## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) ## ----eval=FALSE--------------------------------------------------------------- # if (!require("BiocManager")) { # install.packages("BiocManager") # } # BiocManager::install("glmSparseNet") ## ----packages, message=FALSE, warning=FALSE, results='hide'------------------- library(futile.logger) library(ggplot2) library(glmSparseNet) library(survival) # Some general options for futile.logger the debugging package flog.layout(layout.format("[~l] ~m")) options("glmSparseNet.show_message" = FALSE) # Setting ggplot2 default theme as minimal theme_set(ggplot2::theme_minimal()) ## ----------------------------------------------------------------------------- data("cancer", package = "survival") xdata <- survival::ovarian[, c("age", "resid.ds")] ydata <- data.frame( time = survival::ovarian$futime, status = survival::ovarian$fustat ) ## ----------------------------------------------------------------------------- resAge <- separate2GroupsCox(c(age = 1, 0), xdata, ydata) ## ----echo=FALSE--------------------------------------------------------------- resAge$km ## ----echo=FALSE--------------------------------------------------------------- resAge$plot ## ----------------------------------------------------------------------------- resAge4060 <- separate2GroupsCox(c(age = 1, 0), xdata, ydata, probs = c(.4, .6) ) ## ----echo=FALSE--------------------------------------------------------------- resAge4060$km ## ----echo=FALSE--------------------------------------------------------------- resAge4060$plot ## ----------------------------------------------------------------------------- resAge6040 <- separate2GroupsCox( chosenBetas = c(age = 1, 0), xdata, ydata, probs = c(.6, .4), stopWhenOverlap = FALSE ) ## ----echo=FALSE--------------------------------------------------------------- cat("Kaplan-Meier results", "\n") resAge6040$km ## ----echo=FALSE--------------------------------------------------------------- resAge6040$plot ## ----sessionInfo-------------------------------------------------------------- sessionInfo()