## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) ## ---- eval=FALSE-------------------------------------------------------------- # if (!require("BiocManager")) # install.packages("BiocManager") # BiocManager::install("glmSparseNet") ## ----packages, message=FALSE, warning=FALSE----------------------------------- library(futile.logger) library(ggplot2) library(glmSparseNet) # Some general options for futile.logger the debugging package .Last.value <- flog.layout(layout.format('[~l] ~m')) .Last.value <- loose.rock::show.message(FALSE) # Setting ggplot2 default theme as minimal theme_set(ggplot2::theme_minimal()) ## ----------------------------------------------------------------------------- data('ovarian', package = 'survival') xdata <- ovarian[,c('age', 'resid.ds')] ydata <- data.frame(time = ovarian$futime, status = ovarian$fustat) ## ----------------------------------------------------------------------------- res.age <- separate2GroupsCox(c(age = 1, 0), xdata, ydata) ## ---- echo=FALSE-------------------------------------------------------------- res.age$km ## ---- echo=FALSE-------------------------------------------------------------- res.age$plot ## ----------------------------------------------------------------------------- res.age.40.60 <- separate2GroupsCox(c(age = 1, 0), xdata, ydata, probs = c(.4, .6)) ## ---- echo=FALSE-------------------------------------------------------------- res.age.40.60$km ## ---- echo=FALSE-------------------------------------------------------------- res.age.40.60$plot ## ----------------------------------------------------------------------------- res.age.60.40 <- separate2GroupsCox( chosen.btas = c(age = 1, 0), xdata, ydata, probs = c(.6, .4), stop.when.overlap = FALSE ) ## ---- echo=FALSE-------------------------------------------------------------- cat('Kaplan-Meier results','\n') res.age.60.40$km ## ---- echo=FALSE-------------------------------------------------------------- res.age.60.40$plot