README.md

In LittleBeannie/demo: a R package for demo in Roche inernship

Accessment of Time-To-Event endpoints basd on Interim data

How to edit this package?

• Step1: Modify the functions, ect...(Ctrl+Shift+Alt+R can be used to generate a templet for the description of the functions)

• Step2: Generate the needed documents (such as DESCRIPTION, NAMESPACE) by "devtools::document()".

• Setp3: Build the package by "Ctrl + Shift + B".

• Step4: Update the online package by using GitHub Desktop.

How to use this package?

Install

library(knitr)
library(devtools)
library(roxygen2)
library(testthat)
devtools::install_github("littlebeannie/demo")

Example 1: KM curve

library(survival)
attach(veteran)
km_plot(Surv(time, status),covariate=trt,dataset = veteran,plot_fancy = T)

Example 2: a more fancy KM curve

km_plot_fancy( survfit(Surv(time, status)~ sex, data=lung),
               pvalue.TF  = TRUE,
               conf.int.TF = TRUE,
               x.lab = "Time in Days",
               x.interval = 200,
               risk.table.style = "absolute",
               n.censor.plot.TF= FALSE,
               surv.median.line.style = "hv",
               legend = c("group 1", "group 2"))

Example 3: log rank test

log_rank_test(Surv(time, status),covariate = trt,dataset=veteran)

Example 4: cox model

cox_reg(Surv(time, status),covariate = trt,dataset=veteran)

Example 5: predict the PFS curve

curve_predict(Surv(time, status),covariate = trt,dataset=veteran,family="exp",futuretime=3)

Example 6: multi-test by recycle p-value

multi_test_recy_pvalue(Surv(time, status),trt,veteran,
                       Surv(time, status),trt,veteran,
                       Surv(time, status),prior,veteran,
                       Surv(time, status),trt,veteran,
                       Surv(time, status),trt,veteran,
                       Surv(time, status),prior,veteran,
                       ratio.compare1 = c(3,3,19),
                       ratio.compare2 = c(3,3,19),
                       two.side=TRUE)

Example7: Forest Plot

forest_plot(Surv(time,status)~trt + celltype + karno +diagtime + age +prior, dataset = veteran)

LittleBeannie/demo documentation built on Aug. 12, 2020, 8:17 p.m.