ALR, CLR, and relative abundance). This function is defined in a separate script and needs to be sourced before use:

source("abund_coxnet2.R")