## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----setup, warning = FALSE--------------------------------------------------- library(BayesSurvival) library(survival) library(ggplot2) ## ----------------------------------------------------------------------------- cancer$status[cancer$status == 1] <- 0 #censored cancer$status[cancer$status == 2] <- 1 #died table(cancer$status) ## ----------------------------------------------------------------------------- res <- BayesSurv(df = cancer, #our data frame time = "time", #name of column with survival/censoring times event = "status", #name of column with status indicator prior = "Dependent", #use dependent Gamma prior ) ## ---- warning = FALSE, fig.width = 5------------------------------------------ PlotBayesSurv(bayes.surv.object = res, object = "survival") ## ---- warning = FALSE, fig.width = 5------------------------------------------ PlotBayesSurv(bayes.surv.object = res, object = "survival", color = "orange", plot.title = "Survival function") ## ---- warning = FALSE, fig.width = 5------------------------------------------ gg <- PlotBayesSurv(bayes.surv.object = res, object = "survival") km <- survfit( Surv(time, status) ~ 1, data = cancer ) #Kaplan-Meier df.km <- data.frame(t = km$time, km = km$surv) gg <- gg + geom_line(data = df.km, aes(x = t, y = km), colour = "black", size = 1, lty = 6) gg <- gg + labs(title = "With Kaplan-Meier + CI's") gg ## ---- warning = FALSE, fig.width = 5------------------------------------------ PlotBayesSurv(bayes.surv.object = res, object = "cumhaz", plot.title = "Cumulative hazard") ## ---- warning = FALSE, fig.width = 5------------------------------------------ PlotBayesSurv(bayes.surv.object = res, object = "hazard", plot.title = "Hazard") ## ----------------------------------------------------------------------------- res <- BayesSurv(df = cancer, #our data frame time = "time", #name of column with survival/censoring times event = "status", #name of column with status indicator prior = "Independent", #use independent Gamma prior ) ## ---- warning = FALSE, fig.width = 5------------------------------------------ PlotBayesSurv(bayes.surv.object = res, object = "survival", plot.title = "Survival") PlotBayesSurv(bayes.surv.object = res, object = "cumhaz", plot.title = "Cumulative hazard") PlotBayesSurv(bayes.surv.object = res, object = "hazard", plot.title = "Hazard")