CompareKM: Compare KM curve of full population vs. BEP

Description Usage Arguments Note Author(s) Examples

Description

This function provides K-M curves to compare full population vs. BEP.

Usage

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CompareKM(data, tte, cens, trt = NULL, bep, bep.indicator = 1,
  bep.name = "Biomarker Evaluable", itt.name = "All",
  col.itt = "palegreen4", col.bep = "lightpink2", col.ci = "lightcyan",
  shaded.ci = TRUE, xlim = NULL, xat = NULL, ylab = paste(tte,
  "Survival Probability"), xlab = "Time", main = "",
  surv.conf.type = "plain", pdf.name = NULL, pdf.param = list(height = 5),
  par.param = list(mar = c(4, 4, 3, 2)), ...)

Arguments

data

Input data frame. Rows are patients and columns are variables (e.g. demographics variables, time to event variables, biomarker variables, treatment indicator, etc.). One patient per row.

tte

column name that indicates the time to event variable

cens

column name that indicates the censoring variable associated to tte. 1 indicates event and 0 indicates censoring

trt

name of the treatment column. If trt is specified, the analysis will be performed within treatment arm. if it is NULL, the comparison will be performed using all samples.

bep

name of the column which indicates biomarker evaluable population. If it is null, patients who have non NA records in biomarker variable will be used as BEP.

bep.indicator

In the subpopulation column, which value is used to define the biomarker evaluable population.

bep.name

preferred display name of the biomarker evaluable population. If it is NULL, bep will be used.

itt.name

preferred display name of the full population (e.g. ITT). If it is NULL, "All" will be used.

col.itt, col.bep, col.ci

Color for itt curve, bep curve and confidence interval curve (CI)

shaded.ci

Whether add background shade to disply CI

xlim, xat, ylab, xlab, main

see plot

surv.conf.type

confidence interval type. Default is "plain". see conf.type in survfit

pdf.name

name of output pdf file. If it is NULL (default), the plots will be displayed but not saved as pdf

pdf.param

A list of parameters that define pdf graphics device. See pdf. for example, pdf.param=list(width=10, height=5)

par.param

A list of parameters that define graphcial parameters. See par. for example, par.param=list(mfrow=c(3,1), mar=c(4,4,3,2))

...

additional parameters for plot

Note

This function generates KM curves to compare full population vs BEP, within each treatment arm.

Author(s)

Ning Leng [email protected], Alexey Pronin [email protected], and previous team members (see DESCRIPTION)

Examples

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data(input)
sample.data <- input
CompareKM(data=sample.data, tte="OS",cens="OS.event", main="OS ITT", bep="BEP")

lengning/gClinBiomarker documentation built on May 9, 2019, 2:55 p.m.